annotate pangolin.xml @ 0:0ec813ad2910 draft

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

<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>