Mercurial > repos > anton > vcfallelicprimitives

changeset 1:797a0f9a9845 draft default tip

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Uploaded
author anton
date Tue, 10 Jun 2014 12:01:30 -0400
parents 058c705d3873
children
files vcfallelicprimitives.xml
diffstat 1 files changed, 4 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/vcfallelicprimitives.xml	Thu May 08 14:56:43 2014 -0400
+++ b/vcfallelicprimitives.xml	Tue Jun 10 12:01:30 2014 -0400
@@ -5,9 +5,9 @@
   <description>Split alleleic primitives (gaps or mismatches) into multiple VCF lines</description>
   <command>cat "${input}" | vcfallelicprimitives ${m_option} -t "${t_option}" > "${out_file1}"</command>
   <inputs>
-    <param name="m_option" type="boolean" checked="true" truevalue="-m" falsevalue="" label="Retain MNPs as separate events" help="-use-mnps option"/>
-    <param name="t_option" size="20" type="text" value="Split primitives" label="Mark records which are split with this tag" help="-tag-parsed option"/>
-    <param format="vcf" name="input" type="data" label="From"/>
+    <param format="vcf" name="input" type="data" label="Select VCF dataset"/>
+    <param name="m_option" type="boolean" checked="true" truevalue="-m" falsevalue="" label="Retain MNPs as separate events" help="--use-mnps option"/>
+    <param name="t_option" size="20" type="text" value="Split primitives" label="Mark records which are split with this tag" help="--tag-parsed option"/>
   </inputs>
   <outputs>
     <data format="vcf" name="out_file1" />
@@ -24,7 +24,7 @@
 
 If multiple alleleic primitives (gaps or mismatches) are specified in a single VCF record, this tools splits the record into multiple lines, but drops all INFO fields.  "Pure" MNPs are split into multiple SNPs unless the -m flag is provided.  Genotypes are phased where complex alleles have been decomposed, provided genotypes in the input.
 
-The tool has the following options::
+The options are::
                                                                                                                            
     --use-mnps (-m)
     Retain MNPs as separate events