view ucsc_xenabrowser.xml @ 3:98b498545a52

Fixed xena_delete to delete the files from the Xena files directory as well as from the database

<?xml version="1.0"?>
<!--
    If the value of 'URL_method' is 'get', the request will consist of the value of 'URL' coming back in
    the initial response.  If value of 'URL_method' is 'post', any additional params coming back in the
    initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
-->
<tool name="UCSC Xena Browser" id="ucsc_xenabrowser" tool_type="data_source">
    <description>Run the UCSC Xena Browser as a Galaxy tool.</description>
    <command interpreter="python">ucsc_xena_download.py $genomic $clinical $__app__.config.output_size_limit</command>   
    <inputs action="https://genome-cancer.ucsc.edu/proj/site/hgHeatmap-cavm/" check_values="false" method="get">
        <display>go to UCSC Xena Browser $GALAXY_URL</display>
        <param name="GALAXY_URL" type="baseurl" value="/tool_runner" />
        <param name="tool_id" type="hidden" value="ucsc_xenabrowser" />
    </inputs>
    <request_param_translation>
        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" />
        <request_param galaxy_name="URL" remote_name="URL" missing="" />
    </request_param_translation>
    <uihints minwidth="800"/>
    <outputs>
        <data name="genomic" format="tabular" label="#echo $URL.rsplit('/',1)[1].rsplit('.',1)[0]+' genomic'" />
        <data name="clinical" format="tabular" label="#echo $URL.rsplit('/',1)[1].rsplit('.',1)[0]+' clinical'"/>
    </outputs>
    <options sanitize="False" refresh="True"/>
</tool>