genetorrent.xml

<tool id="cghub_genetorrent" name="CGHub GeneTorrent" version="1.0.0">
	<description>download BAM files from CGHub</description>
	<requirements>
		<container type="docker">genetorrent</container>
	</requirements>
	<command interpreter="python">
genetorrent.py $uuid $outfile $outfile.dataset.dataset.id
#if str($cred_file) != 'None':
--cred-file $cred_file
#end if
--server "${gnos_endpoint}"
	</command>
	<inputs>
		<param name="uuid" type="text" size="50" label="Analysis ID"/>
		<param name="cred_file" type="select" label="Download Credentials" optional="True">
			<options from_file="cghub_credentials.loc">
				<column name="name" index="0"/>
				<column name="value" index="1"/>
			</options>
		</param>
		<param name="gnos_endpoint" type="text" size="50"  label="GNOS Server" help="example: cghub.ucsc.edu" value="cghub.ucsc.edu"/>
	</inputs>
	<outputs>
		<data name="outfile" format="bam" label="${uuid}.bam"/>
	</outputs>
	<help>
Download BAM files from CGHub
	</help>
</tool>