# HG changeset patch
# User p.lucas
# Date 1644420851 0
# Node ID 5b3d3fc3fda6f3ffe7199eea2fb7fe244f669bef

Uploaded xml

diff -r 000000000000 -r 5b3d3fc3fda6 varscan_readcount.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/varscan_readcount.xml	Wed Feb 09 15:34:11 2022 +0000
@@ -0,0 +1,51 @@
+<tool id="varscan" name="VarScan Readcount" version="2.4.4">
+    <description>To use varscan readcount tool</description>
+
+    <requirements>
+        <requirement type="package" version="2.4.4">varscan</requirement>
+    </requirements>
+
+    <stdio>
+        <regex match="Exception" source="both" level="fatal" description="Tool exception"/>
+        <regex match=".*" source="both" level="log" description="tool progress"/>
+    </stdio>
+
+    <version_command><![CDATA[
+varscan 2>&1 | head -n 1
+    ]]></version_command>
+
+    <command><![CDATA[
+        varscan readcounts ${input} --min-coverage ${min_cov} --min-base-qual ${min_base_qual} --output-file ${output}
+    ]]></command>
+
+    <inputs>
+        <param format="pileup" name="input" type="data" label="Pileup dataset" help=""/>
+        <param name="min_cov" type="integer" value="1" min="1" max="2000" label="Minimum read depth" help="Minimum depth at a position to make a call [1]"/>
+        <param name="min_base_qual" type="integer" value="20" min="1" max="500" label="Minimum base quality" label="Minimum base quality at a position to count a read [20]"/>
+    </inputs>
+
+    <outputs>
+        <data name="output" format="vcf"/>
+    </outputs>
+
+    <help>
+
+command: varscan readcounts --help
+
+Min coverage:   1
+Min base qual:  20
+USAGE: java -jar VarScan.jar readcounts [pileup] OPTIONS
+        OPTIONS:
+        --variants-file A list of variants at which to report readcounts
+        --output-file   Output file to contain the readcounts
+        --min-coverage  Minimum read depth at a position to make a call [1]
+        --min-base-qual Minimum base quality at a position to count a read [20]
+
+    </help>
+
+    <citations>
+        <citation type="doi">10.1101/gr.129684.111</citation>
+    </citations>
+</tool>
+
+