view data_manager/add_ctat_ref_lib.xml @ 11:1d8ffed7a312 draft

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<tool id="ctat_genome_ref_lib_data_manager" 
    name="CTAT Genome Reference Library Data Manager" 
    version="1.0.0" tool_type="manage_data">
    <description>Retrieve, and/or Specify the location of, a CTAT Genome Reference Library. 
    </description>
    <requirements>
        <requirement type="package" version="2.7">python</requirement>
    </requirements>
    <command detect_errors="default">
        <![CDATA[
        echo "Current directory and contents" && pwd && ls -la . &&
        echo "Tool directory and contents are" && echo "$__tool_directory__" && ls -la "$__tool_directory__" &&
        python $__tool_directory__/add_ctat_ref_lib.py ${download}
            --ref_genome "${genome_name}"
            --destination_path "${destination}" 
            -o "${out_file}"
        ]]>
    </command>
    <inputs>
        <param name="download" type="boolean" checked="false"
             truevalue="--download" falsevalue="" label="Need to Download? (yes/no)" />
        <param name="genome_name" type="text" label="Reference Genome name" />
        <param name="destination" type="text" label="Local Destination (full path)" />
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json" />
    </outputs>
    <help>
        Retrieve, and/or specify the location of, a CTAT Genome Reference Library.
        When download is true, the file retrieved and processed is https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/GRCh38_gencode_v26_CTAT_lib_Nov012017.plug-n-play.tar.gz.
        Specify the Full Path of the location where the CTAT Reference Library should be placed.
        You will need approximately 30GB of space for this library.
        If you already have the library, specify the full path of the location where it exists and leave the download box unchecked.
        The Reference Genome name may be left empty if downloading. The name will be used as the selector text of the entry in the data table.
        For more information on CTAT Genome Reference Libraries, see <a http="https://github.com/FusionFilter/FusionFilter/wiki">FusionFilter</a>
    </help>
</tool>