--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/varscan_mpileup.xml	Tue Jul 10 13:36:03 2018 -0400
@@ -0,0 +1,101 @@
+<tool id="varscan_mpileup" name="VarScan mpileup" version="@VERSION@.0">
+    <description>for variant detection</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command><![CDATA[
+        ## Set up samples list file.
+        #if $sample_names.strip() != '':
+           echo $sample_names | awk -F ',' '{ for (i = 1; i <= NF; i++) { print \$i; } }' > samples_list.txt &&
+        #end if
+
+        ## Set up command + input.
+        varscan ${cmd} '${input}'
+            --min-coverage ${min_coverage} 
+            --min-reads2 ${min_reads2} 
+            --min-avg-qual ${min_avg_qual}
+            --min-var-freq ${min_var_freq}
+            --min-freq-for-hom ${min_freq_for_hom}
+            --p-value ${p_value}
+
+            #if str($strand_filter) == 'yes':
+              --strand-filter 1
+            #end if
+
+            ## Report only variants in consensus.
+            #if str($cmd) == 'mpileup2cns':
+              --variants
+            #end if
+            
+            ## Set up outputs.
+            --output-vcf 1 > '$output'
+
+            #if $sample_names.strip() != '':
+                --vcf-sample-list samples_list.txt
+            #end if
+
+    ]]></command>
+    <inputs>
+        <param name="input" format="pileup" type="data" label="Samtools pileup dataset" help=""/>
+
+        <param name="cmd" type="select" label="Analysis type">
+          <option value="mpileup2snp" selected="True">single nucleotide variation</option>
+          <option value="mpileup2indel">insertions and deletions</option>
+          <option value="mpileup2cns">consensus genotype</option>
+        </param>
+
+        <expand macro="min_coverage" />
+        <expand macro="min_reads2" />
+        <expand macro="min_avg_qual" />
+        <expand macro="min_var_freq" value="0.01" />
+        <expand macro="min_freq_for_hom" />
+        <expand macro="p_value" value="0.99" label="Default p-value threshold for calling variants"/>
+        <expand macro="strand_filter" />
+        <param name="sample_names" type="text" value="" help="Separate sample names by comma; leave blank to use default sample names."/>
+    </inputs>
+    <outputs>
+        <data name="output" format="vcf"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="test_in1.pileup" />
+            <param name="cmd" value="mpileup2cns" />
+            <param name="min_coverage" value="8" />
+            <param name="min_reads2" value="2" />
+            <param name="min_avg_qual" value="15" />
+            <param name="min_var_freq" value="0.01" />
+            <param name="min_freq_for_hom" value="0.75" />
+            <param name="p_value" value="0.99" />
+            <param name="strand_filter" value="no" />
+            <param name="sample_names" value="" />
+            <output name="output" file="varscan_mpileup_result1.vcf" lines_diff="0" />
+        </test>
+    </tests>
+
+    <help>
+**VarScan Overview**
+
+VarScan_ performs variant detection for massively parallel sequencing data, such as exome, WGS, and transcriptome data.
+It calls variants from a mpileup dataset and produces a VCF 4.1. Full documentation is available online_.
+
+This tool detects variants from pileups.
+
+.. _VarScan: http://dkoboldt.github.io/varscan/
+.. _online: http://dkoboldt.github.io/varscan/using-varscan.html
+
+**Input**
+
+::
+
+  mpileup file - The SAMtools mpileup file
+ 
+
+**Output**
+
+VarScan produces a VCF 4.1 dataset as output.
+
+    </help>
+    <expand macro="citations" />
+</tool>