diff pangolin.xml @ 0:0ec813ad2910 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pangolin.xml	Mon Apr 12 20:31:42 2021 +0000
@@ -0,0 +1,73 @@
+<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@" profile="20.01">
+    <description>Phylogenetic Assignment of Outbreak Lineages</description>
+    <macros>
+        <token name="@TOOL_VERSION@">2.3.8</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">pangolin</requirement>
+        <requirement type="package" version="0.22.0">csvtk</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        pangolin
+        --threads \${GALAXY_SLOTS:-1}
+        $alignment
+        --outfile report.csv 
+        --max-ambig $max_ambig
+        --min-length $min_length
+        '$input1'
+        && csvtk csv2tab report.csv | tail -n-1 >'$output1'
+        #if $alignment
+            && mv sequences.aln.fasta '$align1'
+        #end if 
+    ]]></command>
+    <inputs>
+      <param type="data" name="input1" format="fasta" label="Input FASTA File(s)" /> 
+      <param name="alignment" type="boolean" label="Generate output alignment" 
+            truevalue="--alignment" falsevalue="" /> 
+      <param argument="--max-ambig" type="float" label="Maximum proportion of Ns allowed" 
+          value="0.5" min="0" max="1" help="Maximum proportion of Ns allowed for pangolin to attempt assignment" />
+      <param argument="--min-length" type="integer" label="Minimum query length allowed" 
+          value="10000" min="0" help="Minimum query length allowed for pangolin to attempt assignment"/>
+    </inputs>
+    <outputs>
+        <data name="output1" format="tabular" label="pangolin on ${on_string}">
+            <actions>
+                <action name="column_names" type="metadata" default="taxon,lineage,probability,pangoLEARN_version,status,note" />
+            </actions>
+        </data>
+        <data name="align1" format="fasta" label="pangolin alignment on ${on_string}">
+            <filter>alignment</filter>
+        </data>
+    </outputs>
+    <tests>
+      <test expect_num_outputs="1">
+          <param name="input1" value="test1.fasta"/>
+          <output name="output1" file="result1.tsv" ftype="tabular" />
+      </test>
+      <test expect_num_outputs="2">
+          <param name="alignment" value="--alignment" />
+          <param name="input1" value="test1.fasta" />
+          <output name="output1" file="result1.tsv" ftype="tabular" />
+          <output name="align1" file="aln1.fasta" ftype="fasta" />
+      </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+`Pangolin <https://cov-lineages.org/pangolin.html>`_ (Phylogenetic Assignment of Named Global Outbreak LINeages) 
+is used to assign a SARS-CoV-2 genome sequence the most likely lineage based on the PANGO nomenclature system.
+
+    ]]></help>
+    <citations>
+      <citation type="bibtex">
+      @misc{githubpangolin,
+        author = {O'Toole, Áine},
+        year = {2020},
+        title = {pangolin},
+        publisher = {GitHub},
+        journal = {GitHub repository},
+        url = {https://github.com/cov-lineages/pangolin},
+      }</citation>
+    </citations>
+</tool>