annotate macros.xml @ 4:584c09b1967a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit 2e9b45d5a41ee014d84a5be9e9c672b3b531a814

<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">0.2.1</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <xml name="edam_topics">
        <edam_topics>
            <edam_topic>topic_3175</edam_topic>
        </edam_topics>
    </xml>
    <xml name="edam_operations">
        <edam_operations>
            <edam_operation>operation_3197</edam_operation>
        </edam_operations>
    </xml>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">sansa</requirement>
        </requirements>
    </xml>
    <xml name="version_command">
        <version_command><![CDATA[sansa -v | grep "Sansa " | cut -d "v" -f 3]]></version_command>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1093/bioinformatics/bts378</citation>
        </citations>
    </xml>

    <!-- input -->

    <xml name="fg">
        <section name="fg" title="Feature and gene annotation options" expanded="true">
            <param argument="--gtf" type="data" format="gtf,gff3" label="Select file"/>
            <param argument="--id" type="text" value="gene_name" label="Set GTF/GFF3 attribute">
                <option value="exon_id">exon_id</option>
                <option value="gene_id">gene_id</option>
                <option value="gene_name">gene_name</option>
                <option value="Name">Name</option>
            </param>
            <param argument="--feature" type="text" value="gene" label="Set GTF/GFF3 feature">
                <option value="gene">gene</option>
                <option value="exon">exon</option>
            </param>
            <param argument="--distance" type="integer" min="0" value="1000" label="Set maximum distance" help="0: overlapping features only"/>
            <param argument="--contained" type="boolean" truevalue="-c" falsevalue="" label="Report contained genes?" help="Useful for CNVs
            but potentially long list of genes."/>
        </section>
    </xml>
    <xml name="s">
        <section name="s" title="SV annotation options" expanded="true">
            <param argument="--db" type="data" format="vcf,bcf" label="Select database file"/>
            <param argument="--bpoffset" type="integer" value="50" label="Set maximum breakpoint offset"/>
            <param argument="--ratio" type="float" min="0.0" max="1.0" value="0.8" label="Set minimum size ratio smaller SV to larger SV"/>
            <param argument="--strategy" type="select" label="Select matching strategy">
                <option value="best" selected="true">Best</option>
                <option value="all">All</option>
            </param>
            <param argument="--notype" type="boolean" truevalue="-n" falsevalue="" label="Require matching SV types?"/>
            <param argument="--nomatch" type="boolean" truevalue="-m" falsevalue="" label="Report SVs without match in database?"/>
        </section>
    </xml>
</macros>