view varscan2_from_bam.xml @ 3:436d89c21432

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<?xml version="1.0" encoding="UTF-8"?>
<tool id="varscan2_from_bam" name="VarScan2 from BAM">
	<description>VarScan2 reading a *.bam file to avoid massive I/O resourcing.</description>
	<requirements>
		<requirement type="package" version="1.0.19">samtools-mpileup-parallel</requirement>
		<requirement type="package" version="2.3.6">VarScan</requirement>
	</requirements>
	<command interpreter="bash">
		<!--
			VarScan2 url:
			http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.6.jar?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fvarscan%2Ffiles%2F&ts=1377264954&use_mirror=freefr
			
			The following script is written in the "Cheetah" language:
			http://www.cheetahtemplate.org/docs/users_guide_html_multipage/contents.html
		-->
		samtools mpileup -t $threads -f $reference_genome
		#for $sample in $samples
			 ${sample.mapped_reads}
		#end for
		 | java -jar VarScan.v2.2.jar pileup2snp > $output_table
	</command>
	
	<input type="text" name="threads" value="8" min="1" />
	
	<inputs>
		<repeat name="samples" title="Samples" min="1">
			<param format="bam,sam" name="mapped_reads" type="data" label="Alignment file" help="Mapped reads in BAM or SAM format."/>
		</repeat>
		
		<param format="fa,fasta" name="reference_genome" type="data" label="Gene Model Annotations" help="Reference genome (genome.fa) that corresponds to the *.bam file." />
	</inputs>
	
	<outputs>
		<data format="tabular" name="output_table" label="${tool.name}" />
	</outputs>
	
	<help>
		VarScan2.3.6 is NOT compatible with the latest versions (0.1.16 and 0.1.19) of samtools.
		It is compatible with 0.1.6, until this is fixed please stay stick to 0.1.6.
	</help>
</tool>