Mercurial > repos > nick > allele_counts

changeset 0:28c40f4b7d2b

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Uploaded xml description
author nick
date Fri, 24 May 2013 10:32:56 -0400
parents
children 49bb46c3a1af
files allele-counts.xml
diffstat 1 files changed, 24 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/allele-counts.xml	Fri May 24 10:32:56 2013 -0400
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+<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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