Mercurial > repos > trinity_ctat > ctat_lncrna_annotations_data_manager
diff data_manager/add_ctat_lncrna_annotations.xml @ 0:a3aa3f9e1702 draft default tip
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author | trinity_ctat |
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date | Mon, 16 Jul 2018 20:42:55 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/add_ctat_lncrna_annotations.xml Mon Jul 16 20:42:55 2018 -0400 @@ -0,0 +1,61 @@ +<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>