dpclust.xml

<tool id="dpclust" name="DPClust" version="2.1.3">
    <stdio>
        <exit_code range="1:" />
    </stdio>
	<description>VCF clustering</description>
	<requirements>
		<container type="docker">dpclust</container>
	</requirements>
	<command interpreter="Rscript"><![CDATA[
		dpc.R ${input_vcf} ${sample_number} ${input_battenberg} ${input_cellularity}
	]]></command>

	<inputs>
		<param format="vcf" name="input_vcf" type="data" label="VCF file" help="" />
		<param format="txt" name="input_battenberg" type="data" label="Battenberg file" help="" />
		<param format="txt" name="input_cellularity" type="data" label="Cellularity file" help="" />
		<param type="integer" name="sample_number" label="Sample number" help="The ith sample column in the VCF file" value="1"/>
	</inputs>

	<outputs>
		<data format="png" name="output_png" label="DirichletProcessplotBinomial PNG" from_work_dir="DirichletProcessplotBinomial.png"/>
		<data format="txt" name="cellularity" label="Cellularity (Sub Challenge 1A)" from_work_dir="subchallenge1A.txt"/>
		<data format="txt" name="no_clusters" label="Number Clusters (Sub Challenge 1B)" from_work_dir="subchallenge1B.txt"/>
		<data format="txt" name="proportions" label="Cluster Proportions (Sub Challenge 1C)" from_work_dir="subchallenge1C.txt"/>
		<data format="txt" name="assignments" label="Cluster Assignments (Sub Challenge 2A)" from_work_dir="subchallenge2A.txt"/>
		<data format="txt" name="co_clustering" label="Co-Cluster (Sub Challenge 2B)" from_work_dir="subchallenge2B.txt"/>
	</outputs>

	<help>
        DPClust pipeline implementation
	</help>

	<tests>
		<test>
		</test>
	</tests>

</tool>