diff vcffixup.xml @ 0:a03f346b6aae draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcffixup.xml	Thu Mar 19 14:30:34 2015 -0400
@@ -0,0 +1,30 @@
+<tool id="vcffixup" name="VCFfixup:" version="0.0.3">
+  <description>Count the allele frequencies across alleles present in each record in the VCF file</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"></expand>
+  <expand macro="stdio" />
+  <command>vcffixup "${input1}" > "${out_file1}"</command>
+  <inputs>
+    <param format="vcf" name="input1" type="data" label="Select VCF dataset"/>
+  </inputs>
+  <outputs>
+    <data format="vcf" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input1" value="vcflib.vcf"/>
+      <output name="out_file1" file="vcffixup-test1.vcf"/>
+    </test>
+    </tests>
+  <help>
+
+Uses genotypes from the selected VCF dataset to correct AC (alternate allele count), AF (alternate allele frequency), NS (number of called), in the VCF records.
+
+----
+
+Vcffixup @IS_PART_OF_VCFLIB@
+</help>
+  <expand macro="citations" />
+</tool>