view gdcwebapp.xml @ 32:1edc869cd008 draft

Uploaded 20170607

<?xml version="1.0"?>
<tool name="GDCWebApp" id="data_source_gdcwebapp" tool_type="data_source_async" hidden="False" display_interface="False" version="1.0.0" force_history_refresh="True">
    <description>an intuitive interface to filter, extract, and convert Genomic Data Commons experiments</description>
    <requirements>
        <requirement type="package" version="2.7.10">python</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>
    <command>
        <![CDATA[
            mkdir -p tmp && 
            python ${__tool_directory__}/json_collect_data_source.py "${__app__.config.output_size_limit}" --json_param_file "${output1}" --path "." --appdata "tmp"
        ]]>
    </command>
    <inputs check_values="False" action="http://bioinf.iasi.cnr.it/gdcwebapp/app.php">
        <display>Go to GDCWebApp service $GALAXY_URL</display>
        <param name="GALAXY_URL" type="baseurl" value="/async/data_source_gdcwebapp" />
    </inputs>
    <outputs>
        <collection name="list_output" type="list:list" label="${tool.name} Output Collection">
            <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)_(?P&lt;ext&gt;[^_]+)_(?P&lt;dbkey&gt;[^_]+)" ext="auto" visible="False" directory="tmp" />
        </collection>
        <data name="output1" format="auto" label="${tool.name} Output Data" />
    </outputs>
    <options sanitize="False" refresh="True" />
</tool>