# HG changeset patch
# User nick
# Date 1369400129 14400
# Node ID 7c95db468ad5bf6c3968512954bf51462f38a159
# Parent  57e85db3f13c498e54ad8386b1addcedc4a67b9d
Uploaded xml

diff -r 57e85db3f13c -r 7c95db468ad5 allele-counts.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/allele-counts.xml	Fri May 24 08:55:29 2013 -0400
@@ -0,0 +1,24 @@
+<tool id="allele_counts_1" version="1.0" name="Count alleles">
+  <description>and minor allele frequencies</description>
+  <command interpreter="python">allele-counts.py -i $input -o $output -f $freq -c $covg $header</command>
+  <inputs>
+    <param name="input" type="data" format="vcf" label="Input variants from Naive Variants Detector"/>
+    <param name="freq" type="float" value="1.0" min="0" max="100" label="Minor allele frequency threshold"/>
+    <param name="covg" type="integer" value="10" min="0" label="Coverage threshold (per strand)"/>
+    <param name="header" type="boolean" truevalue="-H" falsevalue="" checked="False" label="Write header line" />
+  </inputs>
+  <outputs>
+    <data name="output" format="tabular"/>
+  </outputs>
+  <stdio>
+    <exit_code range="1:" err_level="fatal"/>
+    <exit_code range=":-1" err_level="fatal"/>
+  </stdio>
+
+  <help>
+This tool parses the output of Naive Variant Detector, counting variants, calculating numbers of alleles, and minor allele frequency. It applies filters based on coverage, strand bias, and minor allele frequency cutoffs.
+
+**Note**: The VCF file from the Naive Variant Detector must include counts *per strand*.
+  </help>
+
+</tool>
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