Mercurial > repos > nml > filter_vcf

diff filtervcf.xml @ 0:93ea196681c8 draft

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"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
author nml
date Tue, 27 Aug 2019 12:31:30 -0400
parents
children 48922d9ca355
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filtervcf.xml	Tue Aug 27 12:31:30 2019 -0400
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+<tool id="filtervcf" name="Filter vcf" version ="1.8.2">
+  <description>filter out indels and complex SNVS</description>
+  <requirements>
+    <requirement type="package" version="1.8.2">snvphyl-tools</requirement>
+  </requirements>
+ <command detect_errors="exit_code">
+	filterVcf.pl --noindels  $vcf
+	-o $vcfout
+  </command>
+  <inputs>
+    <param name="vcf" type="data"  label="VCF file" format="vcf"/>
+  </inputs>
+  <outputs>
+    <data format="vcf" name="vcfout" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="vcf" value="filterVcf.input.1.vcf"/>
+      <output name="vcfout" file="filterVcf.output.1.vcf"/>
+    </test>
+  </tests>
+  <help>
+  Filter out indels and complex variants from VCF file
+  </help>
+<citations>
+</citations>
+</tool>