Mercurial > repos > anton > vcfcheck

changeset 3:dfe0b3d70972 draft

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Uploaded
author anton
date Tue, 10 Jun 2014 12:30:55 -0400
parents 2a60fa33b3ba
children fd7faee2c5fc
files vcfcheck.xml
diffstat 1 files changed, 3 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/vcfcheck.xml	Tue May 20 17:23:23 2014 -0400
+++ b/vcfcheck.xml	Tue Jun 10 12:30:55 2014 -0400
@@ -1,7 +1,6 @@
 <tool id="vcfcheck" name="VCFcheck:" version="0.0.1">
 <requirements>
     <requirement type="package" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">vcflib</requirement>
-    <!-- <requirement type="package" version="0.1.18">samtools</requirement> -->
 </requirements>
   <description>Verify that the reference allele matches the reference genome</description>
   <command>
@@ -25,7 +24,7 @@
            </options>
 	   <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
          </param>
-	 <param name="input_vcf" type="data" format="vcf" label="VCF dataset to check">
+	 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset">
 	   <!-- Validators are commented to allow users apply too to any build. May need to be revised in the future
 		<validator type="unspecified_build" />
 		<validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
@@ -34,7 +33,7 @@
        </when>
        <when value="history"> <!-- FIX ME!!!! -->
          <param name="ref_file" type="data" format="fasta" label="Using reference file" />
-	 <param name="input_vcf" type="data" format="vcf" label="VCF dataset to check" />
+	 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset" />
        </when>
      </conditional>
      <param name="failure_selector" type="select" display="radio" label="Exclude or include failed sites">
@@ -61,7 +60,7 @@
 
 Verifies that the VCF REF field matches the reference as described.  
 
-Options::
+The options are::
 
     -x, --exclude-failures If a record fails, don't print it.  Otherwise do.
     -k, --keep-failures    Print if the record fails, otherwise not.