view data_manager/add_ctat_ref_lib.xml @ 0:fcf82328f066 draft default tip

new version. Not tested yet.

<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>
        <requirement type="package" version="0.3.0">gmap-fusion</requirement>
        <!-- gmap-fusion is required in order to process downloaded libraries 
             to create all of the required files and indexes. It includes gmap
             and FusionFilter, programs from both of which are needed.
        -->
    </requirements>
    <command detect_errors="default">
        <![CDATA[
        python $__tool_directory__/add_ctat_ref_lib.py 
            --genome_name "${genome_name}"
            --destination_path "${destination}" 
            --output_filename "${out_file}"
            #if str(${download}) == "true":
                --download "${filename}"
            #end if
        ]]>
    </command>
    <inputs>
        <!--
        <param name="download" type="boolean" checked="false"
             truevalue="- -download" falsevalue="" label="Need to Download? (yes/no)" />
            <param name="download" type="select" label="Need to Download?">
                <option value="single" selected="true">Single Dataset</option>
                <option value="paired_collection">Paired Collection</option>
            <when value="paired_collection">
                 <param name="fastq_input" format="fastqsanger" type="data_collection" collection_type="paired" label="Select dataset pair" help="Specify paired dataset collection containing paired reads"/>
            </when>
        -->
        <conditional name="download_question">
            <param name="download" type="boolean" checked="false" label="Need to Download? (yes/no)" />
            </param>
            <when value="true">
                 <param name="filename" type="select" label="Select File" display="radio" 
                     dynamic_options="get_ctat_genome_filenames()" help="Select a CTAT Genome Reference Library to Download." />
            </when>
        </conditional>

        <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>
    <code file="add_ctat_ref_lib.py"
</tool>