view generate_pyclone_input.xml @ 0:6882251af034 draft

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<tool id="generate_pyclone_input" name="Generate PyClone input" version="14.2">
	<description>
		Generate PyClone input files from SNV and copy number data
	</description>
	
	<requirements>
		<requirement type="package" version="1.0">generate_pyclone_input</requirement>
		<requirement type="package" version="14.2">morinlab_scripts</requirement>
		<requirement type="set_environment">MORINLAB_SCRIPTS</requirement>
	</requirements>

	<stdio>
	   <exit_code range="1:" level="warning" />
	   <exit_code range=":-1" level="warning" />
	   <regex match="Error:" />
	   <regex match="Exception:" />
	</stdio>

	<command>
		Rscript \$MORINLAB_SCRIPTS/generate_pyclone_input/generate_pyclone_input.R
		$segments $segments_mode $maf $sample_id .;

		mv ./${sample_id}_pyclone_in.tsv $pyclone_input;
	</command>

	<inputs>
		<!-- Required inputs -->
		<param type="data" name="segments" format="tabular" label="Sequenza, Titan, OncoSNP, or IGV-friendly segments file"/>
		<param name="segments_mode" label="Specify the source of the segments file" type="select">
			<option value="S">Sequenza</option>
			<option value="T">Titan</option>
			<option value="I">IGV-friendly</option>
		</param>
		<param type="data" name="maf" format="tabular" label="Patient MAF file"/>
		<param type="text" name="sample_id" size="20" label="Sample ID"/>
	</inputs>

	<outputs>
		<data format="tabular" name="pyclone_input"/>
	</outputs>

	<tests>
	</tests>

	<help>
	</help>

</tool>