From 493071bb80e74ca06934ad00390acb51f2f55895 Mon Sep 17 00:00:00 2001
From: Paula Ruiz Rodriguez <50167687+Paururo@users.noreply.github.com>
Date: Sun, 16 Aug 2026 16:40:16 +0200
Subject: [PATCH 1/3] feat(galaxy): add tool wrappers for all five subcommands

Five Galaxy tools, one per subcommand, sharing a macros.xml. The layout matches
galaxyproject/tools-iuc, so submitting there is a directory copy rather than a
rewrite.

pathotypr is already on Bioconda with a BioContainer built from it and is
registered on bio.tools, so the wrappers declare the conda package and nothing
is vendored.

Verified with planemo: lint is clean on all five with no warnings, and all 8
tests pass. The test suite was itself checked by mutation: changing the output
prefix so it no longer matches from_work_dir fails both classify tests, which is
how we know the assertions read the real outputs.

The test data is 64 KB of synthetic input, generated deterministically by a
script kept alongside it. It is not filler. The generator asserts that every
marker k-mer occurs exactly once in the reference, in both orientations, because
a marker matching in two places would make the tests pass for the wrong reason.
The expected calls follow from how the samples are built, and they cross-check
each other: split-fastq on a sample's reads produces the same summary as
classify on its assembly, which is the property the marker format promises.

Three things had to be worked around, none of which is visible from the CLI
help and all of which were found by running the tools:

  * classify and split-fastq take the sample name from the input filename.
    Galaxy datasets arrive as dataset_NNN.dat, so outputs would have been named
    after a Galaxy id. Inputs are symlinked to stable names first.
  * match writes the absolute paths of its inputs into the report's first
    column, which would differ between instances. Same fix.
  * --min-alt-percent is parsed as an integer. A Galaxy float parameter renders
    95.0, which the tool rejects with "invalid digit found in string". It is
    declared as an integer, which also means fractional thresholds such as
    99.5% are not reachable.

Marker panels and models come from the history for now. A data manager and a
.loc table would let an administrator install the published MTBC panels once,
which is how Galaxy usually handles reference data; that is left as its own
piece of work rather than half-built.
---
 galaxy/tools/pathotypr/.shed.yml              |  18 +
 galaxy/tools/pathotypr/README.md              |  74 +++
 galaxy/tools/pathotypr/macros.xml             |  85 ++++
 galaxy/tools/pathotypr/pathotypr_classify.xml | 143 ++++++
 galaxy/tools/pathotypr/pathotypr_match.xml    | 128 ++++++
 galaxy/tools/pathotypr/pathotypr_predict.xml  |  78 ++++
 .../tools/pathotypr/pathotypr_split_fastq.xml | 144 ++++++
 galaxy/tools/pathotypr/pathotypr_train.xml    | 135 ++++++
 .../pathotypr/test-data/make_testdata.py      | 178 ++++++++
 galaxy/tools/pathotypr/test-data/markers.tsv  |   9 +
 .../pathotypr/test-data/model.pathotypr.zst   | Bin 0 -> 563 bytes
 galaxy/tools/pathotypr/test-data/query.fasta  |  70 +++
 .../tools/pathotypr/test-data/reference.fasta |  35 ++
 .../pathotypr/test-data/references.fasta      |  70 +++
 .../tools/pathotypr/test-data/sample1.fasta   |  35 ++
 .../pathotypr/test-data/sample1_R1.fastq.gz   | Bin 0 -> 2140 bytes
 .../pathotypr/test-data/sample1_R2.fastq.gz   | Bin 0 -> 1995 bytes
 .../tools/pathotypr/test-data/sample2.fasta   |  35 ++
 .../tools/pathotypr/test-data/training.fasta  | 420 ++++++++++++++++++
 19 files changed, 1657 insertions(+)
 create mode 100644 galaxy/tools/pathotypr/.shed.yml
 create mode 100644 galaxy/tools/pathotypr/README.md
 create mode 100644 galaxy/tools/pathotypr/macros.xml
 create mode 100644 galaxy/tools/pathotypr/pathotypr_classify.xml
 create mode 100644 galaxy/tools/pathotypr/pathotypr_match.xml
 create mode 100644 galaxy/tools/pathotypr/pathotypr_predict.xml
 create mode 100644 galaxy/tools/pathotypr/pathotypr_split_fastq.xml
 create mode 100644 galaxy/tools/pathotypr/pathotypr_train.xml
 create mode 100644 galaxy/tools/pathotypr/test-data/make_testdata.py
 create mode 100644 galaxy/tools/pathotypr/test-data/markers.tsv
 create mode 100644 galaxy/tools/pathotypr/test-data/model.pathotypr.zst
 create mode 100644 galaxy/tools/pathotypr/test-data/query.fasta
 create mode 100644 galaxy/tools/pathotypr/test-data/reference.fasta
 create mode 100644 galaxy/tools/pathotypr/test-data/references.fasta
 create mode 100644 galaxy/tools/pathotypr/test-data/sample1.fasta
 create mode 100644 galaxy/tools/pathotypr/test-data/sample1_R1.fastq.gz
 create mode 100644 galaxy/tools/pathotypr/test-data/sample1_R2.fastq.gz
 create mode 100644 galaxy/tools/pathotypr/test-data/sample2.fasta
 create mode 100644 galaxy/tools/pathotypr/test-data/training.fasta

diff --git a/galaxy/tools/pathotypr/.shed.yml b/galaxy/tools/pathotypr/.shed.yml
new file mode 100644
index 0000000..416aed8
--- /dev/null
+++ b/galaxy/tools/pathotypr/.shed.yml
@@ -0,0 +1,18 @@
+categories:
+  - Sequence Analysis
+  - Variant Analysis
+description: Lineage classification and marker-driven genotyping from assemblies or raw reads
+long_description: |
+  pathotypr classifies microbial genomes into lineages and genotypes them
+  against user-defined marker panels. It works from assembled genomes (FASTA)
+  and from raw reads (FASTQ) without aligning them, and it carries no assumption
+  about the organism: the marker panel supplied defines what is typed.
+homepage_url: https://pathogenomics-lab.github.io/pathotypr/
+remote_repository_url: https://github.com/PathoGenOmics-Lab/pathotypr
+owner: iuc
+suite:
+  name: suite_pathotypr
+  description: Lineage classification and marker-driven genotyping with pathotypr
+  long_description: |
+    A suite of the five pathotypr commands: train, predict, classify,
+    split-fastq and match.
diff --git a/galaxy/tools/pathotypr/README.md b/galaxy/tools/pathotypr/README.md
new file mode 100644
index 0000000..a4733cc
--- /dev/null
+++ b/galaxy/tools/pathotypr/README.md
@@ -0,0 +1,74 @@
+# Galaxy wrappers for pathotypr
+
+Five tools, one per subcommand, sharing `macros.xml`.
+
+| Tool | Wraps | Outputs |
+|---|---|---|
+| `pathotypr_train` | `train` | model, and optionally the two feature-importance reports |
+| `pathotypr_predict` | `predict` | predictions TSV |
+| `pathotypr_classify` | `classify` | per-marker hits, summary, optionally masked FASTA |
+| `pathotypr_split_fastq` | `split-fastq` | per-marker calls, summary |
+| `pathotypr_match` | `match` | best-match report |
+
+## Running the tests
+
+```bash
+python3 -m venv .venv && .venv/bin/pip install planemo
+.venv/bin/planemo lint tools/pathotypr/*.xml
+.venv/bin/planemo test tools/pathotypr/
+```
+
+`planemo test` resolves `pathotypr` from Bioconda. On a machine where that
+package has no build for the local platform, put a `pathotypr` binary on `PATH`
+and add `--no_dependency_resolution`; that still exercises the command lines,
+the outputs and the assertions, and leaves only the dependency resolution to CI.
+
+## The test data
+
+Everything under `test-data/` is synthetic and generated deterministically:
+a 2 kb reference, eight markers, two samples, paired reads at about 18x, and a
+twelve-genome training set in two classes. 64 KB in total.
+
+It is not filler. The generator asserts that **every marker k-mer occurs exactly
+once in the reference**, in both orientations, because a marker that matched in
+two places would make the tests pass for the wrong reason. The expected calls
+follow from how the samples were built:
+
+- `sample1` carries the L2 to L2.1 to L2.1.1 path plus the RIF marker, so
+  `classify` calls L2 and reports `rpoB` / `S450L`.
+- `sample2` carries L3 to L3.2 plus the INH marker.
+- `split-fastq` on `sample1`'s reads produces the **same summary** as `classify`
+  on its assembly, which is the property the marker format promises.
+- `predict` assigns the two held-out queries to L2 and L3.
+- `match` picks `ref_A`, which is `sample1`'s own genome.
+
+## Three things the wrappers have to work around
+
+1. **Sample names come from filenames.** Galaxy datasets arrive as
+   `dataset_NNN.dat`, so `classify` and `split-fastq` would name their outputs
+   after a Galaxy id. Each input is symlinked to a stable name first.
+2. **`match` echoes input paths into its report.** Same fix, otherwise the first
+   column is full of absolute paths that differ between instances.
+3. **`--min-alt-percent` is an integer.** A Galaxy `float` parameter renders
+   `95.0`, which the tool rejects outright. It is declared as an integer, so
+   fractional thresholds such as 99.5% are not available.
+
+## Submitting to the IUC
+
+The directory layout matches `galaxyproject/tools-iuc`, so submission is a copy:
+
+```bash
+cp -r galaxy/tools/pathotypr <tools-iuc>/tools/pathotypr
+```
+
+then a pull request against that repository. Their CI runs the same planemo
+lint and tests on Linux, where the Bioconda package resolves.
+
+## Not done yet
+
+Marker panels and models come from the history. A **data manager** plus a
+`.loc` table would let an administrator install the published MTBC panels once
+so users pick them from a dropdown, which is how Galaxy normally handles
+reference data. That is a separate piece of work and was left out deliberately
+rather than half-built: shipping a data table with nothing to populate it moves
+the burden to administrators without helping anyone.
diff --git a/galaxy/tools/pathotypr/macros.xml b/galaxy/tools/pathotypr/macros.xml
new file mode 100644
index 0000000..c42bac2
--- /dev/null
+++ b/galaxy/tools/pathotypr/macros.xml
@@ -0,0 +1,85 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.0.2</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">23.0</token>
+
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">pathotypr</requirement>
+        </requirements>
+    </xml>
+
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">pathotypr</xref>
+        </xrefs>
+    </xml>
+
+    <xml name="version_command">
+        <version_command>pathotypr --version</version_command>
+    </xml>
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.64898/2026.03.24.714002</citation>
+            <citation type="doi">10.5281/zenodo.19210044</citation>
+        </citations>
+    </xml>
+
+    <!-- Threads. Galaxy sets GALAXY_SLOTS; without it a tool helps itself to
+         every core on a shared node. -->
+    <token name="@THREADS@">-t \${GALAXY_SLOTS:-1}</token>
+
+    <xml name="kmer_size" token_default="31" token_help="">
+        <param argument="--kmer-size" type="integer" min="1" max="31" value="@DEFAULT@"
+               label="k-mer size"
+               help="Must be between 1 and 31. An odd value centres the variant inside the k-mer, so 31 and 21 are the usual choices. @HELP@"/>
+    </xml>
+
+    <!-- Marker panels and the reference they were called against. They travel
+         together on purpose: positions are 1-based coordinates on that exact
+         sequence, and a panel read against a different assembly produces
+         confident, wrong calls with no warning. -->
+    <xml name="markers_and_reference">
+        <param argument="--markers" type="data" format="tabular" label="Marker panel"
+               help="Tab-separated: position, REF, ALT, then one lineage level per column. The published MTBC panels are on Zenodo, doi:10.5281/zenodo.19210044."/>
+        <param argument="--reference" type="data" format="fasta" label="Reference genome"
+               help="Single-record FASTA. This must be the assembly the marker positions were called against."/>
+    </xml>
+
+    <xml name="nested_classification">
+        <param argument="--nested-classification" type="boolean" truevalue="--nested-classification"
+               falsevalue="" checked="false" label="Nested lineage classification"
+               help="Requires a panel whose lineage hierarchy is spread across one column per level."/>
+    </xml>
+
+    <token name="@MARKER_HELP@">
+**Marker file format**
+
+Tab-separated, no header required. Column order:
+
+::
+
+    position  REF  ALT  level1  level2  ...  (empty)  gene  mutation
+
+Positions are 1-based on the reference genome you supply. The lineage hierarchy
+runs from column 4 until the first empty cell; whatever follows that empty cell
+is read as gene and mutation. SNPs and equal-length MNVs work everywhere;
+indels are accepted by *classify* and skipped by *split-fastq*.
+
+The full rules are at
+https://pathogenomics-lab.github.io/pathotypr/marker_format/
+
+Ready-made panels for the *M. tuberculosis* complex, and a pre-trained model,
+are published on Zenodo: https://doi.org/10.5281/zenodo.19210044
+    </token>
+
+    <token name="@ORGANISM_NOTE@">
+**A note on other organisms**
+
+Nothing in pathotypr is hard-coded to one organism: the panel you supply defines
+what is typed. In practice it has only been validated on the *M. tuberculosis*
+complex, so treat other organisms as exploratory and check the calls against a
+truth set you trust.
+    </token>
+</macros>
diff --git a/galaxy/tools/pathotypr/pathotypr_classify.xml b/galaxy/tools/pathotypr/pathotypr_classify.xml
new file mode 100644
index 0000000..0ad6544
--- /dev/null
+++ b/galaxy/tools/pathotypr/pathotypr_classify.xml
@@ -0,0 +1,143 @@
+<tool id="pathotypr_classify" name="pathotypr classify" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>genotypes assembled genomes against a marker panel</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="exit_code"><![CDATA[
+## Galaxy datasets arrive as dataset_NNN.dat, and pathotypr takes the sample
+## name from the filename. Link each one to the element identifier so the
+## output names the sample rather than a Galaxy id.
+## The extension is stripped before it is re-added, or an identifier that
+## already ends in .fasta becomes sample.fasta.fasta, and that name is what the
+## summary reports back in the genome column.
+#import re
+#set $safe = lambda s: re.sub('[.](fasta|fa|fna|fas)$', '', re.sub('[^A-Za-z0-9_.-]', '_', str(s)))
+#for $i, $g in enumerate($genomes)
+    ln -s '$g' '${safe($g.element_identifier)}.fasta' &&
+#end for
+#if $annotation.use_gff == 'yes'
+    #for $i, $f in enumerate($annotation.gff_files)
+        ln -s '$f' '${safe($f.element_identifier)}.gff' &&
+    #end for
+#end if
+
+pathotypr classify
+    --markers '$markers'
+    --reference '$reference'
+    --input-files
+#for $g in $genomes
+    '${safe($g.element_identifier)}.fasta'
+#end for
+#if $annotation.use_gff == 'yes'
+    --gff-files
+    #for $f in $annotation.gff_files
+        '${safe($f.element_identifier)}.gff'
+    #end for
+#end if
+    --output-prefix 'result'
+    --kmer-size $kmer_size
+    --min-flank-bases $min_flank_bases
+    $nested_classification
+    $output_masked_fasta
+    @THREADS@
+    ]]></command>
+    <inputs>
+        <param name="genomes" type="data" format="fasta" multiple="true" label="Assembled genomes"
+               help="One or more FASTA assemblies to genotype."/>
+        <expand macro="markers_and_reference"/>
+        <conditional name="annotation">
+            <param name="use_gff" type="select" label="Annotate hits with a GFF">
+                <option value="no" selected="true">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no"/>
+            <when value="yes">
+                <param name="gff_files" type="data" format="gff,gff3" multiple="true" label="GFF annotation"
+                       help="Matched to the genomes by filename, so the names must correspond."/>
+            </when>
+        </conditional>
+        <expand macro="kmer_size" default="31"/>
+        <param argument="--min-flank-bases" type="integer" min="0" value="10"
+               label="Minimum flanking bases"
+               help="Bases required on each side of the allele inside the marker k-mer. At the defaults this caps usable alleles at 11 bp."/>
+        <expand macro="nested_classification"/>
+        <param argument="--output-masked-fasta" type="boolean" truevalue="--output-masked-fasta"
+               falsevalue="" checked="false" label="Also write masked FASTA"
+               help="Writes each genome with the marker positions replaced by N."/>
+    </inputs>
+    <outputs>
+        <data name="detailed" format="tabular" label="${tool.name} on ${on_string}: per-marker hits"
+              from_work_dir="result.tsv"/>
+        <data name="summary" format="tabular" label="${tool.name} on ${on_string}: summary"
+              from_work_dir="result_summary.tsv"/>
+        <collection name="masked" type="list" label="${tool.name} on ${on_string}: masked FASTA">
+            <filter>output_masked_fasta</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)_masked\.fasta" format="fasta" directory="."/>
+        </collection>
+    </outputs>
+    <tests>
+        <!-- One genome carrying the L2 -> L2.1 -> L2.1.1 path and a RIF marker. -->
+        <test expect_num_outputs="2">
+            <param name="genomes" value="sample1.fasta" ftype="fasta"/>
+            <param name="markers" value="markers.tsv" ftype="tabular"/>
+            <param name="reference" value="reference.fasta" ftype="fasta"/>
+            <output name="summary">
+                <assert_contents>
+                    <has_text text="major_lineage"/>
+                    <has_text text="L2;L2.1;L2.1.1"/>
+                </assert_contents>
+            </output>
+            <output name="detailed">
+                <assert_contents>
+                    <has_text text="rpoB"/>
+                    <has_text text="S450L"/>
+                    <has_n_lines n="5"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Two genomes at once, and the second one is a different lineage. -->
+        <test expect_num_outputs="2">
+            <param name="genomes" value="sample1.fasta,sample2.fasta" ftype="fasta"/>
+            <param name="markers" value="markers.tsv" ftype="tabular"/>
+            <param name="reference" value="reference.fasta" ftype="fasta"/>
+            <param name="kmer_size" value="21"/>
+            <output name="summary">
+                <assert_contents>
+                    <has_text text="L2"/>
+                    <has_text text="L3"/>
+                    <has_n_lines n="3"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+`pathotypr classify` calls a panel of diagnostic variants directly on assembled
+genomes. For each marker it builds a k-mer centred on the variant, looks for it
+in the assembly, and reports which allele was found. Hits are then collapsed
+into a lineage call per genome.
+
+It produces two tables:
+
+- **per-marker hits**: one row per marker found, with the k-mer, its position,
+  the reference and alternate alleles, the lineage the marker belongs to and,
+  where the panel carries them, the gene and amino-acid change.
+- **summary**: one row per genome, with the count of hits per lineage and the
+  major lineage call.
+
+@MARKER_HELP@
+
+@ORGANISM_NOTE@
+
+**Choosing between classify and split-fastq**
+
+Use this tool when you have assemblies. Use *pathotypr split-fastq* when you
+have raw reads and would rather not assemble them. Both read the same panel and
+agree on the call; only the input differs.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
diff --git a/galaxy/tools/pathotypr/pathotypr_match.xml b/galaxy/tools/pathotypr/pathotypr_match.xml
new file mode 100644
index 0000000..17c4209
--- /dev/null
+++ b/galaxy/tools/pathotypr/pathotypr_match.xml
@@ -0,0 +1,128 @@
+<tool id="pathotypr_match" name="pathotypr match" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>finds which reference genome a set of reads is closest to</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="exit_code"><![CDATA[
+## The report echoes the input paths back into the first column, so the reads
+## are linked to fixed names to keep that column readable and reproducible
+## rather than full of Galaxy dataset ids.
+#if $reads.layout == 'paired'
+    #set $ext = 'fastq.gz' if $reads.fwd.is_of_type('fastqsanger.gz') else 'fastq'
+    ln -s '$reads.fwd' 'sample_R1.$ext' &&
+    ln -s '$reads.rev' 'sample_R2.$ext' &&
+#else
+    #set $ext = 'fastq.gz' if $reads.single.is_of_type('fastqsanger.gz') else 'fastq'
+    ln -s '$reads.single' 'sample.$ext' &&
+#end if
+
+pathotypr match
+    --references '$references'
+#if $reads.layout == 'paired'
+    -i 'sample_R1.$ext' 'sample_R2.$ext'
+#else
+    -i 'sample.$ext' --no-auto-paired
+#end if
+    --output 'match.tsv'
+    --kmer-size $kmer_size
+    --min-kmer-count $min_kmer_count
+#if float($early_stop_confidence) > 0
+    --early-stop-confidence $early_stop_confidence
+    --early-stop-min-kmers $early_stop_min_kmers
+#end if
+    $strict_percentages
+    @THREADS@
+    ]]></command>
+    <inputs>
+        <conditional name="reads">
+            <param name="layout" type="select" label="Read layout">
+                <option value="paired" selected="true">Paired end</option>
+                <option value="single">Single end</option>
+            </param>
+            <when value="paired">
+                <param name="fwd" type="data" format="fastqsanger,fastqsanger.gz" label="Forward reads"/>
+                <param name="rev" type="data" format="fastqsanger,fastqsanger.gz" label="Reverse reads"/>
+            </when>
+            <when value="single">
+                <param name="single" type="data" format="fastqsanger,fastqsanger.gz" label="Reads"/>
+            </when>
+        </conditional>
+        <param argument="--references" type="data" format="fasta" label="Reference genomes"
+               help="A single multi-FASTA holding every candidate reference. Each record is one candidate."/>
+        <expand macro="kmer_size" default="31"/>
+        <param argument="--min-kmer-count" type="integer" min="1" value="2"
+               label="Minimum k-mer count"
+               help="Query k-mers seen fewer times than this are discarded as sequencing noise. Set to 1 to keep singletons. Only applied once the query has more than 100,000 unique k-mers."/>
+        <param argument="--early-stop-confidence" type="float" min="0" max="1" value="0"
+               label="Early-stop confidence"
+               help="Stop the exact phase once the leader is this far ahead. 0 disables it and scores everything. Useful values are 0.98 to 0.999."/>
+        <param argument="--early-stop-min-kmers" type="integer" min="1" value="1000000"
+               label="Minimum k-mers before early stop"
+               help="Ignored unless early-stop confidence is above 0."/>
+        <param argument="--strict-percentages" type="boolean" truevalue="--strict-percentages"
+               falsevalue="" checked="false" label="Legacy shared k-mer percentages"
+               help="Reproduces the older weighted-count definition of the shared fraction. For comparing against earlier runs."/>
+    </inputs>
+    <outputs>
+        <data name="report" format="tabular" label="${tool.name} on ${on_string}: best match"
+              from_work_dir="match.tsv"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <conditional name="reads">
+                <param name="layout" value="paired"/>
+                <param name="fwd" value="sample1_R1.fastq.gz" ftype="fastqsanger.gz"/>
+                <param name="rev" value="sample1_R2.fastq.gz" ftype="fastqsanger.gz"/>
+            </conditional>
+            <param name="references" value="references.fasta" ftype="fasta"/>
+            <output name="report">
+                <assert_contents>
+                    <has_text text="Best_Match_Reference"/>
+                    <has_text text="ref_A"/>
+                    <has_n_lines n="2"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+`pathotypr match` answers one question: of the reference genomes you supply,
+which one do these reads look most like? It counts how many of the query's
+k-mers are contained in each reference and reports the best one with the shared
+fraction behind the call.
+
+Typical uses are picking the closest reference before mapping, and sanity
+checking that a sample is the species you think it is.
+
+**The output**
+
+=============================  ================================================
+Column                         Meaning
+=============================  ================================================
+``Query_Files``                The read files that went in
+``Best_Match_Reference``       The record name of the winning reference
+``Shared_Kmer_Fraction``       Fraction of query k-mers contained in it, 0 to 1
+=============================  ================================================
+
+A fraction near 1 means the reads are essentially that reference. A low fraction
+for every candidate means the right reference is not in your set, and the tool
+will still name a winner, so read the fraction and not only the name.
+
+.. class:: warningmark
+
+**This is the most memory-hungry of the pathotypr tools.** Each batch loads a
+reference genome and its k-mer set, and both time and memory scale with the
+number of references multiplied by the number of reads. On a shared Galaxy
+instance, keep the reference set to the candidates you actually mean to compare,
+rather than a whole database.
+
+**Early stopping** trades exhaustiveness for speed: once a leader is far enough
+ahead, the remaining references are not scored exactly. Leave it at 0 when you
+want the shared fractions of every candidate to be comparable.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
diff --git a/galaxy/tools/pathotypr/pathotypr_predict.xml b/galaxy/tools/pathotypr/pathotypr_predict.xml
new file mode 100644
index 0000000..a384f06
--- /dev/null
+++ b/galaxy/tools/pathotypr/pathotypr_predict.xml
@@ -0,0 +1,78 @@
+<tool id="pathotypr_predict" name="pathotypr predict" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>assigns lineages to genomes using a trained model</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="exit_code"><![CDATA[
+pathotypr predict
+    --input '$input'
+    --model '$model'
+    --output 'predictions.tsv'
+    @THREADS@
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="fasta" label="Genomes to classify"
+               help="A FASTA of sequences with unknown lineage. Headers are reported back unchanged."/>
+        <param name="model" type="data" format="data" label="Trained model"
+               help="Produced by pathotypr train. A pre-trained model for the M. tuberculosis complex is on Zenodo, doi:10.5281/zenodo.19210044."/>
+    </inputs>
+    <outputs>
+        <data name="predictions" format="tabular" label="${tool.name} on ${on_string}: predictions"
+              from_work_dir="predictions.tsv"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input" value="query.fasta" ftype="fasta"/>
+            <param name="model" value="model.pathotypr.zst" ftype="data"/>
+            <output name="predictions">
+                <assert_contents>
+                    <has_text text="Predicted_Lineage"/>
+                    <has_text text="query_a"/>
+                    <has_text text="query_b"/>
+                    <has_n_lines n="3"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+`pathotypr predict` applies a model built by *pathotypr train* to new sequences.
+It streams the input in batches, so memory stays flat regardless of how many
+genomes you give it.
+
+The output has one row per input sequence:
+
+=========================  ====================================================
+Column                     Meaning
+=========================  ====================================================
+``Header``                 The FASTA header of the input sequence, unchanged
+``Predicted_Lineage``      The class the ensemble voted for
+``Confidence``             Fraction of trees that voted for it, 0 to 1
+``Confidence_Margin``      The gap to the runner-up
+``Other_Votes``            The remaining classes and their shares
+=========================  ====================================================
+
+**Reading the confidence**
+
+Confidence is a vote share among the classes the model was trained on, not a
+probability that the answer is right. A genome from a lineage that was never in
+the training set will still be assigned to the nearest class it knows, and can
+do so confidently. The margin is the more useful number of the two: a high
+confidence with a small margin means two classes were nearly tied.
+
+.. class:: warningmark
+
+A model only knows the labels it was trained on, and those come from the first
+whitespace-separated token of each header in the training FASTA. If a model was
+trained on genomes with unedited public-archive headers it will have one class
+per accession, and its predictions will be meaningless however confident they
+look.
+
+@ORGANISM_NOTE@
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
diff --git a/galaxy/tools/pathotypr/pathotypr_split_fastq.xml b/galaxy/tools/pathotypr/pathotypr_split_fastq.xml
new file mode 100644
index 0000000..a85256c
--- /dev/null
+++ b/galaxy/tools/pathotypr/pathotypr_split_fastq.xml
@@ -0,0 +1,144 @@
+<tool id="pathotypr_split_fastq" name="pathotypr split-fastq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>genotypes raw reads against a marker panel without aligning them</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="exit_code"><![CDATA[
+## The sample name is taken from the input filename, so the reads are linked to
+## fixed names and the outputs are predictable rather than named after a Galaxy
+## dataset id.
+#if $reads.layout == 'paired'
+    #set $ext = 'fastq.gz' if $reads.fwd.is_of_type('fastqsanger.gz') else 'fastq'
+    ln -s '$reads.fwd' 'sample_R1.$ext' &&
+    ln -s '$reads.rev' 'sample_R2.$ext' &&
+#else
+    #set $ext = 'fastq.gz' if $reads.single.is_of_type('fastqsanger.gz') else 'fastq'
+    ln -s '$reads.single' 'sample.$ext' &&
+#end if
+
+pathotypr split-fastq
+    --markers '$markers'
+    --reference '$reference'
+#if $reads.layout == 'paired'
+    -i 'sample_R1.$ext' -i 'sample_R2.$ext'
+#else
+    -i 'sample.$ext' --no-auto-paired
+#end if
+    --output-prefix 'result'
+    --kmer-size $kmer_size
+    --min-depth $min_depth
+    --min-alt-percent $min_alt_percent
+    $nested_classification
+    @THREADS@
+    ]]></command>
+    <inputs>
+        <conditional name="reads">
+            <param name="layout" type="select" label="Read layout">
+                <option value="paired" selected="true">Paired end</option>
+                <option value="single">Single end</option>
+            </param>
+            <when value="paired">
+                <param name="fwd" type="data" format="fastqsanger,fastqsanger.gz" label="Forward reads"/>
+                <param name="rev" type="data" format="fastqsanger,fastqsanger.gz" label="Reverse reads"/>
+            </when>
+            <when value="single">
+                <param name="single" type="data" format="fastqsanger,fastqsanger.gz" label="Reads"/>
+            </when>
+        </conditional>
+        <expand macro="markers_and_reference"/>
+        <expand macro="kmer_size" default="31"/>
+        <param argument="--min-depth" type="integer" min="1" value="10" label="Minimum depth"
+               help="Reads required at a marker position before a variant is called."/>
+        <!-- Whole percent only: pathotypr parses this as an integer, so 95.5
+             is rejected outright rather than rounded. -->
+        <param argument="--min-alt-percent" type="integer" min="0" max="100" value="95"
+               label="Minimum alternate allele frequency (%)"
+               help="How much of the depth must carry the alternate allele, in whole percent. Lower this for mixed or low-coverage samples, knowing that it also admits sequencing error."/>
+        <expand macro="nested_classification"/>
+    </inputs>
+    <outputs>
+        <data name="mutations" format="tabular" label="${tool.name} on ${on_string}: per-marker calls"
+              from_work_dir="result_sample_mutations.tsv"/>
+        <data name="summary" format="tabular" label="${tool.name} on ${on_string}: summary"
+              from_work_dir="result_summary.tsv"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2">
+            <conditional name="reads">
+                <param name="layout" value="paired"/>
+                <param name="fwd" value="sample1_R1.fastq.gz" ftype="fastqsanger.gz"/>
+                <param name="rev" value="sample1_R2.fastq.gz" ftype="fastqsanger.gz"/>
+            </conditional>
+            <param name="markers" value="markers.tsv" ftype="tabular"/>
+            <param name="reference" value="reference.fasta" ftype="fasta"/>
+            <output name="summary">
+                <assert_contents>
+                    <has_text text="major_lineage"/>
+                    <has_text text="L2;L2.1;L2.1.1"/>
+                </assert_contents>
+            </output>
+            <output name="mutations">
+                <assert_contents>
+                    <has_text text="alt_fraction"/>
+                    <has_text text="L2;L2.1;L2.1.1"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- A depth threshold above the coverage of the test data must call nothing. -->
+        <test expect_num_outputs="2">
+            <conditional name="reads">
+                <param name="layout" value="paired"/>
+                <param name="fwd" value="sample1_R1.fastq.gz" ftype="fastqsanger.gz"/>
+                <param name="rev" value="sample1_R2.fastq.gz" ftype="fastqsanger.gz"/>
+            </conditional>
+            <param name="markers" value="markers.tsv" ftype="tabular"/>
+            <param name="reference" value="reference.fasta" ftype="fasta"/>
+            <param name="min_depth" value="500"/>
+            <output name="mutations">
+                <assert_contents>
+                    <has_n_lines n="1"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+`pathotypr split-fastq` genotypes a marker panel straight from sequencing reads,
+with no alignment and no assembly. It builds a diagnostic k-mer for each allele
+of each marker, streams the reads past a Bloom filter, and counts how many reads
+carry the reference allele and how many carry the alternate one.
+
+Because it streams, memory does not grow with the number of reads.
+
+Two tables come out:
+
+- **per-marker calls**: position, both alleles, the read counts behind each, the
+  alternate fraction, and the lineage the marker belongs to.
+- **summary**: the count of hits per lineage and the major lineage call, in the
+  same shape *pathotypr classify* produces, so the two are directly comparable.
+
+**Depth and frequency**
+
+A marker is only called when it has at least *minimum depth* reads and the
+alternate allele reaches *minimum alternate frequency*. The defaults, 10 reads
+and 95%, are strict on purpose: they are chosen for a clonal sample. Lower the
+frequency if you expect mixed infections, and expect more sequencing error to
+come with it.
+
+.. class:: warningmark
+
+**Indels are skipped here.** A marker whose REF and ALT differ in length is
+dropped, because short reads across repetitive regions give unreliable k-mer
+matches for insertions and deletions. Detect those with *pathotypr classify* on
+an assembly instead.
+
+@MARKER_HELP@
+
+@ORGANISM_NOTE@
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
diff --git a/galaxy/tools/pathotypr/pathotypr_train.xml b/galaxy/tools/pathotypr/pathotypr_train.xml
new file mode 100644
index 0000000..f8a22d3
--- /dev/null
+++ b/galaxy/tools/pathotypr/pathotypr_train.xml
@@ -0,0 +1,135 @@
+<tool id="pathotypr_train" name="pathotypr train" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>fits a Random Forest lineage classifier on labelled genomes</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="exit_code"><![CDATA[
+pathotypr train
+    --input '$input'
+    --output 'model.pathotypr.zst'
+    --kmer-size $kmer_size
+    --max-depth $max_depth
+    --min-samples-leaf $min_samples_leaf
+#if $accuracy.method == 'cv'
+    --cv-folds $accuracy.cv_folds
+#else
+    --test-split $accuracy.test_split
+#end if
+    @THREADS@
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="fasta" label="Labelled genomes"
+               help="A FASTA whose headers carry the class label. See the warning below about how the label is read."/>
+        <expand macro="kmer_size" default="21"/>
+        <conditional name="accuracy">
+            <param name="method" type="select" label="How to estimate accuracy"
+                   help="The final model is trained on all of the data either way. This only changes how the accuracy figure is obtained.">
+                <option value="split" selected="true">A single held-out split</option>
+                <option value="cv">Stratified cross-validation</option>
+            </param>
+            <when value="split">
+                <param argument="--test-split" type="float" min="0" max="0.99" value="0.2"
+                       label="Fraction held out"/>
+            </when>
+            <when value="cv">
+                <param argument="--cv-folds" type="integer" min="2" value="5" label="Number of folds"
+                       help="Must not exceed the number of samples. Preferable to a single split on small or imbalanced sets."/>
+            </when>
+        </conditional>
+        <param argument="--max-depth" type="integer" min="1" value="20" label="Maximum tree depth"
+               help="Lower values reduce overfitting on small datasets."/>
+        <param argument="--min-samples-leaf" type="integer" min="1" value="5"
+               label="Minimum samples per leaf"
+               help="Higher values act as regularisation, stopping a tree memorising individual genomes."/>
+        <param name="want_reports" type="boolean" checked="false"
+               label="Also output the feature importance reports"
+               help="Which hash buckets the forest split on most, and where the k-mers behind them sit in the training sequences."/>
+    </inputs>
+    <outputs>
+        <data name="model" format="data" label="${tool.name} on ${on_string}: model"
+              from_work_dir="model.pathotypr.zst"/>
+        <data name="importance" format="tabular" label="${tool.name} on ${on_string}: feature importance"
+              from_work_dir="model.pathotypr.importance.tsv">
+            <filter>want_reports</filter>
+        </data>
+        <data name="coords" format="tabular" label="${tool.name} on ${on_string}: discriminant k-mer coordinates"
+              from_work_dir="model.pathotypr.importance.coords.tsv">
+            <filter>want_reports</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input" value="training.fasta" ftype="fasta"/>
+            <conditional name="accuracy">
+                <param name="method" value="cv"/>
+                <param name="cv_folds" value="3"/>
+            </conditional>
+            <output name="model">
+                <assert_contents>
+                    <has_size min="100"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="3">
+            <param name="input" value="training.fasta" ftype="fasta"/>
+            <param name="want_reports" value="true"/>
+            <output name="importance">
+                <assert_contents>
+                    <has_text text="rank"/>
+                    <has_text text="importance_pct"/>
+                </assert_contents>
+            </output>
+            <output name="coords">
+                <assert_contents>
+                    <has_text text="lineage"/>
+                    <has_text text="position"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+`pathotypr train` turns a labelled set of genomes into a Random Forest that
+*pathotypr predict* can then apply to new sequences. Each sequence is hashed
+into a fixed-size k-mer feature vector, so there is no vocabulary to fit and the
+features at prediction time are identical to those at training time by
+construction.
+
+The accuracy figure it reports comes either from a single held-out split or from
+stratified cross-validation. Either way the **model it saves is trained on all
+of your data**; the split only exists to produce the estimate. An out-of-bag
+accuracy is also computed from the bootstrap samples and costs nothing extra.
+
+.. class:: warningmark
+
+**The label is the first whitespace-separated token of the FASTA header.**
+Everything after the first space is ignored. This is the single most common
+mistake with this tool: genomes downloaded from a public archive keep headers
+like ``>GCF_000195955.2 Mycobacterium tuberculosis H37Rv``, which yields one
+class per accession rather than one class per group, and nothing warns you.
+Rewrite the headers to the labels you actually want predicted::
+
+    >L2 sample_A collected_2021
+    >L2 sample_B
+    >L4.3 sample_C
+
+Labels are compared as flat strings. ``L4`` and ``L4.1`` are two unrelated
+classes; the tool knows nothing about the hierarchy in the name. If you want
+hierarchical calls, use a marker panel with *pathotypr classify* or
+*pathotypr split-fastq* instead.
+
+**How much data**
+
+Nothing enforces a minimum per class, but a class represented by one or two
+genomes contributes almost nothing the forest can generalise from. Aim for ten
+or more per class, and prefer cross-validation over a single split when the set
+is small or imbalanced.
+
+@ORGANISM_NOTE@
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
diff --git a/galaxy/tools/pathotypr/test-data/make_testdata.py b/galaxy/tools/pathotypr/test-data/make_testdata.py
new file mode 100644
index 0000000..32ebf29
--- /dev/null
+++ b/galaxy/tools/pathotypr/test-data/make_testdata.py
@@ -0,0 +1,178 @@
+#!/usr/bin/env python3
+"""Generate the smallest test data that still exercises every pathotypr module.
+
+Everything is deterministic: a fixed seed, and every derived file is built from
+the same reference so the expected calls can be reasoned about rather than
+copied out of a run.
+
+Size matters here. tools-iuc carries this data forever, so the reference is a
+couple of kb rather than a genome.
+"""
+import gzip
+import os
+import random
+import sys
+
+random.seed(20260816)
+
+OUT = sys.argv[1] if len(sys.argv) > 1 else "test-data"
+os.makedirs(OUT, exist_ok=True)
+
+REF_LEN = 2000
+K = 31            # default --kmer-size
+FLANK = 10        # default --min-flank-bases
+READ_LEN = 100
+DEPTH = 20        # comfortably above the default --min-depth of 10
+
+
+def w(name, text):
+    with open(os.path.join(OUT, name), "w") as fh:
+        fh.write(text)
+    return os.path.join(OUT, name)
+
+
+def revcomp(s):
+    return s.translate(str.maketrans("ACGT", "TGCA"))[::-1]
+
+
+# ---------------------------------------------------------------- reference
+# Random sequence, but every k-mer window around a marker has to be unique or
+# the diagnostic k-mers match in more than one place. Random 2 kb over a 31-mer
+# window is unique with overwhelming probability; asserted below rather than
+# assumed.
+ref = "".join(random.choice("ACGT") for _ in range(REF_LEN))
+
+# Marker positions are 1-based. Keep them clear of the ends so a centred 31-mer
+# with 10 flanking bases always fits.
+MARKERS = [
+    # pos, alt, lineage levels, gene, mutation
+    (200,  "L1",),
+    (400,  "L2",),
+    (600,  "L2", "L2.1"),
+    (800,  "L2", "L2.1", "L2.1.1"),
+    (1000, "L3",),
+    (1200, "L3", "L3.2"),
+]
+ANNOTATED = [
+    (1400, "RIF", "rpoB", "S450L"),
+    (1600, "INH", "katG", "Ser315Thr"),
+]
+
+
+def alt_of(base):
+    return {"A": "G", "G": "A", "C": "T", "T": "C"}[base]
+
+
+rows = ["#position\tref\talt\tlevel1\tlevel2\tlevel3"]
+marker_alts = {}
+for m in MARKERS:
+    pos, levels = m[0], list(m[1:])
+    r = ref[pos - 1]
+    a = alt_of(r)
+    marker_alts[pos] = (r, a)
+    rows.append("\t".join([str(pos), r, a] + levels))
+for pos, lineage, gene, mut in ANNOTATED:
+    r = ref[pos - 1]
+    a = alt_of(r)
+    marker_alts[pos] = (r, a)
+    # The empty cell after the lineage is what makes gene and mutation be read
+    # as annotations rather than as two more lineage levels.
+    rows.append("\t".join([str(pos), r, a, lineage, "", gene, mut]))
+
+# Every marker k-mer must be unique in the reference, otherwise a hit is
+# ambiguous and the test data would be testing the wrong thing.
+half = K // 2
+for pos in marker_alts:
+    kmer = ref[pos - 1 - half: pos + half]
+    assert len(kmer) == K, f"marker {pos} too close to the end"
+    assert ref.count(kmer) == 1 and ref.count(revcomp(kmer)) == 0, (
+        f"marker k-mer at {pos} is not unique")
+    assert pos - 1 - half >= FLANK and pos + half <= REF_LEN - FLANK
+
+w("reference.fasta", ">MTB_test_ref synthetic 2 kb reference\n" +
+  "\n".join(ref[i:i + 60] for i in range(0, len(ref), 60)) + "\n")
+w("markers.tsv", "\n".join(rows) + "\n")
+
+
+def genome_with(alt_positions, name, desc):
+    """The reference with the ALT allele substituted at the given positions."""
+    g = list(ref)
+    for pos in alt_positions:
+        g[pos - 1] = marker_alts[pos][1]
+    seq = "".join(g)
+    w(name, f">{desc}\n" + "\n".join(seq[i:i + 60] for i in range(0, len(seq), 60)) + "\n")
+    return seq
+
+
+# sample1 carries the full L2 -> L2.1 -> L2.1.1 path plus the RIF marker.
+s1 = genome_with([400, 600, 800, 1400], "sample1.fasta", "sample1")
+# sample2 carries L3 -> L3.2 and the INH marker.
+s2 = genome_with([1000, 1200, 1600], "sample2.fasta", "sample2")
+
+# ------------------------------------------------------------------- FASTQ
+def reads(seq, path, depth=DEPTH, read_len=READ_LEN, paired=True):
+    """Tile the genome so every position, markers included, is covered `depth`
+    times. Tiling rather than random sampling keeps the file small and the
+    coverage guaranteed."""
+    step = max(1, (read_len * 2) // depth)
+    r1, r2 = [], []
+    n = 0
+    for start in range(0, len(seq) - read_len * 2, step):
+        f = seq[start:start + read_len]
+        rc = revcomp(seq[start + read_len: start + read_len * 2])
+        if len(f) < read_len or len(rc) < read_len:
+            continue
+        n += 1
+        q = "I" * read_len
+        r1.append(f"@read{n}/1\n{f}\n+\n{q}\n")
+        r2.append(f"@read{n}/2\n{rc}\n+\n{q}\n")
+    if paired:
+        with gzip.open(path + "_R1.fastq.gz", "wt") as fh:
+            fh.write("".join(r1))
+        with gzip.open(path + "_R2.fastq.gz", "wt") as fh:
+            fh.write("".join(r2))
+    return n
+
+
+n1 = reads(s1, os.path.join(OUT, "sample1"))
+
+# ---------------------------------------------------------------- training
+# train takes the label from the first whitespace-separated token of the
+# header. Several genomes per class, each a mutated copy, so the forest has
+# something to separate.
+def mutate(seq, n_changes, rng):
+    g = list(seq)
+    for _ in range(n_changes):
+        i = rng.randrange(len(g))
+        g[i] = alt_of(g[i])
+    return "".join(g)
+
+
+rng = random.Random(7)
+train_records = []
+for i in range(6):
+    train_records.append((f"L2 train_L2_{i}", mutate(s1, 20, rng)))
+for i in range(6):
+    train_records.append((f"L3 train_L3_{i}", mutate(s2, 20, rng)))
+
+w("training.fasta", "".join(
+    f">{h}\n" + "\n".join(s[j:j + 60] for j in range(0, len(s), 60)) + "\n"
+    for h, s in train_records))
+
+# query set for predict: two unseen genomes, one per class
+w("query.fasta", "".join(
+    f">{h}\n" + "\n".join(s[j:j + 60] for j in range(0, len(s), 60)) + "\n"
+    for h, s in [("query_a", mutate(s1, 20, rng)), ("query_b", mutate(s2, 20, rng))]))
+
+# ------------------------------------------------------------- match refs
+w("references.fasta",
+  ">ref_A\n" + "\n".join(s1[i:i + 60] for i in range(0, len(s1), 60)) + "\n" +
+  ">ref_B\n" + "\n".join(s2[i:i + 60] for i in range(0, len(s2), 60)) + "\n")
+
+print(f"reference   {REF_LEN} bp")
+print(f"markers     {len(marker_alts)} ({len(MARKERS)} lineage, {len(ANNOTATED)} annotated)")
+print(f"reads       {n1} pairs, ~{n1 * READ_LEN * 2 / REF_LEN:.0f}x")
+print(f"training    {len(train_records)} records, 2 classes")
+print()
+for f in sorted(os.listdir(OUT)):
+    print(f"  {os.path.getsize(os.path.join(OUT, f)):>8} B  {f}")
diff --git a/galaxy/tools/pathotypr/test-data/markers.tsv b/galaxy/tools/pathotypr/test-data/markers.tsv
new file mode 100644
index 0000000..a0d38c5
--- /dev/null
+++ b/galaxy/tools/pathotypr/test-data/markers.tsv
@@ -0,0 +1,9 @@
+#position	ref	alt	level1	level2	level3
+200	C	T	L1
+400	G	A	L2
+600	G	A	L2	L2.1
+800	T	C	L2	L2.1	L2.1.1
+1000	A	G	L3
+1200	C	T	L3	L3.2
+1400	A	G	RIF		rpoB	S450L
+1600	A	G	INH		katG	Ser315Thr
diff --git a/galaxy/tools/pathotypr/test-data/model.pathotypr.zst b/galaxy/tools/pathotypr/test-data/model.pathotypr.zst
new file mode 100644
index 0000000000000000000000000000000000000000..d1a7536afa42458a126651d3c605226d3efa69ca
GIT binary patch
literal 563
zcmV-30?hp=wJ-euSXB`KR@6>EATQXA0a(7D@cRN{Y{C!GW=8x)vl^41Q?z*i-z<_~
zC@3I}Y8W6RU`}%K#f^RWehOAzhq|(R61yk2NlF1b06+jd0IW2ek#Xg;PL9eqRuMn+
z0D2eVyeA;2HROj29N5{dv;A8>5GUI+F>Ov_ej+i=Ie<HRTtEU*0ExH;<oE)d-Kqcz
z`JsHO0r=o?+lw{^%w8&Sk1jfdrV&2rDsNJSqls4~^W|Xr5}d{ppDH2tn?m!Kr$1DL
zcjf5?nA?3((L)L~5QX8sMA$>{>xC2PSlx<f$Kbp_k%msJ>%=_TRQ^q5xILB3nyICU
zcLPScrUK_JiinEtR^|{_Y^-8K8d&}I2w1o=M&@KxY}<G!U{p-zwyy*Cw;=_B9+#E+
zu+lx&J{}2|$l?MZ)Izj4d|jTsq+Wo>sF2jK#(<L~NjefBF%S<TNC*@HxIrR8F#=_U
z5#gxkHZm3I-`7M^X>KKvN;Juu=f>V%1=TbJH28ICKvnjHVNGpU4{i3%_=!!+N8~wk
zoOA-(r1XDF18EZ{liaDiWulH}Xl^$<`H85R&|Aaln*9#g*pQ85G;L!TH=GHis6lW^
z`K&Ot(%285Mh_w4llQGryEky7?MYQG;X$6n>kXFDl4PHaxmc2hY%a_^!$~+EN~h5@
zB?;kX;u(C1!-vQ>SWJkTugrPHe8WS*i{(X9Gm1a(!h{JHY+O1p`O@%HhuJZG{REV?
B2}A$@

literal 0
HcmV?d00001

diff --git a/galaxy/tools/pathotypr/test-data/query.fasta b/galaxy/tools/pathotypr/test-data/query.fasta
new file mode 100644
index 0000000..ccc6788
--- /dev/null
+++ b/galaxy/tools/pathotypr/test-data/query.fasta
@@ -0,0 +1,70 @@
+>query_a
+CGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGACACTCAACTTCCCA
+GTAGCGCTGATAGGGAAGGACTGACAGGCGTGAACCGGGTCCAGCGCCGGGGGATGCGTT
+AATGAAACTCCTTAGAATAGAGTTAGATTCCTACCTTTGTGGGGTGGTGCTTCACCAGGG
+TCTGTGACCACTCGACCCGCGCTAGATTTTCGGCGTCTACCTGTATAACTTATGTCCGCT
+CGCGGTACCTAGTATTGTGTTGGACCTCCACTCTCGAAGTCGAGATAAGAACATCCACTT
+AAAGGGTGTCAAGTAGTTTTCCTATGGGGGATTGCTCGGCTGGAGGAACACATCGTGATA
+CTACTAATATTTCCTTCACCGACCCTATGCCGTATCCCCACAGATTAATCGTTTGTCATC
+AGGGGCTGGTACGATTTTCGCTTTGTCGAAGATATTTCCCCGTTAACTTTATTCTGGCAG
+AAGTCTCATGTCCGATATACTAAGTCATGTTAAAGATCTCCGACCCGGGTAGTAAAATCC
+GTTTGACAACTAAGTACAAGCAGGTTAAGCAACTAGGTTGCGCCGTCAGAAGTGGCTCTA
+GTCGGAATAAACTTGAAAAAGGACAGCGGCAACGATACTCTTGCTAGACGCCTGGAACTT
+GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACAGATTCAAAGAATCCCATGCCCCA
+GGCGTACGTACGGTCTGGGAGTGCTGGCGAGCGATCCTATAGAAGGCCTGTATGACACCT
+TTTATGTAGGCGCGTTGTACCAACCGATACGTGCTAGTTCGTCACAATTCCCGTTATACA
+TCGCTGGGGTGGACAACACCTTTGAAAGGAACAAATCCGGAACGATGTCCCGTCACTGCA
+ATGGTAGAGAAGTGGCAGGTTGGATTACAGCGCCATATACGGTTGCGTACTGCTGTCTCA
+GAATTTCTAACATAGTAAATCGTCTTGATCTAGCGGAATATGCCGACGCCAAGTTTCGGT
+CATAGTAAGGTGTGGTGCTAGGGGCTCCTATACGCCCAGTGTGGGCGACTGATTTGCGTA
+CGGAGCGACTTAATGCGTCCCAGGTCTCTAACCGCGAAGCTTGCCTTCAATGTCGGGGCA
+AAAACTGCACCTCTTATCGCGCTTAGGGCCGACGTGCACTATCTTCTCCGCCCCAGACAC
+CGATTGGAACTGATGATCGCGAGAAACTCTACTGTACTTGGAGATAGGCTATTCATCACC
+CGCTGCACGATCGGTCATCGAGGGGCGGGAGGGATAGCCCGGGTCACAGAAGCTGCAGGG
+GGTCGTCCATGACATGGATGGGCTAGCTAGATACATGCAACGGTCATATGCTACCCTATC
+TGCGTCCTCAGGAAACCCCGCGTAAATTAATACAGTGAATATTTCTCACAAATATAGCAC
+ATTTTTTTAACTAAATCTCAGCGAATGGCGACGAGTGATGCTTAAACAATGGTTACGTGT
+GCTCTAAGCTACTCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA
+ATGGCTTCCACGCCTGCTATAGCGGCCCAAACATCTTTGATCCGTTAAAGCCTGCGGCCC
+CCATCCTAGCGTTGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCTTATA
+CCTTGCACCATGACTTCAGTCCTGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA
+TGATTAGCAATCTCCGGCTAAGAGATGAGCAGTACACGCGTGGCTACCTATCCAATGCTG
+GCTACGCTAGTGGTAACAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG
+GAATCCATGCGCGGAGTACCTGGCTGCAAGCGGCATACTGATCCGTGTTGTTCCCTAGAC
+GCTGGGTGTCTCGTCGGACGATAATTCACATTGCTGGTTCCTATAGTCTCCTGTCACAGG
+ATCACGGCAGAAAGGAGGGG
+>query_b
+TGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGACACTCAGCTTCCCA
+GTAGCGCTGATAGGGAAGGACTGACAGGCGTGAACCGGGTCCAGCGCTGGGGGATGCGTT
+AATGAAATTCCTTAGAACAGAGTTGGATTCCTACCTTTGTGGGGTGGTGCTTCACCAGGG
+TCTGTGACCACTCGACCCGCGCTAGATCTCCGACGTCTACCTGTACAACTTATGTCTGCT
+CGCGGTACCTAATATTGTGTTGGACCTCCACTCTCGAAGTCGAGATAAGAACATCCACTT
+AAAGAGTGTTAAGTAGTTTTCCTATGGGGGATCGCTCGGCTGGAGGAACACATCGTGATA
+CTACTAATATTTCCTTCACCGACCCTATGCTGTATCCCCGCAGATTAATCGTTTGTCATC
+AGGGGTTAGTACGATTTTCGCTTTGTCGAAGATATTTCCCCGTTAACTTTATTCTGGCAG
+AAGTCTCATGTCCGATATACTAAGTCATGTTAAAGACCTCCGACCCGGGTAGTAAAATCC
+GTTTGACAACTAAGTACAAGCAGGTTAAGCAACTAGGTTGCGCCGTCAGAAGTGGCTCTG
+GTCGGAATAAACTTGAAAAAGGACAGCGGCAACGATACTCTTGCTAGACGCCTGGAACTT
+GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACGGATTCAAAGAATCCTATGCCCCA
+GGCGTACGTACGGTCTGGGAGTGCCAGCGAGCGATCCTATAGAAGGCCTGCATGACACCT
+TTTATGTAGGCGCGTTGTATCAACCGACACGTGCTAGTTCATCACAATTCCCGTTATACA
+TCGCTGGGGTGGACAACACCTTTGAAAGGAACAAATCCGGAACGATGTCCCGTCACTGCA
+ATAGTAGAGAAGTGGCAGGTTGGATTACAGCGCCATATACGGTTGCGTACTGCTGTCTCA
+GAATTTCTAACGTAGTAAATCGTCTTAATCTAGCGGAATGTGCCGACGCCAAGTTTCGGT
+CATAGTAAGGTGTGGTGCTAGGGGCTCCTATACGCCCAGTGTGGGCGACTGATTTGCGTA
+CGGAGCGACTTAATGCGTTCCAGGTCTCTAACCGCGAAGCTTGCCTTCAATGTCGGGGCA
+AAAACTGCACCTCTTATCGCACTTAGGGCCGACGTGCACTATCTTCTCCGCCCCAGACAT
+CGATTGGAACTGATGATCGCGAGAAACTCTGCTATACTTGGAGATAGGCTATTCATTGCC
+CGCTGCACGATCGGTCATCGAGGGGCGGGAGGGATAGCCCGGGTCACAGAAGCTGCAGGG
+GGTCGTCCATGACATGGATGGGCTAGCTAGATACATGCAACGGTCATATGCTACCCTATC
+TGCGTCCTCAGGAAACCCCACGTAAATTAATACAGTGAATATTTCTCACAAATATAGCAC
+ATTTTTTTAACTAAATCTCAGCGAATGGCGACGAGTGATGCTTAAACAATGGTTACGTGT
+GCTCTAAGCTACTCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA
+ATGGCTTCCACGCCTGCTATAGCGGCCCAAACATCTTTGGTCCGTTAAAGCCTGCGGCCC
+CCATCCTAGCGTTGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCTTATA
+CCTTGCACCATGACTTCAGTCCTGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA
+TGATTAGCAATCTCCGGCTAAGAGATGAGCAGTACACGCGTGGCTACCTACCCAATGCTG
+GCTACGCTAGTGGTAACAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG
+GAATCCATGCGCGGAGTACCTGGCTGCAAGCGGCATACTGATCCGTGTTGTTCCCTAGAC
+GCTGGGTGTCTCGTCGGACGATAGTTCACATTGCTGATTCCTATAGTCTCCTGTCACAGG
+ATCACGGCAGAAAGGAGGGG
diff --git a/galaxy/tools/pathotypr/test-data/reference.fasta b/galaxy/tools/pathotypr/test-data/reference.fasta
new file mode 100644
index 0000000..258cfee
--- /dev/null
+++ b/galaxy/tools/pathotypr/test-data/reference.fasta
@@ -0,0 +1,35 @@
+>MTB_test_ref synthetic 2 kb reference
+TGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGACACTCAACTTCCCA
+GTAGCGCTGATAGGGAAGGACTGACAGGCGTGAACCGGGTCCAGCGCTGGGGGATGCGTT
+AATGAAATTCCTTAGAACAGAGTTAGATTCCTACCTTTGTGGGGTGGTGCTTCACCAGGG
+TCTGTGACCACTCGACCCGCGCTAGATTTCCGACGTCTACCTGTACAACTTATGTCCGCT
+CGCGGTACCTAGTATTGTGTTGGACCTCCACTCTCGAAGTCGAGATAAGAACATCCACTT
+AAAGGGTGTTAAGTAGTTTTCCTATGGGGGATCGCTCGGCTGGAGGAACACATCGTGATA
+CTACTAATATTTCCTTCACCGACCCTATGCTGTATCCCCGCAGATTAATCGTTTGTCATC
+AGGGGCTAGTACGATTTTCGCTTTGTCGAAGATATTTCCCCGTTAACTTTATTCTGGCAG
+AAGTCTCATGTCCGATATACTAAGTCATGTTAAAGATCTCCGACCCGGGTAGTAAAATCC
+GTTTGACAACTAAGTACAAGCAGGTTAAGCAACTAGGTTGCGCCGTCAGAAGTGGCTCTG
+GTCGGAATAAACTTGAAAAAGGACAGCGGCAACGATACTCTTGCTAGACGCCTGGAACTT
+GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACGGATTCAAAGAATCCCATGCCCCA
+GGCGTACGTACGGTCTGGGAGTGCTGGCGAGCGATCCTATAGAAGGCCTGTATGACACCT
+TTTATGTAGGCGCGTTGTATCAACCGACACGTGCTAGTTCATCACAATTCCCGTTATACA
+TCGCTGGGGTGGACAACACCTTTGAAAGGAACAAATCCGGAACGATGTCCCGTCACTGCA
+ATAGTAGAGAAGTGGCAGGTTGGATTACAGCGCCATATACGGTTGCGTACTGCTGTCTCA
+GAATTTCTAACATAGTAAATCGTCTTAATCTAGCGGAATATGCCGACGCCAAGTTTCGGT
+CATAGTAAGGTGTGGTGCTAGGGGCTCCTATACGCCCAGTGTGGGCGACTGATTTGCGTA
+CGGAGCGACTTAATGCGTTCCAGGTCTCTAACCGCGAAGCTTGCCTTCAATGTCGGGGCA
+AAAACTGCACCTCTTATCGCACTTAGGGCCGACGTGCACTATCTTCTCCGCCCCAGACAC
+CGATTGGAACTGATGATCGCGAGAAACTCTGCTGTACTTGGAGATAGGCTATTCATCACC
+CGCTGCACGATCGGTCATCGAGGGGCGGGAGGGATAGCCTGGGTCACAGAAGCTGCAGGG
+GGTCGTCCATGACATGGATGGGCTAGCTAGATACATGCAACGGTCATATGCTACCCTATC
+TGCGTCCTCAGGAAACCCCACGTAAATTAATACAGTGAATATTTCTCACAAATATAGCAC
+ATTTTTTTAACTAAATCTCAGCGAATGGCGACGAGTGATGCTTAAACAATGGTTACGTGT
+GCTCTAAGCTACTCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA
+ATGGCTTCCACGCCTGCTATAGCGGCCCAAACATCTTTGATCCGTTAAAGCCTGCGGCCC
+CCATCCTAGCGTTGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCTTATA
+CCTTGCACCATGACTTCAGTCCTGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA
+TGATTAGCAATCTCCGGCTAAGAGATGAGCAGTACACGCGTGGCTACCTATCCAATGCTG
+GCTACGCTAGTGGTAACAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG
+GAATCCATGCGCGGAGTACCTGGCTGCAAGCGGCATACTGATCCGTGTTGTTCCCTAGAC
+GCTGGGTGTCTCGTCGGACGATAATTCACATTGCTGGTTCCTATAGTCTCCTGTCACAGG
+ATCACGGCAGAAAGGAGGGG
diff --git a/galaxy/tools/pathotypr/test-data/references.fasta b/galaxy/tools/pathotypr/test-data/references.fasta
new file mode 100644
index 0000000..4022036
--- /dev/null
+++ b/galaxy/tools/pathotypr/test-data/references.fasta
@@ -0,0 +1,70 @@
+>ref_A
+TGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGACACTCAACTTCCCA
+GTAGCGCTGATAGGGAAGGACTGACAGGCGTGAACCGGGTCCAGCGCTGGGGGATGCGTT
+AATGAAATTCCTTAGAACAGAGTTAGATTCCTACCTTTGTGGGGTGGTGCTTCACCAGGG
+TCTGTGACCACTCGACCCGCGCTAGATTTCCGACGTCTACCTGTACAACTTATGTCCGCT
+CGCGGTACCTAGTATTGTGTTGGACCTCCACTCTCGAAGTCGAGATAAGAACATCCACTT
+AAAGGGTGTTAAGTAGTTTTCCTATGGGGGATCGCTCGGCTGGAGGAACACATCGTGATA
+CTACTAATATTTCCTTCACCGACCCTATGCTGTATCCCCACAGATTAATCGTTTGTCATC
+AGGGGCTAGTACGATTTTCGCTTTGTCGAAGATATTTCCCCGTTAACTTTATTCTGGCAG
+AAGTCTCATGTCCGATATACTAAGTCATGTTAAAGATCTCCGACCCGGGTAGTAAAATCC
+GTTTGACAACTAAGTACAAGCAGGTTAAGCAACTAGGTTGCGCCGTCAGAAGTGGCTCTA
+GTCGGAATAAACTTGAAAAAGGACAGCGGCAACGATACTCTTGCTAGACGCCTGGAACTT
+GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACGGATTCAAAGAATCCCATGCCCCA
+GGCGTACGTACGGTCTGGGAGTGCTGGCGAGCGATCCTATAGAAGGCCTGTATGACACCT
+TTTATGTAGGCGCGTTGTACCAACCGACACGTGCTAGTTCATCACAATTCCCGTTATACA
+TCGCTGGGGTGGACAACACCTTTGAAAGGAACAAATCCGGAACGATGTCCCGTCACTGCA
+ATAGTAGAGAAGTGGCAGGTTGGATTACAGCGCCATATACGGTTGCGTACTGCTGTCTCA
+GAATTTCTAACATAGTAAATCGTCTTAATCTAGCGGAATATGCCGACGCCAAGTTTCGGT
+CATAGTAAGGTGTGGTGCTAGGGGCTCCTATACGCCCAGTGTGGGCGACTGATTTGCGTA
+CGGAGCGACTTAATGCGTTCCAGGTCTCTAACCGCGAAGCTTGCCTTCAATGTCGGGGCA
+AAAACTGCACCTCTTATCGCACTTAGGGCCGACGTGCACTATCTTCTCCGCCCCAGACAC
+CGATTGGAACTGATGATCGCGAGAAACTCTGCTGTACTTGGAGATAGGCTATTCATCACC
+CGCTGCACGATCGGTCATCGAGGGGCGGGAGGGATAGCCTGGGTCACAGAAGCTGCAGGG
+GGTCGTCCATGACATGGATGGGCTAGCTAGATACATGCAACGGTCATATGCTACCCTATC
+TGCGTCCTCAGGAAACCCCGCGTAAATTAATACAGTGAATATTTCTCACAAATATAGCAC
+ATTTTTTTAACTAAATCTCAGCGAATGGCGACGAGTGATGCTTAAACAATGGTTACGTGT
+GCTCTAAGCTACTCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA
+ATGGCTTCCACGCCTGCTATAGCGGCCCAAACATCTTTGATCCGTTAAAGCCTGCGGCCC
+CCATCCTAGCGTTGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCTTATA
+CCTTGCACCATGACTTCAGTCCTGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA
+TGATTAGCAATCTCCGGCTAAGAGATGAGCAGTACACGCGTGGCTACCTATCCAATGCTG
+GCTACGCTAGTGGTAACAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG
+GAATCCATGCGCGGAGTACCTGGCTGCAAGCGGCATACTGATCCGTGTTGTTCCCTAGAC
+GCTGGGTGTCTCGTCGGACGATAATTCACATTGCTGGTTCCTATAGTCTCCTGTCACAGG
+ATCACGGCAGAAAGGAGGGG
+>ref_B
+TGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGACACTCAACTTCCCA
+GTAGCGCTGATAGGGAAGGACTGACAGGCGTGAACCGGGTCCAGCGCTGGGGGATGCGTT
+AATGAAATTCCTTAGAACAGAGTTAGATTCCTACCTTTGTGGGGTGGTGCTTCACCAGGG
+TCTGTGACCACTCGACCCGCGCTAGATTTCCGACGTCTACCTGTACAACTTATGTCCGCT
+CGCGGTACCTAGTATTGTGTTGGACCTCCACTCTCGAAGTCGAGATAAGAACATCCACTT
+AAAGGGTGTTAAGTAGTTTTCCTATGGGGGATCGCTCGGCTGGAGGAACACATCGTGATA
+CTACTAATATTTCCTTCACCGACCCTATGCTGTATCCCCGCAGATTAATCGTTTGTCATC
+AGGGGCTAGTACGATTTTCGCTTTGTCGAAGATATTTCCCCGTTAACTTTATTCTGGCAG
+AAGTCTCATGTCCGATATACTAAGTCATGTTAAAGATCTCCGACCCGGGTAGTAAAATCC
+GTTTGACAACTAAGTACAAGCAGGTTAAGCAACTAGGTTGCGCCGTCAGAAGTGGCTCTG
+GTCGGAATAAACTTGAAAAAGGACAGCGGCAACGATACTCTTGCTAGACGCCTGGAACTT
+GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACGGATTCAAAGAATCCCATGCCCCA
+GGCGTACGTACGGTCTGGGAGTGCTGGCGAGCGATCCTATAGAAGGCCTGTATGACACCT
+TTTATGTAGGCGCGTTGTATCAACCGACACGTGCTAGTTCATCACAATTCCCGTTATACA
+TCGCTGGGGTGGACAACACCTTTGAAAGGAACAAATCCGGAACGATGTCCCGTCACTGCA
+ATAGTAGAGAAGTGGCAGGTTGGATTACAGCGCCATATACGGTTGCGTACTGCTGTCTCA
+GAATTTCTAACATAGTAAATCGTCTTAATCTAGCGGAATGTGCCGACGCCAAGTTTCGGT
+CATAGTAAGGTGTGGTGCTAGGGGCTCCTATACGCCCAGTGTGGGCGACTGATTTGCGTA
+CGGAGCGACTTAATGCGTTCCAGGTCTCTAACCGCGAAGCTTGCCTTCAATGTCGGGGCA
+AAAACTGCACCTCTTATCGCACTTAGGGCCGACGTGCACTATCTTCTCCGCCCCAGACAT
+CGATTGGAACTGATGATCGCGAGAAACTCTGCTGTACTTGGAGATAGGCTATTCATCACC
+CGCTGCACGATCGGTCATCGAGGGGCGGGAGGGATAGCCTGGGTCACAGAAGCTGCAGGG
+GGTCGTCCATGACATGGATGGGCTAGCTAGATACATGCAACGGTCATATGCTACCCTATC
+TGCGTCCTCAGGAAACCCCACGTAAATTAATACAGTGAATATTTCTCACAAATATAGCAC
+ATTTTTTTAACTAAATCTCAGCGAATGGCGACGAGTGATGCTTAAACAATGGTTACGTGT
+GCTCTAAGCTACTCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA
+ATGGCTTCCACGCCTGCTATAGCGGCCCAAACATCTTTGGTCCGTTAAAGCCTGCGGCCC
+CCATCCTAGCGTTGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCTTATA
+CCTTGCACCATGACTTCAGTCCTGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA
+TGATTAGCAATCTCCGGCTAAGAGATGAGCAGTACACGCGTGGCTACCTATCCAATGCTG
+GCTACGCTAGTGGTAACAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG
+GAATCCATGCGCGGAGTACCTGGCTGCAAGCGGCATACTGATCCGTGTTGTTCCCTAGAC
+GCTGGGTGTCTCGTCGGACGATAATTCACATTGCTGGTTCCTATAGTCTCCTGTCACAGG
+ATCACGGCAGAAAGGAGGGG
diff --git a/galaxy/tools/pathotypr/test-data/sample1.fasta b/galaxy/tools/pathotypr/test-data/sample1.fasta
new file mode 100644
index 0000000..d29bd70
--- /dev/null
+++ b/galaxy/tools/pathotypr/test-data/sample1.fasta
@@ -0,0 +1,35 @@
+>sample1
+TGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGACACTCAACTTCCCA
+GTAGCGCTGATAGGGAAGGACTGACAGGCGTGAACCGGGTCCAGCGCTGGGGGATGCGTT
+AATGAAATTCCTTAGAACAGAGTTAGATTCCTACCTTTGTGGGGTGGTGCTTCACCAGGG
+TCTGTGACCACTCGACCCGCGCTAGATTTCCGACGTCTACCTGTACAACTTATGTCCGCT
+CGCGGTACCTAGTATTGTGTTGGACCTCCACTCTCGAAGTCGAGATAAGAACATCCACTT
+AAAGGGTGTTAAGTAGTTTTCCTATGGGGGATCGCTCGGCTGGAGGAACACATCGTGATA
+CTACTAATATTTCCTTCACCGACCCTATGCTGTATCCCCACAGATTAATCGTTTGTCATC
+AGGGGCTAGTACGATTTTCGCTTTGTCGAAGATATTTCCCCGTTAACTTTATTCTGGCAG
+AAGTCTCATGTCCGATATACTAAGTCATGTTAAAGATCTCCGACCCGGGTAGTAAAATCC
+GTTTGACAACTAAGTACAAGCAGGTTAAGCAACTAGGTTGCGCCGTCAGAAGTGGCTCTA
+GTCGGAATAAACTTGAAAAAGGACAGCGGCAACGATACTCTTGCTAGACGCCTGGAACTT
+GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACGGATTCAAAGAATCCCATGCCCCA
+GGCGTACGTACGGTCTGGGAGTGCTGGCGAGCGATCCTATAGAAGGCCTGTATGACACCT
+TTTATGTAGGCGCGTTGTACCAACCGACACGTGCTAGTTCATCACAATTCCCGTTATACA
+TCGCTGGGGTGGACAACACCTTTGAAAGGAACAAATCCGGAACGATGTCCCGTCACTGCA
+ATAGTAGAGAAGTGGCAGGTTGGATTACAGCGCCATATACGGTTGCGTACTGCTGTCTCA
+GAATTTCTAACATAGTAAATCGTCTTAATCTAGCGGAATATGCCGACGCCAAGTTTCGGT
+CATAGTAAGGTGTGGTGCTAGGGGCTCCTATACGCCCAGTGTGGGCGACTGATTTGCGTA
+CGGAGCGACTTAATGCGTTCCAGGTCTCTAACCGCGAAGCTTGCCTTCAATGTCGGGGCA
+AAAACTGCACCTCTTATCGCACTTAGGGCCGACGTGCACTATCTTCTCCGCCCCAGACAC
+CGATTGGAACTGATGATCGCGAGAAACTCTGCTGTACTTGGAGATAGGCTATTCATCACC
+CGCTGCACGATCGGTCATCGAGGGGCGGGAGGGATAGCCTGGGTCACAGAAGCTGCAGGG
+GGTCGTCCATGACATGGATGGGCTAGCTAGATACATGCAACGGTCATATGCTACCCTATC
+TGCGTCCTCAGGAAACCCCGCGTAAATTAATACAGTGAATATTTCTCACAAATATAGCAC
+ATTTTTTTAACTAAATCTCAGCGAATGGCGACGAGTGATGCTTAAACAATGGTTACGTGT
+GCTCTAAGCTACTCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA
+ATGGCTTCCACGCCTGCTATAGCGGCCCAAACATCTTTGATCCGTTAAAGCCTGCGGCCC
+CCATCCTAGCGTTGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCTTATA
+CCTTGCACCATGACTTCAGTCCTGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA
+TGATTAGCAATCTCCGGCTAAGAGATGAGCAGTACACGCGTGGCTACCTATCCAATGCTG
+GCTACGCTAGTGGTAACAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG
+GAATCCATGCGCGGAGTACCTGGCTGCAAGCGGCATACTGATCCGTGTTGTTCCCTAGAC
+GCTGGGTGTCTCGTCGGACGATAATTCACATTGCTGGTTCCTATAGTCTCCTGTCACAGG
+ATCACGGCAGAAAGGAGGGG
diff --git a/galaxy/tools/pathotypr/test-data/sample1_R1.fastq.gz b/galaxy/tools/pathotypr/test-data/sample1_R1.fastq.gz
new file mode 100644
index 0000000000000000000000000000000000000000..46a949383bb7b23f38045319776958485a37770c
GIT binary patch
literal 2140
zcmV-i2&4BOiwFpi#(`=A|8rq&aBO8UUs5qHW?^%5aR9`fOO7Kq5JdNV6)!AG_1#S(
z7lik`fC2jgzW>6^2v)-fa6}KfHInKBysoNbGC#pz|NQ;uU+wqyHTvk$N6!Do$jF>;
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literal 0
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diff --git a/galaxy/tools/pathotypr/test-data/sample1_R2.fastq.gz b/galaxy/tools/pathotypr/test-data/sample1_R2.fastq.gz
new file mode 100644
index 0000000000000000000000000000000000000000..cedc88d2258e2f080885e317792413f7ebdf530c
GIT binary patch
literal 1995
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literal 0
HcmV?d00001

diff --git a/galaxy/tools/pathotypr/test-data/sample2.fasta b/galaxy/tools/pathotypr/test-data/sample2.fasta
new file mode 100644
index 0000000..d5ce268
--- /dev/null
+++ b/galaxy/tools/pathotypr/test-data/sample2.fasta
@@ -0,0 +1,35 @@
+>sample2
+TGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGACACTCAACTTCCCA
+GTAGCGCTGATAGGGAAGGACTGACAGGCGTGAACCGGGTCCAGCGCTGGGGGATGCGTT
+AATGAAATTCCTTAGAACAGAGTTAGATTCCTACCTTTGTGGGGTGGTGCTTCACCAGGG
+TCTGTGACCACTCGACCCGCGCTAGATTTCCGACGTCTACCTGTACAACTTATGTCCGCT
+CGCGGTACCTAGTATTGTGTTGGACCTCCACTCTCGAAGTCGAGATAAGAACATCCACTT
+AAAGGGTGTTAAGTAGTTTTCCTATGGGGGATCGCTCGGCTGGAGGAACACATCGTGATA
+CTACTAATATTTCCTTCACCGACCCTATGCTGTATCCCCGCAGATTAATCGTTTGTCATC
+AGGGGCTAGTACGATTTTCGCTTTGTCGAAGATATTTCCCCGTTAACTTTATTCTGGCAG
+AAGTCTCATGTCCGATATACTAAGTCATGTTAAAGATCTCCGACCCGGGTAGTAAAATCC
+GTTTGACAACTAAGTACAAGCAGGTTAAGCAACTAGGTTGCGCCGTCAGAAGTGGCTCTG
+GTCGGAATAAACTTGAAAAAGGACAGCGGCAACGATACTCTTGCTAGACGCCTGGAACTT
+GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACGGATTCAAAGAATCCCATGCCCCA
+GGCGTACGTACGGTCTGGGAGTGCTGGCGAGCGATCCTATAGAAGGCCTGTATGACACCT
+TTTATGTAGGCGCGTTGTATCAACCGACACGTGCTAGTTCATCACAATTCCCGTTATACA
+TCGCTGGGGTGGACAACACCTTTGAAAGGAACAAATCCGGAACGATGTCCCGTCACTGCA
+ATAGTAGAGAAGTGGCAGGTTGGATTACAGCGCCATATACGGTTGCGTACTGCTGTCTCA
+GAATTTCTAACATAGTAAATCGTCTTAATCTAGCGGAATGTGCCGACGCCAAGTTTCGGT
+CATAGTAAGGTGTGGTGCTAGGGGCTCCTATACGCCCAGTGTGGGCGACTGATTTGCGTA
+CGGAGCGACTTAATGCGTTCCAGGTCTCTAACCGCGAAGCTTGCCTTCAATGTCGGGGCA
+AAAACTGCACCTCTTATCGCACTTAGGGCCGACGTGCACTATCTTCTCCGCCCCAGACAT
+CGATTGGAACTGATGATCGCGAGAAACTCTGCTGTACTTGGAGATAGGCTATTCATCACC
+CGCTGCACGATCGGTCATCGAGGGGCGGGAGGGATAGCCTGGGTCACAGAAGCTGCAGGG
+GGTCGTCCATGACATGGATGGGCTAGCTAGATACATGCAACGGTCATATGCTACCCTATC
+TGCGTCCTCAGGAAACCCCACGTAAATTAATACAGTGAATATTTCTCACAAATATAGCAC
+ATTTTTTTAACTAAATCTCAGCGAATGGCGACGAGTGATGCTTAAACAATGGTTACGTGT
+GCTCTAAGCTACTCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA
+ATGGCTTCCACGCCTGCTATAGCGGCCCAAACATCTTTGGTCCGTTAAAGCCTGCGGCCC
+CCATCCTAGCGTTGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCTTATA
+CCTTGCACCATGACTTCAGTCCTGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA
+TGATTAGCAATCTCCGGCTAAGAGATGAGCAGTACACGCGTGGCTACCTATCCAATGCTG
+GCTACGCTAGTGGTAACAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG
+GAATCCATGCGCGGAGTACCTGGCTGCAAGCGGCATACTGATCCGTGTTGTTCCCTAGAC
+GCTGGGTGTCTCGTCGGACGATAATTCACATTGCTGGTTCCTATAGTCTCCTGTCACAGG
+ATCACGGCAGAAAGGAGGGG
diff --git a/galaxy/tools/pathotypr/test-data/training.fasta b/galaxy/tools/pathotypr/test-data/training.fasta
new file mode 100644
index 0000000..e878ffe
--- /dev/null
+++ b/galaxy/tools/pathotypr/test-data/training.fasta
@@ -0,0 +1,420 @@
+>L2 train_L2_0
+TGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGACACTCAACTTCCCA
+GTAGCGCTGATAGGGAGGGACTGACAGGCGTGAACCGGATCCAGCGCTGGGGGATGCGCT
+AATGAAATTCCTTAGAACAGAGTTAGATCCCTACCTTTGTGGGGTGGTGCTTCACCGGGG
+TCTGTGACCACTTGACCCGCGCTAGATTTCCGACGTCTACCTGTACAACTTATGTCCGCT
+CGCGGTACCTAGTATTGTGTTGGACCTCCACTCTCGAAGTCGAGATAAGAACATCCACTT
+AAAGGGTGCTAAGTAGTTTTCCTATGGGGGATCGCTCGGCTGGAGGAACACATCGTGATA
+CTACTAATATTTCCTTCACCGACCCTATGCTGTATCCCCACAGATTAATCGTTTGTCATC
+AGGGGCTAGTACGATTTTCACTTTGTCGAAGATATTTCCCCGTTAACTTTATTCTGGCAG
+AAGTCTCATGTCCGATATACTAAGTCATGTTAAAGATCTCCGACCCGGGTAGTAAAATCC
+GTTTGACAACTAAGTACAAGCAGGTTAAGCAACTAGGTTGCGCCGTCAGAAGTGGCTCTA
+GTCGGAATAAACTTGAAAAAGGACAGCGGCAACGATACTCTTGCTAGACGCCTGGAACTT
+GGGTAGGCTCATACCTCATGCACCAGCCCCCTAAACGGATTCAAAGAATCCCATGCCCCA
+GGCGTACGTACGGTCTGGGAGTGCTGGCAAGCGATCCTATAGAAGGCCTGTATGACACCT
+TTTATGTAGGCGCGTTGTACCAACCGACGCGTGCTAGTTCATCACAATTCCCGTTATACA
+TCGCTGGGGTGGACAATACCTTTGAAAGGAACAAATCCGGAACGATGTTCCGTCACTGCA
+ATAGTAGAGAAGTGGCAGGTTGGATTACAGCGCCATATACGGTTGCGTACTGCTGTCTCA
+GAATTTCTAACATAGTAAATCGTCTTAATCTAGCGGAATATGCCGACGCCAAGTTTCGGT
+CATAGTAAGGTGTGGTGCTGGGGGCTCCTATACGCCCAGTGTGGGCGACTGATTTGCGTA
+CGGAGCGACTTAATGCGCTCCAGGTCTCTAACCGCGAAGCTTGCCTTCAATGTCGGGGCA
+AAAACTGCACCTCTTATCGCACTTAGGGCCGACGTGCACTATCTTCTCCGCCCTAGACAC
+CGATTGGAACTGATGATCGCGAGAAACTCTGCTGTACTTGGAGATAGGCTATTCATCACC
+CGCTGCACGATCGGTCATCGAGGGGCGGGAGGGATAGCCTGGGTCACAGAAGCTGCAGGG
+GGTCGTCCATGACGTGGATGGGCTAGCTAGATACATGCAACGGTCATATGCTACCCTATC
+TGCGTCCTCAGGAAACCCCGCGTAAATTAATACAGTGAATATTTCTCACAAATATAGCAC
+ATTTTTTTAACTAAATCTCAGCGAATGGCGACGAGTGATGCTTAAACAATGGTTACGTGT
+GCTCTAAGCTACTCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA
+ATGGCTTCCACGCCTGCTATAGCGGCCCAAACATCTTTGATCCGTTAAAGCCTGCGGCCC
+CCATCCTAGCGTTGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCTTATA
+CTTTGCACCATGACTTCAGTCCTGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA
+TGATTAGCAATCTCCGGCTAAGAGATGAGCAGTACACGCGTGGCTACCTATCCAATGCTG
+GCTACGCTAGTGGTAACAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG
+GAACCCATGCGCGGAGTACCTGGCTGCAAGCGGCATACTGATCCGTGTTGTTCCCTAGAC
+GCTGGGTGTCTCGTCGGACGACAATTCACATTGCTGGTTCCTATAGTCTCCTGTCACAGG
+ATCACGGCAGAAAGGAGGGG
+>L2 train_L2_1
+TGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGACACTCAACTTCCCA
+GTAGCGCTGATAGGGAAGGACTGACAGGCGTGAACCGGGTCTAGCGCTGGGGGATGCGTT
+AGTGAAGTTCCTTAGAACAGAGTCAGATTCCTACCTTTGTGGGGTGGTGCTTCACCAGGG
+TCTGTAACCACTCGACCCGCGCTAGATTTCCGACGTCTACCTGTACAACTTATGTCCGCT
+CGCGGTACCTAGTGTTGTGTTGGACCTCCACTCTCGAAGTCGAGATAAGAACATCCACTT
+AAAGGGTGTTAAGTAGTTTTCCTATGGGGGATCGCTCGGCTGGAGGAACACATCGTGATA
+CTACTAATATTTCCTTCACCGACCCTATGCTGTATCCCCACAGATTAATCGTTTGTCATC
+AGGGGCTAGTACGATTTTCGCTTTGTCGAAGATATTTTCCCGTTAACTTTATTCTGGCAG
+AAGTCTCATGTCTGATATACTAAGTCATGTTAAAGATCTCCGACCCGGGTAGTAAAATCC
+GTTTGACAACTAAGTACAAGCAGGTTAAGCAACTAGGTTGCGCCGTCAGAAGTGGCTCTA
+GTCGGAATAAACTTGAAAAAGGACAGCGGCAACGATACTCTTGCTAGACGCCTGGAACTT
+GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACGGATTCAAAGAATCCCATGCCCCA
+GGCGTACGTACGGTCTGGGAGTGCTGGCGAGCGATCCTATAGAAGGCCTGTATGACACCT
+TTTATGTAGGCGCGTTGTACCAACCGACACGTACTAGTTCATCACAATTCCCGTTATACA
+TCGCTGGGGTGGACAACACCTTTGAAAGGGACAAATCCGGAACGATGTCCCGTCACTGCA
+ATAGTAGAGAAGTGGCAGGTTGGATTACAGCGCCATATACGGTTGCGTACTGCTGTCTCA
+GAATTTCTAACATAGTAAATCGTCTTAATCTAGCGGAATATGCCGACGCCAAGTTTCGGT
+CATAGTAAGGTGTGGTGCTAGGGGCTCCTATACGCCCAGTGTGGGCGACTGATTTGCGTA
+CGGAGCGACTTAATGCGTTCCAGGTCTCTAACCGCGAAGCTTGCCTTCGATGTCGGGGCA
+AAAACTGCACCTCTTATCACACTTAGGGCCGACGTGCACTACCTTCTCCGCCCTAGACAT
+CGATTGGAACTGATGATCGCGAGAAACTCTGCTGTACTTGGAGATAGGCTATTCATCACC
+CGCTGCACGATCGGTCATCGAGGGACGGGAGAGATAGCCTGGGTCACAGAAGCTGCAGGG
+GGTCGTCCATGACATGGATGGGCTAGCTAGATACATGCAACGGTCATATGCTACCCTATC
+TGCGTCCTCAGGAAACCCCGCGTAAATTAATACAGTGAATATTTCTCACAAATATAGCAC
+ATTTTTTTAACTAAATCTCAGCGAATGGCGACGAGTGATGCTTAAACAATGGTTACGTGT
+GCTCTAAGCTACTCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA
+ATGGCTTCCACGCCTGCTATAGCGGCCCAAACATCTTTGATCCGTTAAAGCCTGCGGCCC
+CCATCCTAGCGTTGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCTTATA
+CCTTGCACCATGATTTCAGTCCTGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA
+TGATTAGCAATCTCCGGCTAAGAGATGAGCAGTACACGCGTGGCTACCTATCCAATGCTG
+GCTACGCTAGTGGTAACAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG
+GAATCCATGCGCGGAGTACCTGGCTGCAAGCGGCATACTGATCCGTGTTGTTCCCTAGAC
+GCTGGGTGTCTCGTCGGACGATAATTCACATTGCTGGTTCCTATAGTCTCCTGTCACAGG
+ATCACGGCAGAAAGGAGGGG
+>L2 train_L2_2
+TGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGACACTCAACTTCCCA
+GTAGCGCTGATAGGGAAGGACTGACAGGCGTGAACTGGGTCCAGCGCTGGGGGATGCGTT
+AATGAAATTCCTTAGAACAGAGTTAGATTCCTACCTTTGTGGGGTGGTGCTTCACCAGGG
+TCTGTGACCACTCGACCCGCGCTAGATTTCCAACGTCTACCTGTACAACTTATGTCCGCT
+CACGGTACCTAGTATTGTGTTGGACCTCCACTTTCGAAGTCGAGATAAGAACATCTACTT
+AAAGGGTGTTAAGTAGTTTTCCTATGGGGGATCGCTCGGCTGGAGGAACACATCGTGATA
+CTACTAATATCTCCTTCACCGACCCTATGCTGTATCCCCACAGATTAATCGTTTGTCATC
+AGGGGCTAGTACGATTTTCGCTTTGTCGAAGACATTTCCCCGTTAACTTTATTCTGGCAG
+AAGTCTCATGTCCGATATACTAAGTCATGTTAAAGATCTCCGACCCGGGTAGTAAAATCC
+GTTTGACAACTAAGTACAAGCAGGTTAAGCAACTAGGTTGCGCCGTCAGAAGTAGCTCTA
+GTCGGAATAAACTTGAAAAAGGACAGCGGCAGCGATACTCTTGCTAGACGCCTGGAACTT
+GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACGGATTCAAAGAATCCCATGCCCCA
+GGCGTACGTACGGTCTGGGAGTGCTGGCGAGCGATCCTATAGAAGGCCTGTATGACACCT
+TTTATGTAGGCGCGTTGTACCAACCGACACGTGCTAGTTCATCACAATTCCCGTTATACA
+TCGCTGGGGTGGACAACATCTTTGAAAGGAACAAATCCGGAACGATGTCCCGTCACTGCA
+ATAGTAGAGAAGTGGCAGGTTGGATTACAGCGCCATATACGGTTGCGTACTGCTGTCTCA
+GAATTTCTAACATAGTAAATCGTCTTAATCTAGCGGAATATGCCGACGCCAAGTTTCGGT
+CATAGTAAGGTGTGGTGCTAGGGGCTCCTATACGCCCAGTGTGGGCGACTGATTTGCGTA
+CGGAGCGACTTAATGCGTTCCAGGTCTTTAACCGCGAAGCTTGCCTTCAATGTCGGGGCA
+GAAACTGTACCTCTTATCGCACTTAGGGCCGACGTGCACTATCTTCTCCGCTCCAGACAC
+CGATTGGAACTGATGATCGCGAGAAACTCTGCTGTACTTGGAGATAGGCTATTCATCACC
+CGCTGCACGATCGGTCATCGAGGGGCGGGAGGGATAGCCTGGGTCACAGAAGCTGCAGGG
+GGTCGTCCATGACATGGATGGGCTAGCTAGATACATGCAACGGTCATATGCTACCCTATC
+TGCGTCCTCAGGAAACTCCGCGTAAATTAATACAGTGAATATTTCTCACAAATATAGCAC
+ATTTTTTTAACTAAATCTCAGCGAATGGCGACGAGTGATGCTTAAACAATGGTTACGTGT
+GCTCTAAGCTACTCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA
+ATGGCTTCCACGCCTGCTATAGCGGCCCAAACATCTTTGATCCGTTAAAGCCTGCGGCCC
+CCATCCTAGCGTTGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGACGCTTATA
+CCTTGCACCATGACTTCAGTCCTGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA
+TGATTAGCAATCTCCGGCCAAGAGATGAGCAGTACACGCGTGGCTACCTATCCAATGCTG
+GCTACGCTAGTGGTAACAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG
+GAATCCATGCGCGGAGTACCTGGCTGCAAGCGGCATACTGATCCGTGTTGTTCCCTAGAC
+GCTGGGTGTCTCGTCGGACGATAATTCACATTGCTGGTTCCTATAGTCTCCTGTCACAGG
+ATCACGGCAGAAAGGAGGGA
+>L2 train_L2_3
+TGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGACACTCAACTTCCCA
+GTAGCGCTGATAGGGAAGGACTGACAGGCGTGAACCGGGTCCAGCGCTGGGGGATGCGTT
+AACGAAATCCCTTAGAACAGAGTTAGATTCCTACCTTTGTGGGGTGGTGCTTCACCAGGG
+TCTGTGACCACTCGACCCGTGCTAGATTTCCGACGTCTACCTGTACAACTTATGTCCGCT
+CGCGGTACCTAGTATTGTGTTGGACCTCCACTCTCGAAGTCGAGATAAGAACATCCACTT
+AAAGGGTGTTAAGTAGTTTTCCTATGGGGGATCGCTCGGCTGGAGGAACACATCGTGATA
+CTACTAATATTTCCTTCACCGACCTTATGCTGTATCCCCACAGATTAATCGTTTGTCATC
+AAGGGCTAGTACGATTTTCGCTTTGTCGAAGATATTTCCCCGTTAACTTTATTCTGGCAG
+AAGTCTCATGTCCGATATACTAAGTCATGTTAAAGATCTCCGACCCGGGTAGTAAAATCC
+GTTTGACAACTAAGTACAAGCAGGTTAAGCAACTAGGTTGCGCCGTCAGAAGTGGCTCTA
+GTCGGAATAAACTTGAAAAAGGACAGCGGCAACGATACTCTTGTTAGACGCCTGGAACTT
+GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACGGATTCAAAGAATCCCATGCCCCA
+GGCGTACGTACGGTCTGGGAGTGCTGGCGAGCGATCCTATAGGAGGCCTGTATGACACCT
+TTTATGTAGGCGCGTTGTACCAACCGACACGTGCTAGTTCATCACAATTCCCGTTATACA
+TCGCTGGGGTGGACAACACCTTTGAAAGGAACAAACCCGGAACGATGTCCCGTCACTGCA
+ATAGTAGAGAAGTGGCAGGTTGGATTACAGCGCCATATACGGTTGCGTACTGCCGTCTCA
+GAATTTCTAACATAGTAAATCGTCTTAATCTAGCGGAATATGCCGACGCCAAGTTTTGGT
+CATAGTAAGGTGTGGTGCTAGGGGCTCCTATACGCCCAGTGTGGGCGACTGATTTGCGTA
+CGGAGCGATTTAATGCGTTCCAGGTCTCTAACCGCGAAGCTCGCCTTCAATGTCGGGGCA
+AAAACTGCACCTCTTGTCGCACTTAGGGCCGACGTGCACTATCTTCTCCGCCCCAGACAT
+CGATTGGAACTGATGATCGCGAGAAACTCTGCTGTACTTGGAGATAGGCTATTCATCACC
+CGCTGCATGATCGGTCATCGAGGGGCGGGAGGGATAGCCTGGGTCACAAAAGCTGCAGGG
+GGTCGTCCATGACATGGATGGGCTAGCTAGATACATGCAACGGTCATATGCTACCCTATC
+TGCGTCCTCAGGAGACCCCGCGTAAATTAATACAGTGAATATTTCTCACAAATATAGCAC
+ATTTTTTTAACTAAATCTTAGCGAATGGCGACGAGTGATGCTTAAACAATGGTTACGTGT
+GCTCTAAGCTACTCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA
+ATGGCTTCCACGCCTGCTATAGCGGCCCAAATATCTTTGATCCGTTAAAGCCTGCGGCCC
+CCATCCTAGCGTTGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCTTATA
+CCTTGCACCATGACTTCAGTCCTGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA
+TGATTAGCAATCTCCGGCTAAGAGATGAGCAGTACACGCGTGGCTACCTATCCAATGCTG
+GCTACGCTAGTGGTAACAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG
+GAATCCATGCGCGGAGTACCTGGCTGCAAGCAGCATACTGATCCGTGTTGTTCCCTAGAC
+GCTGGGTGTCTCGTCGGACGATAATTCACATTGCTGGTTCCTATAGTCTCCTGTCACAGG
+ATCACGGCAGAAAGGAGGGG
+>L2 train_L2_4
+TGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGACACTCAACTTCCCA
+GTAGCGCTGATAGGGAAGGACTGACAGGCGTGAACCGGGTCCAGCGCTGGGGGATGCGTT
+AATGAAATTCCTTAGAACAGAGTTAGATTCCTACCTTTGTGGGGTGGCGCTTCACCAGGG
+TCTGTGACCACTCGACCCGCGCTAGATTTCCGACGTCTACCTGTACAACTTATGTCCGCT
+CGCGGTACCTAGTATTGTGTTGGACCTCCACTCTCGAAGTCGAGATAAGAACATCCACTT
+AAAGGGTGTTAAGTAGTTTTCCTATGGGGGATCGCTCGGCTGGAGGAACACATCGTGATA
+CTACTAATGTTTCCTTCACCGACCCTATGCTGTATCCCCACAGATTAATCGTTTGTCATC
+AGGGGCTAGTACGATTTTCGCTTTGTCGAAGATATTTCCCCGTTAACTTTATTCTGGCAG
+AAGTCTCATGTCCGATATATTAAGTCATATTAAAGATCTCCGACCCGGGTAGTAAAATCC
+GTTTGACAACTAAGTACAAGCAGGTTAAGCAACTAGGTTGCGCCGTCAGGAGTGGCTCTA
+GTCGGAATAAACTCAAAAAAGGACAGCGGCAACGATACTCTTGCTAGACGCCTGGAACTT
+GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACGGATTCAGAGAATCCCATGCCCCA
+GGCGTACGTACGGTCTGGGAATGCTGGCGAGCGATCCTATAGAAGGCCTGTATGACACCT
+TTTATGTAGGCGCGTTGTACCAACCGACACGTGCTAGTTCATCACAATTCCCGTTATACA
+TCGCTGGGGTGGACAACACCTTTGAAAGGAACAAATCCGGAACGATGTCCCGTCACTGCA
+ATAGTAGAGAAGTGGCAGGCTGGATTACGGCGCCATATACGGTTGCGTACTGCTGTCTCA
+GAATTTCTAACATAGTAAATCGTCTTAATCTAGCGGAATATGCCGACGCCAAGCTTCGGT
+CATAGTAAGGTGTGGTGCTAGGGGCTCCTATACGCCCAGTGTGGGCGACTGATTTACGTA
+CGGAGCGACTTAATGCGTTCCAGGTCTCTAACCGCGAAGCTTGCCTTCAATGTCGGGGCA
+AAAACTGCACCTCTTATCGCACTTAGGGCCGACGTGTACTATCTTCTCCGCCCCAGACAC
+CGATTGGAACTGATGATCGCGAGAAACTCTGCTGTACTTGGAGATAGACTATTCATCACC
+CGCTGCACGATCGGTCATCGAGGGGCGGGAGGGATAGCCTGGGTCACAGAAGCTGCAGGG
+GGTCGTCCATGACATGGATGGGCTAGCTAGATACATGCAACGGTCATATGCTACCCTATC
+TGCGTCCTCAGGAAACCCCGCGTAAATTAATACAGTGAATATTTCTCACAAGTATAGCAC
+ATTTTTTTAACTAAATCTCAGCGAATGGCGACGAGTGATGCTTAAACAATGGTCACGTGT
+GCTCTAAGCTACTCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA
+ATGGCTTCCACGCCTGCTATAGCGGCCCAAACATCTTCGATCCGTTAAAGCCTGCGGCCC
+CCATCCCAGCGTTGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCTTATA
+CCTTGCACCATGACTTCAGTCCTGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA
+TGATTAGCAATCTCCGGCTAAGAGATGAGCAGTACACGCGTGGCTACCTATCTAATGCTG
+GCTACGCTAGTGGTAACAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG
+GAATCCATGCGCGGAGTACCTGGCTGCAAGCGGCATACTGATCCGTGTTGTTCCCTAGAC
+GCTGGGTGTCTCGTCGGACGATAATTCACATTGCTGGTTCCTATAGTCTCCTGTCACAGG
+ATCACGGCAGAAAGGAGGGG
+>L2 train_L2_5
+TGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGACACTCAACTTCCCA
+GTAGCGCTGATAGGGAAGGATTGACAGGCGTGAACCGGGTCCAGCGCTGGGGGATGCGTT
+AATGAAATTCCTTAGAACAGAGTTAGATTTCTACCTTTATGGGGTGGTGCTTCACCAGGG
+TCTGTGACCACTCGACCCGCGCTAGATTTCCGACGTCTACCTGTACAACTTATGTCCGCT
+CACGGTACCTAGTATTGTGTTGGACCTCCACTCTCGAAGTCGAGATAAGAACATCCACTT
+AAAGGGTGTTAGGTAGTTTTCCTATGGGGGATCGCTCAGCTGGAGGAACACATCGTGATA
+CTACTAATATTTCCTTCACCGACCCTATGCTGTATCCCCACAGATTAATCGTTTGTCATC
+AGGGGCTAGTACGATTTTCGCTTTGTCGAAGATATTTCCCCGTTAACTTTATTCTGGCAG
+AAGTCTCATGTCCGATATACTAAGTCATGTTAAAGATCTCCGACCCGGGTAGTAAAATCC
+GTTTGACAACTAAGTACAAGCAGGTTAAGCAACTAGGTTGCGCCGTCAGAAGTGGCTCTA
+GTCGGAATAAACTTGAAAAAGGACAGCGGCAACGATACTCTTGCTAGACGCCTGGAACTT
+GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACGGATCCAAAGAATCCCATGCCCCA
+GGCGTACGTACGGTCTGGGAGTGCTGGCGAGCGATCCTATAGAAGGCCTGTATGACACCT
+TTTATGTAGGCGCGTTGTACCAACCGACACGTGCTAGTTCATCACAATTCCCGTTATACA
+TCGCTGGGGTGGACAATACCTTTAAAAGGAACAAATCCGGAACGATGTCCCGTCACTGCA
+ATAGTAGAGAAGTGGCAGGTTGGATTACAGCGCCATATACGGTTGCGTACTGCTGTCTCA
+GAATTTCTAACATAGTAAATCGTCTTAATCTAGCGGAATATACCGACGCCAAGTTTCGGT
+CATAGTAAGGTGTGGTGCTAGGGGCTCCCATACGCCCAGTGTGGGCGACTGATTTGCGTA
+CGGAGCGACTTAATGCGTTCCAGGTCTCTAACCGCGAAGCTTGCCTTCAATGTCGGGGCA
+AAGACTGCACCTCTTATCGCACTTAGGGCCGACATGCACTATCTTCTCCGCCCCAGACAC
+CGATTGGAACTGATGATCGCGAGAAACTCTGCTGTACTTGGAGATAGGCTATTCATCACC
+CGCTGCACGATCGGTCATCGAGGGGCGGGAGGGATAGCCTGGGTCACAGAAGCTGCAGGG
+GGTCGTCCATGACATGGATGGGCTAGCTAGATACATGCAACGGTCATACGCTACCCTATC
+TGCGTCCTCAGGAAACCCCGCGTAAATTAATACAGTGAATATTTCTCACAAATATAGCAC
+ATTTTTTTAACTAAATCTCAGCGAATGGCGACGAGTGATGCTTAAACAATGGTTACGTGT
+GCTCTAAGCTACTCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCATCAATTTAAA
+ATGGCCTCCACGCCTGCTATAGCGGCCCAAACATCTTTGATCCGTTAAAGCCTGCGACCC
+CCATCCTAGCGTTGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCTTATA
+CCTTGCACCATGACTTCAGTCCTGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA
+TGATTAGCAATCTCCGGCTAAGAGATGAGCAGTACACGCGTGGCTACCTATCTAATGCTG
+GCTACGCTAGTGGTAACAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG
+GAATCCATGCGCGGAGTACCTGGCTGCAAGCGGCATACTGATCCGTGTTGTCCCCTAGAC
+GCTGGGTGTCTCGTCGGACGATAATTCACATTGCTGGTTCCTATAGTCTCTTGTCACAGG
+ATCACGGCAGAAAGGAGGGG
+>L3 train_L3_0
+TGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGACACTCAACTTCCCA
+GTAGCGCTGATAGGGAAGGACTGACAGGCGTGAACCGGGTCCAGCGCTGGGGGATGCGTT
+AATGGAATTCCTTGGAACAGGGTTAGATTCCTACCTTTGTGGGGTGGTGCTTCACCAGGG
+TCTGTGACCACCCGACCCGCGCTAGATTTCCGACGTCTACCTGTACAACTTATGTCCGCT
+CGCGGTACCTAGTATTGTGTTGGACCTCCACTCTCGAAGTCGAGATAAGAACATCCACTT
+AAAGGGTGTTAAGTAGTTTTCCTATGGGGGATCGCTCGGCTGGAGGAACACATCGTGATA
+CTACTAATATTTCCTTCACCGACCCTATGCTGTATCCCCGCAGATTAATCGTTTGTCATC
+AGGGGCTAGTACGATTTTCGCTTTGTCGAAGATATTTCCCCGTTAACTTTATTCTGGCAG
+AAGTCTCATGTCCGATATACTAAGTCATGTTAAAGATCTCCGACCCGGGTAGTAAAATCC
+GTTTGACAACTAGGTACAAGCAGGTTAAGCAACTAGGTTGCGCCGTCAGAAGTGGCTCTG
+GTCGGAATAAACTTGAAAAAGGACAGCGGCAACGATACTCTTACTAGACGCCTGGAACTT
+GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACAGATTCAAAGAATCCCATGCCTCA
+GGCGTACGTACGGTCTGGGAGTGCTGGCGAGCGATCCTATAGAAGGCCTGTATGACACCT
+TTTATGTAGGCGCGTTGTATCAACCGACACGTGCTAGTTCATCACAATTCCCGTTATACA
+TCGCTGGGGTGGACAACACCTTTGAAAGGAACAAATCCGGAACGATGTCCCGTCACTGCA
+ATAGTAGAGAAGTGGCAGGTTGGATTACAGCGCCGTATACGGTTGCGTACTGCTGTCTCA
+GAATTTCTAATATAGTAAATCGTCTTAATCTAGCGGAATGTGCCGACGCCAAGTTTCAGT
+CATAGTAAGGTGTGGTGCTAGGGGCTCCTATACGCCCAGTGTGGGCGACTGATTTGCGTA
+CGGAGCGACTTAATGCGTTCCAGGTCTCTAACCGCGAAGCTTGCCTTCAATGTCGGGGCA
+AAAACTGCACCTCTTATCGCACTTAGGGCCGACGTGCACTATCTTCTTCGCCCCAGACAT
+CGATTGGAACTGATGATTGCGAGAAACTCTGCTGTACTTGGAGATAGGCTATTCATCACC
+CGCTGCACGATCGGTCATCGAGGGGCGGGAGGGATAGCCTGGGTCACAGAAGCTGCAGGG
+GGTCGTCCATGACATGGATGGGCTAGCTAGATACATGCAATGGTCATATGCTACCCTATC
+TGCGTCCTCAGGAAACCCCACGTAAATTAATACAGTGAATATTCCTCGCAAATATAGCAC
+ATTTTTTTAACTAAATCTCAGCGAATGGCGACGAGTGATGCTTAAACAATGGTTACGTGT
+GCTCTAAGCTACTCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA
+ATGGCTTCCACGCCTGCTATAGCGGCCCAAACATCTTTGGTCCGTTAAAGCCTGCGGCCC
+CCATCCTAGCGTCGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCCTATA
+CCTTGCACCATGACTTCAGTCCTGAGCCGATTGATTGAGCAAGCGCTGCCAGCGCTCATA
+TGATTAGCAATCTCCGGCTAAGAGATGAGCAGTACACGCGTGGCTACCTATCCAATGCTG
+GCTACGCTAGTGGTAACAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG
+GAATCCATGCGCGGAGTACCTGGCTGCAAGCGGCATACTGATCCGTGTTGTTCCCTAGAC
+GCTGGGTGTCTCGTTGGACGATAATTCACATTGCTGGTTCCTATAGTCTCCTGTCACAGG
+ATCACGGCAGAAAGGAGGGG
+>L3 train_L3_1
+TGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGATACTCAACTTCCCA
+GTAGCGCTGATAGGGAAGGACTGACAGGCGTGAACCGGGTCCAGCGCTGGGGGATGCGTT
+AATGAAATTCCTTAGAACAGAGTTAGATTCCTACCTTTGTGGGGTGGTGCTTCACCAGGG
+TCTGTGACCACTCGACCCGCGCTAGATTTCCGACGTCTACCTGTACAACTTATGTCCGCT
+CGCGGTACCTAGTATTGTGTTGGACCTCCACTCTCGAAGTCGAGATAAGAACATCCACTT
+AAAGGGTGTTAAGTAGTTTTCCTATGGGGGATCGCTCGGCTGGAAGAACACATCGTGATA
+CTACTAATATTTCCTTCACCGACCCTATGCTGTATCCCCGCAGATTAATCGTTTGTCATC
+AGGGGCTAGTACGATTTTCGCTTTGTCGAAGATATTTCCCCGTTAACTTTATTCTGGCAG
+AAGTCTCATGTCCGATATACTAAGTCATGTTAAAGATCTCCGACCCGGGTAGTAAAATCC
+GTTTGACAACTAAGTACAAGCAGGTTAAGCAACTAGGTTGCGTCGTCAGAAGTGGCTCTG
+GTCGGAATAAACTTGAAAAAGGACAGCGGCAACGGTACTCTTGCTAGACGCCTGGAACTT
+GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACGGATTCAAAGAATCTCATGCCCCA
+GGCGTACATACGGTCTGGGAGTGCTGGCGAGCGATCCTATAGAAGGCCTGTATGACACCT
+TTTATGTAGGTGCGTTGTATCAACCGACACGTGCTAGTTCATCACAATTCCCGTTATACA
+TCGCTGGGGTGGACAACACCTTTGAAAGGAACAAATCCGGAACGATGTCCCGTCACTGCA
+ATAGTAGAGAAGCGGCAGGTTGGATTACAGCGCCATATACGGTTGTGTACTGCTGTCTCA
+GAATTTCTAACATAGTAAATCGTCTTAATCTAGCGGAATGTGCCGACGCCAAGTTTCGGT
+CATAGTAAGGTGTGGTGCTAGGGGCTCCTATACGCCCAGTGTGGGCGACTGATTTGCGTA
+CGGAGCGACTTAATGCGTTCCAGGTCTCTAACCGCGAAGCTTGCCTTCAATGTCGGGGCA
+AAAACTGCACCTCTTATCGCACTTAGGGCCGACGTGCACTATCCTCTCCGCCCCAGACAT
+CGATTGGAACTGATGATCGCGAGAAACTCTGCTGTACTTGGAGATAGGCTACTCATCACC
+CGCTGCACGATCGGTCATCGAGGGGCGGGAGGGATAGCCTGGGTCACAGAAGCTGCAGGG
+GGTCGCCCATGACATGGATGGGCTAGCTAGATACATGCAACGGTCATATACTACCCTATC
+TGCGTCCTCAGGAAATCCCACGTAAATTAATACAGTGAATATTTCTCACAAATATAACAC
+ATTTTTTTAACTAAATCTCAGCGAATGACGACGAGTGATGCTTAAACAATGGTTACGCGT
+GCTCTAAGCTACTCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA
+ATGGCTTCCACGCCTGCTATAGCGGCCCAAACATCTTTGGTCCGTTAAAGCCTGCGGCCC
+CCATCCTAGCGTTGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCTTATA
+CCTCGCACCATGACTTCAGTCCTGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA
+TGATTAGCAATCTCCGGCTAAGAGATGAGCAGTACACGCGTGGCTACCTATCCAATGCTG
+GCTACGCTAGTGGTAATAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG
+GAATCCATGCGCGGAGTACCTGGCTGCAAGCGGCATACTGATCCGTGTTGTTCCCTAGAC
+GCTGGGCGTCTCGTCGGACGATAATTCACATTGCTGGTTCCTATAGTCTCCTGTCACAGG
+ATCACGGCAGAAAGGAGGGG
+>L3 train_L3_2
+TGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGACACTCAACTTCCCA
+GTAGCGCTGATAGGGAAGGACTGACAGGCGTGAACCGGGTCCAGCGCTGGGGGATGCGTT
+GATGAAATTCCTTAGAACAGAGTTAGATTCCTACCTTTGTGGGGTAGTGCTTCACCAGGG
+TCTGTGACCACTCGACCCGCGCTAGATTTCCGACGTCTACCTGTACAACTTATGTCCGCC
+CGCGGTACCTAGTATTGTGTTGGATCTCCACTCTCGAAGTCGAGATAAGAACATCCACTT
+AAAGGGTGTTAAGTAGTTTTCCTATGGGGGATCGCTCGGCCGGAGGAACACATCGTGATA
+CTACTAATATTTCCTTCACCGACCCTATGCTGTATCCCCGCAGATTAATCGTTTGTCATC
+AGGGGCTAGTACGATTTTCGCTTTGTTGAAGATATTTCCCCGTTAACTTTATTCTGGCAG
+AAGTCTCATGTCCGATATACTAAGTCACGTTAAAGATCTCCGACCCGGGTAGTAAAATCC
+GTTTGACAACTAAGTACAAGCAGGTTAAGTAACTAGGTTGCGCCGTCAAAAGTGGCTCTG
+GTCGGAATAAACTTGAAAAAGGACAGCGGCAACGATACTCTTGCTAGACGCCTGGAACTT
+GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACGGATTCAAAGAATCCCATGCCCCA
+GGCGTACGTACGGTCTGGGAGTGCTGGCGAGCGATCCTATAGAAGGCCTGTATGACACCT
+TTTATGTAGGCGCGTTGTATTAACCGACACGTGCCAGTTCATTACAATTCCCGTTATACA
+TCGCTGGGGTGGACAACACCTTTGAAAGGAACAAATCCGGAACGATGTCCCGTCACTGCA
+ATAGTAGAGAAGTGGCAGGCTGGATTACAGCGCCATATACGGTTGCGTACTGCTGTCTCA
+GAATTTCTAACATAGTAAATCGTCTTAATCTAGCGGAATGTGCCGACGCCAGGTTTTGGT
+CATAGTAAGGTGTGGTGCTAGGGGCTCCTATACGCCCAGTGTGGGCGACTGATTTGCGTA
+CGGAGCGACTTAATGCGTTCCAGGTCTCTAACCGCGAAGCTTGCCCTCAATGTCGGGGCA
+AAAACTGCACCTCTTATCGCACTTAGGGCCGACGTGCACTATCTTCTCCGCCCCAGACAT
+CGATTGGAACTGATGATCGCGAGAAACTCTGCTGTACTTGGAGATAGGCTATTCATCACC
+CGCTGCACGATCGGTCATCGAGGGGCGGGAGGGATAGCCTGGGTCACAGAAGCTGCAGGG
+GGTCGTCCATGACATGGATGGGCTAGCTAGATACATGCAACGGTCATATGCTACCCTATC
+TGCGTCCTCAGGAAACCCCACGTAAATTAATACAGTGAATATTTCTCACAAATATAGCAC
+ATTTTTTTAACTAAATCTCAGCGAATGGCGACGAGTGATGCTTAAACAATGGTTACGTGT
+GCTCTAAGCTACCCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA
+ATGGCTTCCACGCTTGCTATAGCGGCCCAAACATCTTTGGTCCGTTAAAGCCTGCGGCCC
+CCATCCTAGCGTTGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCTTATA
+CCTTGCACCATGACTTCAGTCCTGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA
+TGATTAGCAATCTCCGGCTAAGAGATGAGCAGTACACGCGTGGCCACCTATCCAATGCTG
+GCTACGCTAGTGGTAACAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG
+GAATCCATGCGCGGAGTGCCTGGCTGCAAGCGGCATACTGATCCGTGTTGTTCCCTAGAC
+GCTGGGTGTCTCGTCGGACGATAATTCACATTGCTGGTTCCTATAGTCTCCTGTCACAGG
+ATCACGGCAGAAAGGAGGGG
+>L3 train_L3_3
+TGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGACACTCAACTTCCCA
+GTAGCGCTGATAGGGAAGGACTGACAGGCGTGAACCGGGTCCAGCGCTGGGGGATGCGTT
+AATGAAATTCCTTAGAACAGAGTTAGATTCCTACCTTTGTGGGGTGGTGTTTCACCAGGG
+TCTGTGACCACTCGACCCGCGCTAGATTTCCGACGTCTACCTGTACAACTTATGTCCGCT
+CGCGGTACCTAGTATTGTGTTGGACCTCCACTCTCGAAGTTGAGATAAGAACATCCACTT
+AAAGGGTGTTAAGTAGTTTTCCTATGGGGGATCGCTCGGCTGGAGGAACACATCGTGATA
+TTACTAATATTTCCTTCACCGACCCTATGCTGTATCCCCGCAGATTAATCGTTTGTCATC
+AGGGGCTAGTACGATTTTCGCTTTGTCGAAGATATTTCCCCGTTAACTTTATCCTAGCAG
+AAGTCTCATGTCCGATATACTAAGTCATGTTAAAGATCTCCGACCCGGGTAGTAAAATCC
+GTTTGACAACTAAGTACAAGCAGGTTAAGCGACTAGGTTGCGCCGTCAGAAGTGGCTCTG
+GTCGGAATAAACTTGAAAAAGGACAGCGGCAACGATACTCTTGCTAGACGCCTGGAACTT
+GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACGGATTCAAAGAATCCCATGCCCCA
+GGCGTACGTACGGTTTGGGAGTGCTGGCGAGCGATCCTATAGAAGGCCTGTATGACACCC
+TTTATGTAGGCGCGTTGTATCAACCGACACGTGCTAGTTCATCACAATTCCCGTTATACA
+TCGCTGGGGTAGACAACACCTTTGAAAGGAACAAATCCGGAGCGATGTCCCGTCACTGCA
+ATAGTAGAGAAGTGGCAGGTTGGATTACAGCGCCATATACGGTTGCGTACTGCTGTCTCA
+GAATTTCTAACATAGTAAATCGTCTTAATCTAGCGGAATGTGCCGACGCCAAGTTTCGGT
+CATAGTAAGGTGTGGTGCTAGGGGCTCCTATACGCCCAGTGTGGGCGACTGATTTGCGTA
+CGGAGCGACTTAATGCGTTCCAGGTCTCTAACCGCGAAGCTTGCCTCCAATGTCGGGGCA
+AAAACTGCACCTCTTATCGCACTTAGGGCCGACGTGCACTATCTTCTCCGCCCCAGACAT
+CGATTGGAACTGATGATCGCGAGAAACTCTGCTGTACTTGGAGATAGGCTATTCATCACC
+CGCTGCACGATCGGTCATCGAGGGGCGGGAGGGATAGCCTGGGTCACAGAAGCTGCAGGG
+GGTCGTCCATGACATGGATGGGCTAGCTAGATACATGCAACGGTCATATGCTACCCTATC
+TGCGTCCTCAGGAAACCCTACGTAAATTAATACAGTGAATATTTCTCACAAATATAGCAC
+ATTTTTCTAACTAAATCTCAGCGAATGGCGACGAGTGATGCTTAAACAATGGTTACGTGT
+GCTCTAAGCTACTCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA
+ATGGCTTCCACGCCTGCTATAGCGGCCCAAACATCTTTGGTCCGTTAAAGCCTGCGGCCC
+CCATCCTAGCGTTGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCTTGTA
+CCTTGCACCATGACTTCAGTCCTGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA
+TGATTAGCAATCTCCGGCTAAGAGATGAGTAGTACACGCGTGGCTACCTATCCAATGCTG
+GCTACGCTAACGGTAACAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG
+GAATCCATGCGCGGAGTACCTGGCTGCAAGCGGCATACTGATCCGTGTTGTTCCCTAGAC
+GCTGGGTGTCTCGTCGGACGATAATTCACATTGCTGGTTCCCATAGTCTCCTGTCACAGG
+ATCACGGCAGAAAGGAGGGG
+>L3 train_L3_4
+TGTGAGTCATGTTCACCTCGGTACGGGACGACAATGCTGGCACAGACACTCAACTTCCCA
+GTAGCGCTGATAGGGAAGGACTGACAGGCGTGAACCGGGTCCAGCGCTGGGGGATGCGTT
+AATGAAATTCCTTAGAACAGAGTTAGATTCCTACCTTTGTGGGGTGGTGCTTCACCAGGG
+TCTGTGACCACTCGACCCGCGCTAGATTTCCGACGTCTACCTGTACAACTTATGTCCGCT
+CGCGGTACCTAGTATTGCGTTGGACCTCCACTCTCGAAGTCGAGATAAGAACATCCACCT
+AAAGGGTGTTAAGTAGTTTTCCTATGGGGGATCGCTCGGCTGGAGGAACACATCGTGATA
+CTACTAATATTTCTTTCACCGACCCTATGCTGTATCCCCGCAGATTAATCGTTTGTCATC
+AGGGGCTAGTACGATTTTCGCTTTGTCGAAGATATTTCCCCGTTAACTTTATTCTGGTAG
+AAGTCTCATGTCCGATATACTAAGTCATGTTAAAGATCTCCGACCCGGGTAGTAAAATTC
+GTTTGACAACTAAGTACAAGCAGGTTAAGCAACTAGGCTGCGCCGTCAGAAGTGGCTCTG
+GTCGGAATAAACTTGAAAAAGGACAGCGGCAACGATACTCTTGCTAGACGCCCGGAACTT
+GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACGGATTCAAAGAATCCCATGCCCCA
+GGCGTACGTACGGTCTGGGAGTGCTGGCGAGCGATCTTATAGAAGGCCTGTATGACACCT
+TTTATGTAGGCGCGTTGTATCAACCGACACGTGCTAGTTCATCACAATTCCCGTTATACA
+TCGCTGGGGTGGACAACATCTTTGAAAGGAACAAATCCGGAACGATGTCCCGTCACTGCA
+ATAGTAGAGAAGTGGCAGGTTGGATTACAGCGCCATATACGGTTGCGTACTGCTGTCTCA
+GAATTTCTAACATAGTAAATCGTCTTAATCTAGTGGAATGTGCCGACGCCAAGTTTCGGT
+CATAGTAAGGTGTGGTGCTAGGGGCTCCTATACGCCCAGTGTGGGCGACTGATTTGCGTA
+CGGAGCGACTTAATACGTTCCAGGTCTCTAACCGCGAAGCTTGCCTTCAATGTCGGGGCA
+AAAACTGCACCTCTTATCGTACTTAGGGCCGACGTGCACTATCTTCTCCGCCCCAGACAT
+CGATTGAAACTGATGATCGCGAGAAACTCTGCTGTACTTGGAGATAGGTTATTCATCACC
+CGCTGCACGATCGGTCATCGAGGGGCGGGAGGGATAGCCTGGGTCACAGAAGCTGCAGGG
+GGTCGTCCATGACATGGATGGGCTAGCTGGATACATGCAACGGTCATATGCTACCCTATC
+TGCGTCCTCAGGAAACCCCACGTAAATTAATACAATGAATATTTCTCACAAATATAGCAC
+ATTTTTTTAACTAAATCTCAGCGAATGGCGACGAGTGATGCTTAAACAATGGTTACGTGT
+GCTCTAAGCTACTCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA
+ATGGCTTCCACGCCTGCTATAGCGGCCCAAACATCTTTGGTCCGTTAAAGCCTGCGGCCC
+CCATCCTAGCGTTGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCTTATA
+CCTTGCACCATGACTTCAGTCCCGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA
+TGATTAGCAATCTCCGGCTAAGAGATGAGCAGTACACGCGTGGCTACCTATCCAATGCTG
+GCTACGCTAGTGGTAACAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG
+GAATCCATGCGCGGAGTACCTGGCTGCAAGCGGCATACTGATCCGTGTTGTTCCCTAGAC
+GCTGGGTGTCTCGTCGGACGATAATTCACATCGCTGGTTCCTATAGTCTCCTGTCACAGG
+ATCACGGCAGAAAGGAGGGG
+>L3 train_L3_5
+TGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGACACTCAACTTCCCA
+GTAGCGCTGATAGGGAAGGACTGACAGGCGTGAACCGGGTCCAGCGCTGGAGGATGCGTT
+AATGAAATTCCTTAGAACAGAGTTAGATTCCTACCTTTGTGGGGTGGTGCTTCACCAGGG
+TCTGTGACCACTCGACCCGCGCTAGATTTCCGACGTCTACCTGTACAACTTATGTCCGCT
+CGCGGTACCTAGTATTGTGTTGGACCTCCACTCTCGAAGTCGAGATAAGAACATCCACTT
+AAAGGGTGTTAAGTAGTTTTCCTATGGGGGATCGCTCGGCTGGAGGAACACATCGTGATA
+CTACTAATATTTCCTTCACCGACCCTATGCTGTATCCCCGCAGATTAATCGTTTGTCATC
+AGGGGCTAGTACGATTTTCGCTTTGTCGAAGATATTTCCCCGTTAACTTTATTCTGGCAG
+AAGTCTCATGTCCGATATACTAAGTCATGTTAAAGATCTCCGACCCGGGTAGTAAAATCC
+GTTTGACAACTAAGTACAAGCAGGTTAAGCAACTAGGTTGCGCCGTCAGAAGTGGCTCTG
+GTCGGAATAAACTTGAAAAAGGACAGCGGCAACGATACTCTTGCTAGACGCCTGGAACTT
+GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACGGATTCAAAGAATCCCATGCCCCA
+GGCGTACGTACGGTCTGGGAGTGCTGGCGAGCGATCCTATAGAAGGCCTGTATGACACCT
+TTTATGTAGGCGCGTTGTATCAATCGACACGTGCTGGCTCATCACAATTCCCGTTATACA
+TCGCTGGGGTGGACAACACCTTTGAAAGGAACAAATCCGGAACGATGTCCCGTCACTGCA
+ATAGTAGAGAAGTGGCAGGTTGGATTACAGCGCCACATACGGTTGCGTACTGCTGTCTCA
+GAATTTCTAACATAGTAAATCGTCTTAATCTAGCGGAATGTGCCGACGCCAAGTTTCGGT
+CATAGTAAGGTGTGGTGCTAGGGGCTCCTATACGCTCAGTGTGGGCGACTGATTTGCGTA
+CGGAGCGACTTAATGCGTTCCAGGTCTCTAACCGCGAAGCTTGCCTTCAATGTCGGGGCA
+AAAACCGCACCTCTTATCGCACTTAGGGCCGACGTGCACTATCTTCTCCGCCCCAGACAT
+CGATTGGAACTGATGATCGCGAGAAACTCTGCTGTACTTGGAGATAGGCTATTCATCACC
+CGCTACACGATCGGTCATCGAGGGGCGGGAGGGATAGCCTGGGTCACAGAAGCTGCAGGG
+GGTCGTCCATGACATGGATGGACTAGCTAGATACATGCAACGGTCATATGCTACCCTATC
+TGCGCCCTCAGGAGACCCCACGTAAATTAATACAGTGAATATTTCTCACAAATATAGCAC
+ATTTTTTTAACTAAATCTCAGCGAATGGCGACGAGTGATGCTTAAACAATGGTTACGTGT
+GCTCTAAGCTACTCCCTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA
+ATGGCTTCCACGCCTGCTATAGCGGCCCAAACATCTTCGGTCCGTTAAAGCCTGCGGCCC
+CCATCCTAGCGTTGCCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCTTATA
+CCTTGCACCATGACTTCAGTCCTGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA
+TGATTAGCAATCTCCGGCTGAGAGATGAGCAGTACACGCGTGGTTACCTATTCAATGCTG
+GCTACGCTAGTGGTAACAAGAAACTCAGTTAGTGGCCACTTGCTGGGAGTAATCGTCTCG
+GAATCCATGCGCGGAGTACCTGGCTGCAAGCGGCATACTGATCCGTGTTGTTCCCTAGAC
+GCTGGGTGTCTCGTCGGACGATAATTTACGTTGCTGGTTCCTATAGTCTCCTGTCACAGG
+ATCACGGCAGAAAGGAGGGG

From b9b079fe889be906ba4b62c733a7aa34a12064bb Mon Sep 17 00:00:00 2001
From: Paula Ruiz Rodriguez <50167687+Paururo@users.noreply.github.com>
Date: Sun, 16 Aug 2026 16:41:17 +0200
Subject: [PATCH 2/3] ci: give the galaxy directory a labeler rule

labeler.yml was written before galaxy/ existed and has no catch-all, so the
pull request adding five Galaxy wrappers arrived with no labels at all. The
list has now aged exactly the way the comment in that file predicts a
file-by-file list would.
---
 .github/labeler.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/labeler.yml b/.github/labeler.yml
index 109d044..bf3373e 100644
--- a/.github/labeler.yml
+++ b/.github/labeler.yml
@@ -71,6 +71,11 @@ area:packaging:
           - "src-tauri/tauri.conf.json"
           - "CITATION.cff"
 
+area:galaxy:
+  - changed-files:
+      - any-glob-to-any-file:
+          - "galaxy/**"
+
 # Everything under .github, not a list of the files there. Naming them one by one
 # would leave this file itself uncovered, so the pull request adding a rule would
 # arrive with no label, which is a small thing that says exactly how such a list

From 940466f9d0e50e73c185bdf32b45b3c47d4da5ff Mon Sep 17 00:00:00 2001
From: Paula Ruiz Rodriguez <50167687+Paururo@users.noreply.github.com>
Date: Sun, 16 Aug 2026 16:57:01 +0200
Subject: [PATCH 3/3] fix(galaxy): bring .shed.yml to the IUC standard and test
 the masked output

Checked against a current tools-iuc tool rather than from memory, which turned
up three things.

.shed.yml was missing name, type and auto_tool_repositories. That last one is
what turns a directory of five tools into five ToolShed repositories, so
without it the suite would not have been built the way the IUC expects. Its
remote_repository_url also pointed at this repository rather than at the path
the wrappers will live at inside tools-iuc.

The masked FASTA output had no test. It is a collection discovered by pattern,
so its naming is exactly the kind of thing that breaks silently. Verified first
that the file is sample1_masked.fasta, that the discovered designation is
sample1, and that it carries exactly eight Ns, one per marker. The input genomes
contain no N at all, so an N in the output can only have come from masking.

detect_errors stays exit_code rather than the aggressive setting the reference
tool uses. That is now a measured decision: pathotypr writes its INFO log to
stderr, and aggressive scans stderr, so a log line containing the word error
would fail an otherwise correct job.

No EDAM annotations. The reference tool carries none either, and wrong
ontology terms are worse than absent ones.

planemo: lint clean on all five, 9 of 9 tests passing.
---
 galaxy/tools/pathotypr/.shed.yml              | 23 +++++++++++--------
 galaxy/tools/pathotypr/pathotypr_classify.xml | 17 ++++++++++++++
 2 files changed, 30 insertions(+), 10 deletions(-)

diff --git a/galaxy/tools/pathotypr/.shed.yml b/galaxy/tools/pathotypr/.shed.yml
index 416aed8..17a0a0f 100644
--- a/galaxy/tools/pathotypr/.shed.yml
+++ b/galaxy/tools/pathotypr/.shed.yml
@@ -1,18 +1,21 @@
-categories:
-  - Sequence Analysis
-  - Variant Analysis
+name: pathotypr
+owner: iuc
 description: Lineage classification and marker-driven genotyping from assemblies or raw reads
 long_description: |
   pathotypr classifies microbial genomes into lineages and genotypes them
   against user-defined marker panels. It works from assembled genomes (FASTA)
   and from raw reads (FASTQ) without aligning them, and it carries no assumption
   about the organism: the marker panel supplied defines what is typed.
+categories:
+- Sequence Analysis
+- Variant Analysis
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathotypr
 homepage_url: https://pathogenomics-lab.github.io/pathotypr/
-remote_repository_url: https://github.com/PathoGenOmics-Lab/pathotypr
-owner: iuc
+type: unrestricted
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: "Wrapper for the pathotypr tool {{ tool_name }}."
 suite:
-  name: suite_pathotypr
-  description: Lineage classification and marker-driven genotyping with pathotypr
-  long_description: |
-    A suite of the five pathotypr commands: train, predict, classify,
-    split-fastq and match.
+  name: "suite_pathotypr"
+  description: A suite of Galaxy tools for the five pathotypr commands.
+  type: repository_suite_definition
diff --git a/galaxy/tools/pathotypr/pathotypr_classify.xml b/galaxy/tools/pathotypr/pathotypr_classify.xml
index 0ad6544..cf3daaf 100644
--- a/galaxy/tools/pathotypr/pathotypr_classify.xml
+++ b/galaxy/tools/pathotypr/pathotypr_classify.xml
@@ -112,6 +112,23 @@ pathotypr classify
                 </assert_contents>
             </output>
         </test>
+        <!-- The masked FASTA is a discovered collection, so its naming deserves
+             a test of its own. The input genomes contain no N at all, so an N in
+             the output can only have come from masking. -->
+        <test expect_num_outputs="3">
+            <param name="genomes" value="sample1.fasta" ftype="fasta"/>
+            <param name="markers" value="markers.tsv" ftype="tabular"/>
+            <param name="reference" value="reference.fasta" ftype="fasta"/>
+            <param name="output_masked_fasta" value="true"/>
+            <output_collection name="masked" type="list" count="1">
+                <element name="sample1" ftype="fasta">
+                    <assert_contents>
+                        <has_text text="&gt;sample1"/>
+                        <has_text text="N"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**