annotate data_manager/add_ctat_lncrna_annotations.xml @ 0:a3aa3f9e1702 draft default tip

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<tool id="ctat_lncrna_annotations_data_manager" 
    name="CTAT lncrna annotations Data Manager" 
    version="1.0.0" tool_type="manage_data">
    <description>Retrieve, and/or specify the location of CTAT lncrna annotations. 
    </description>
    <requirements>
        <requirement type="package" version="2.7">python</requirement>
    </requirements>
    <command detect_errors="default">
        <![CDATA[
        python $__tool_directory__/add_ctat_lncrna_annotations.py 
            --display_name "${display_name}" 
            --destination_path "${destination}" 
            --output_filename "${out_file}" 
            #if str( $download_question.download ) == "true":
                --download_location "\"${download_question.filename}\"" 
                #if str( $download_question.force_download ) == "true":
                    --force_download 
                #end if
            #end if
        ]]>
    </command>
    <inputs>
        <conditional name="download_question">
            <param name="download" type="boolean" checked="false" label="Need to Download?" />
            <when value="true">
                <param name="filename" type="select" label="Select File"
                    dynamic_options="get_ctat_lncrna_annotations_locations()" 
                    help="Select a lncrna annotations to Download." />
                <param name="force_download" type="boolean" checked="false" label="Force New Download?" />
            </when>
        </conditional>

        <param name="display_name" type="text" label="lncrna annotations Display Name" />
        <param name="destination" type="text" label="Local Destination (full path)" />
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json" />
    </outputs>
    <help>
.. class:: infomark
	
Retrieve, and/or specify the location of, a CTAT lncrna annotations.
When download is true, the annotations from this website_ will be downloaded.

Currently mm9,mm10,hg19,hg38 are supported.

.. class:: infomark

Specify the Full Path of the destination where the CTAT lncrna annotations should be placed.
If you already have the annotations, specify the full path of the location where it exists and leave the download box unchecked.

.. class:: infomark

The display_name may be left empty if downloading. 
The display_name will be used as the selector text of the entry in the data table.

.. _website: https://data.broadinstitute.org/Trinity/CTAT/lncrna/annotations.tar.gz         
    </help>
    <code file="add_ctat_lncrna_annotations.py" />
</tool>