annotate cooc_pubmut.xml @ 0:d04ea6b052c5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e

<tool id="cooc_pubmut" name="Cojac: pubmut" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
      profile="@PROFILE@">
    <description>
        render a JSON or YAML file to a pretty table
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools"/>
    <expand macro="requirements">
        <requirement type="package" version="2.12">pandoc</requirement>
    </expand>
    <expand macro="version"/>
    <command detect_errors="exit_code"><![CDATA[
@VOCDIR_COMMAND@
#for $input_file in $cooc_file
    #set $cooc_ext = $input_file.ext
#end for
cooc-pubmut
    -m '$vocdir'
    -a '$amplicons'
    #if $cooc_ext == 'json'
        -j '$cooc_file'
    #else if $cooc_ext == 'yaml'
        -y '$cooc_file'
    #end if
    -o cooc-table.csv
    -q
    $escape
    #if $add_html
        && pandoc cooc-table.csv -o cooc-table.html
        && mkdir -p '$html.files_path'
        && cp cooc-table.html '$html.files_path'
    #end if
    ]]></command>
    <inputs>
        <expand macro="vocdir_input"/>
        <param name="amplicons" type="data" format="yaml" label="List of query amplicons"
               help="File generated by the Cojac mutbamscan tool"/>
        <param name="cooc_file" type="data" format="json,yaml" multiple="true"
               label="Results generated by mutbamscan"/>
        <param argument="--escape" type="boolean" truevalue="--escape" falsevalue=""
               checked="false" label="Use escape characters for newlines"/>
        <param name="add_html" type="boolean" checked="false"
               label="Convert CSV output table to HTML format"/>
    </inputs>
    <outputs>
        <data name="table" format="csv"
              label="${tool.name} on ${on_string}: Mutation cooccurrence (CSV table)"
              from_work_dir="cooc-table.csv">
        </data>
        <data name="html" format="html"
              label="${tool.name} on ${on_string}: Mutation cooccurrence (HTML)"
              from_work_dir="cooc-table.html">
            <filter>add_html</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <conditional name="vocdir_option">
                <param name="choice" value="custom"/>
                <param name="voc_file" value="omicron_ba1_mutations.yaml"/>
            </conditional>
            <param name="amplicons" value="amplicons111.yaml"/>
            <param name="cooc_file" value="cooc-test111.json"/>
            <output name="table" ftype="csv">
                <assert_contents>
                    <has_text text="Amplicon 76"/>
                    <has_text text="Amplicon 81"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
@HELP_HEADER@

Information about **cooc-pubmut** method
========================================

The method renders a JSON or YAML file to a table as in the publication.
You need to open the output CSV in a spreadsheet that understands linebreaks.

    ]]></help>
    <expand macro="citations"/>
</tool>