--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vapor.xml	Wed Aug 24 09:51:46 2022 +0000
@@ -0,0 +1,96 @@
+<tool id="vapor" name="VAPOR" version="@TOOL_VERSION@+galaxy0" profile="21.05">
+    <description>
+        Classify Influenza samples from raw short read sequence data
+    </description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.0.2</token>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">vapor</xref>
+    </xrefs>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">vapor</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        vapor.py
+            --return_best_n $opt.return_best_n
+            #if $output_type == "fasta"
+                --return_seqs
+            #end if
+            -k '$opt.kmer_length'
+            -t '$opt.score_threshold'
+            -c '$opt.min_kmer_cov'
+            -m '$opt.min_kmer_prop'
+            -fa '$fasta_file'
+            -fq '$fastq_file'
+            -f '$opt.top_seed_frac'
+            -q
+        > out_file
+    ]]>    </command>
+    <inputs>
+        <param name="fasta_file" format="fasta" type="data" label="FASTA file" help="Raw short read sequences (full length reference segment sequences)" />
+        <param name="fastq_file" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file(s)" help="WGS reads" />
+        <param name="output_type" type="select" label="Output type">
+            <option value="scores" selected="true">Return scores only</option>
+            <option value="fasta">Return FASTA only</option>
+        </param>
+        <section name="opt" title="Optional arguments" expanded="true">
+            <param name="return_best_n" type="integer" min="1" value="1" label="Returns the highest scoring n queries" help="A list of the best n queries instead of only the highest scoring query" />
+            <param name="kmer_length" type="integer" min="5" max="30" value="21" label="Kmer Length" help="" />
+            <param name="score_threshold" type="float" min="0.0" max="1.0" value="0.2" label="Read kmer filtering threshold" help="" />
+            <param name="min_kmer_cov" type="integer" value="5" label="Min coverage kmer culling" help="Minimum coverage kmer culling" />
+            <param name="min_kmer_prop" type="float" value="0.1" label="Min kmer proportion" help="Minimum proportion of matched kmers allowed for queries" />
+            <param name="top_seed_frac" type="float" min="0.0" max="1.0" value="0.2" label="Fraction of best seeds to extend" help="" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="output_scores" from_work_dir="out_file" format="tabular" label="VAPOR: closest reference">
+            <filter>output_type == "scores"</filter>
+            <actions>
+                <action name="column_names" type="metadata" default="% of query bases in reads,Total score,Query length,Mean score,Reads after culling,Query description" />
+            </actions>
+        </data>
+        <data name="output_fasta" from_work_dir="out_file" format="fasta" label="VAPOR: closest reference (fasta)">
+            <filter>output_type == "fasta"</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="fasta_file" value="HA_sample.fa" />
+            <param name="fastq_file" value="test_reads.fq" />
+            <output name="output_scores" file="output1.tab" />
+        </test>
+        <test expect_num_outputs="1">
+            <param name="fasta_file" value="HA_sample.fa" />
+            <param name="fastq_file" value="test_reads.fq" />
+            <section name="opt">
+                <param name="kmer_length" value="29" />
+                <param name="score_threshold" value="0.5" />
+                <param name="min_kmer_cov" value="7" />
+                <param name="min_kmer_prop" value="0.5" />
+                <param name="top_seed_frac" value="0.5" />
+            </section>
+            <output name="output_scores" file="output2.tab" />
+        </test>
+        <test expect_num_outputs="1">
+            <param name="fasta_file" value="HA_sample.fa" />
+            <param name="fastq_file" value="test_reads.fq" />
+            <param name="output_type" value="fasta" />
+            <section name="opt">
+                <param name="return_best_n" value="3" />
+            </section>
+            <output name="output_fasta" file="output3.fa" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis.
+VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain.
+
+`sub_sample` is not an option here (compared to the tool on GitHub), since you can always build a workflow that preprocesses your reads to a (random) subsample. You can use this output as your reads file for VAPOR.
+    ]]>    </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btz814</citation>
+    </citations>
+</tool>
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