view data_manager/featurecounts_gxfloader.xml @ 2:b3cd759a0064 draft default tip

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<?xml version="1.0"?>
<tool id="featurecounts_gxfloader" name="featurecounts" tool_type="manage_data" version="1.0.1">
    <description>GFF/GTF loader</description>
    <requirements>
        <requirement type="package" version="1.4.6.p5">featurecounts</requirement>
        <requirement type="set_environment">FCOUNT_SCRIPT_PATH</requirement>
    </requirements>
    <stdio>
        <exit_code description="Error" level="fatal" range="1:" />
    </stdio>
    <!-- <version_command>kraken -version | awk '{print $NF}'</version_command> -->
    <command>
    <![CDATA[
        mkdir featurecount_gxf && cp "$gxf" featurecount_gxf/ &&
        cd .. && python \$FCOUNT_SCRIPT_PATH/data_manager/make_json.py --dbkey "${dbkey}" --provider "${provider}" --ref "${ref}"--out "${out_file}"
    ]]>
    </command>
    <inputs>
        <param label="Name for this GFF/GTF" name="dbkey" type="text" />
        <param label="Provider for this GFF/GTF" name="provider" type="text" />
        <param label="Reference URL for this GFF/GTF" name="ref" type="text" />
        <param format="gff,gtf,tabular" label="Select history item" multiple="True" name="gxf" type="data" />        
    </inputs>
    <outputs>
        <data format="data_manager_json" name="out_file" />
    </outputs>

</tool>