annotate pangolin.xml @ 1:f557122d379e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"

<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[
        #if str($db.source) == "download"
            python '$__tool_directory__/fetch_latest_pangolearn.py' &&
        #else if str($db.source) == "builtin"
            ln -s $db.db_release.fields.path datadir &&
        #end if
        pangolin
        --threads \${GALAXY_SLOTS:-1}
        #if str($db.source) == "download" or str($db.source) == "builtin"
            --datadir 'datadir'
        #end if
        $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"/>
      <conditional name="db">
            <param type="select" name="source" label="pangoLEARN source" help="Where to find the pangoLEARN database">
                <option value="download">Download latest from web</option>
                <option value="builtin">Use database from Galaxy server</option>
                <option value="default">Use default database built in to pangolin (not recommended)</option>
            </param>
            <when value="download">
            </when>
            <when value="builtin">
                <param name="db_release" label="pangoLEARN release" type="select">
                    <options from_data_table="pangolearn">
                        <column name="value" index="0" />
                        <column name="name" index="1" />
                        <column name="path" index="3" />                         
                        <filter type="sort_by" column="0"/>
                    </options>
                </param>
            </when>
            <when value="default">
            </when>
      </conditional>
    </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"/>
          <conditional name="db">
              <param name="source" value="download" />
          </conditional>
          <output name="output1">
            <assert_contents>
                <has_text text="B.1.1" />
                <has_text text="passed_qc" />
            </assert_contents>
          </output>
      </test>
      <test expect_num_outputs="2">
          <param name="alignment" value="--alignment" />
          <param name="input1" value="test1.fasta" />
          <conditional name="db">
            <param name="source" value="download" />
          </conditional>
          <output name="output1">
            <assert_contents>
                <has_text text="B.1.1" />
                <has_text text="passed_qc" />
            </assert_contents>
          </output>
          <output name="align1" file="aln1.fasta" ftype="fasta" />
      </test>
      <test expect_num_outputs="1">
        <param name="input1" value="test1.fasta"/>
        <conditional name="db">
            <param name="source" value="builtin" />
        </conditional>
        <output name="output1">
            <assert_contents>
                <has_text text="2021-04-21" />
            </assert_contents>
        </output>
    </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.

Pangolin uses the `pangoLEARN <https://github.com/cov-lineages/pangoLEARN>`_ stored model for lineage assignment. This
model is updated more frequently than the pangolin tool is. In general one should use the most recent model for lineage
assignment, and the default option for this tool is to download the latest version of the model before the pangolin
tool runs. A pangoLEARN data manager exists so that the Galaxy admin can download specific versions of the pangoLEARN
model as required. Finally the pangolin tool can use its default built-in model, but this is **not recommended** as the
default model rapidly becomes out of date.

    ]]></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>