--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/varscan/varscan_mpileup.xml	Fri Mar 07 06:17:32 2014 -0500
@@ -0,0 +1,124 @@
+<tool id="varscan_mpileup" name="VarScan mpileup" version="2.3.5">
+  <description>
+        mutation caller for targeted, exome, and whole-genome resequencing
+  </description>
+  <requirements>
+  	<requirement type="package" version="2.3.5">VarScan</requirement>
+  </requirements>
+  <command interpreter="perl">
+  	
+	varscan_mpileup.pl 
+	"COMMAND::java -jar \$JAVA_JAR_PATH/VarScan.v2.3.5.jar $exe_command" 
+  	"INPUT::$in_file"
+  	"OUTPUT::$output"
+  	"LOG::$log"
+	"OPTION::--min-coverage $min_coverage"
+	"OPTION::--min-reads2 $min_reads2"
+	"OPTION::--min-avg-qual $min_avg_qual"
+	"OPTION::--min-var-freq $min_var_freq"
+	"OPTION::--min-freq-for-hom $min_freq_for_hom"
+	"OPTION::--p-value $p_value"	
+	"OPTION::--strand-filter $strand_filter"	
+	"OPTION::--output-vcf 1"	
+	
+	#if ($vcf_sample_list):
+		"OPTION::--vcf-sample-list $vcf_sample_list"
+	#end if
+	"OPTION::--variants $variants"	
+	
+	
+  	
+  </command>
+
+  <inputs>
+  	
+	<param name="exe_command" type="select" label="Command" help="" optional="false">
+		<option value="mpileup2snp" >mpileup2snp</option>
+		<option value="mpileup2indel">mpileup2indel</option>
+		<option value="mpileup2cns">mpileup2cns</option>
+	</param>
+	<param name="in_file" type="data" format="pileup" label="mpileup file" help="The SAMtools mpileup file" />
+	<param name="min_coverage" type="integer" label="min-coverage" help="" optional="true" value="8"/>
+	<param name="min_reads2" type="integer" label="min-reads2" help="" optional="true" value="2"/>
+	<param name="min_avg_qual" type="integer" label="min-avg-qual" help="" optional="true" value="15"/>
+	<param name="min_var_freq" type="float" label="min-var-freq" help="" optional="true" value="0.01"/>
+	<param name="min_freq_for_hom" type="float" label="min-freq-for-hom" help="" optional="true" value="0.75"/>
+	<param name="p_value" type="text" label="p-value" help="" optional="true" value="0.99"/>
+	<param name="strand_filter" type="integer" label="strand-filter" help="" optional="true" value="1"/>
+	<param name="vcf_sample_list" type="data" label="vcf-sample-list" format="txt" help="" optional="true" />
+	<param name="variants" type="integer" label="variants" help="Set to 1 to report only variants" optional="true" value="1"/>
+	
+	
+  </inputs>
+  <outputs>
+  	<data type="data" format="vcf" name="output" label="${tool.name} result on ${on_string}"/>
+  	<data type="data" format="txt" name="log" label="${tool.name} result on ${on_string} (log) "/>
+  </outputs>
+  	
+  <help> 
+
+.. class:: infomark
+
+**What it does**
+
+::
+
+ VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most  operating systems. It can be used to detect different types of variation:
+
+    Germline variants (SNPs an dindels) in individual samples or pools of samples.
+    Multi-sample variants (shared or private) in multi-sample datasets (with mpileup).
+    Somatic mutations, LOH events, and germline variants in tumor-normal pairs.
+    Somatic copy number alterations (CNAs) in tumor-normal exome data.
+
+
+**Input**
+
+::
+
+  mpileup file - The SAMtools mpileup file
+ 
+
+**Parameters**
+
+::
+
+  commands
+	mpileup2snp		Identify SNPs from an mpileup file
+	mpileup2indel		Identify indels an mpileup file
+	mpileup2cns		Call consensus and variants from an mpileup file
+
+  min-coverage	
+  	Minimum read depth at a position to make a call [8]
+
+  min-reads2	
+  	Minimum supporting reads at a position to call variants [2]
+
+  min-avg-qual	
+  	Minimum base quality at a position to count a read [15]
+
+  min-var-freq	
+        Minimum variant allele frequency threshold [0.01]
+
+  min-freq-for-hom
+  	Minimum frequency to call homozygote [0.75]
+  
+  p-value
+  	Default p-value threshold for calling variants [99e-02]
+  
+  strand-filter
+  	Ignore variants with >90% support on one strand [1]
+  
+  output-vcf
+  	If set to 1, outputs in VCF format
+  
+  vcf-sample-list
+  	For VCF output, a list of sample names in order, one per line
+  
+  variants
+  	Report only variant (SNP/indel) positions [0]
+
+
+  
+  </help>
+</tool>
+