# HG changeset patch
# User yhoogstrate
# Date 1387273267 18000
# Node ID 212cc602c073a97f0201c491428a84060bcf3735

Uploaded

diff -r 000000000000 -r 212cc602c073 varscan2_from_bam.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/varscan2_from_bam.xml	Tue Dec 17 04:41:07 2013 -0500
@@ -0,0 +1,41 @@
+<?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>