# HG changeset patch
# User anton
# Date 1402418268 14400
# Node ID 551d94c28e3be3330e1ec429e7188c41faff0381
# Parent  f91098850a145ee2d242ae5ec9ed8c8e52bc9890
Uploaded

diff -r f91098850a14 -r 551d94c28e3b vcfgeno2haplo.xml
--- a/vcfgeno2haplo.xml	Wed May 21 12:34:16 2014 -0400
+++ b/vcfgeno2haplo.xml	Tue Jun 10 12:37:48 2014 -0400
@@ -1,7 +1,6 @@
 <tool id="vcfgeno2haplo" name="VCFgenotype-to-haplotype:" version="0.0.1">
 <requirements>
     <requirement type="package" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">vcflib</requirement>
-    <!-- <requirement type="package" version="0.1.18">samtools</requirement> -->
 </requirements>
   <description>Convert genotype-based phased alleles into haplotype alleles</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." />
@@ -34,11 +33,11 @@
        </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="window_size" type="text" size="4" value="30" label="compare records up to this many bp away (window size)" help="-w option (default = 30)" />
-     <param name="output_option" type="boolean" truevalue="-o" label="What to report?" help="-o option" />
+     <param name="window_size" type="text" size="4" value="30" label="compare records up to this many bp away (window size)" help="--window-size option (default = 30)" />
+     <param name="output_option" type="boolean" truevalue="-o" label="What to report?" help="--only-variants option" />
 <!--       <option value=" ">Output entire haplotype</option>
        <option value="-o">Don't output the entire haplotype, just concatenate REF/ALT strings (delimited by &quot;:&quot;)</option>
      </param> -->
@@ -47,7 +46,7 @@
     <data format="vcf" name="out_file1" />
   </outputs>
   <stdio>
-    <regex match="index file" source="stderr" level="warning"/>
+    <exit_code range="1:" level="fatal" />
   </stdio>
   <tests>
     <test>
@@ -63,7 +62,7 @@
 
 Convert genotype-based phased alleles within a window size specified by -w option into haplotype alleles. Will break haplotype construction when encountering non-phased genotypes on input.
 
-Options::
+The options are::
 
     -r, --reference FILE    FASTA reference file, required with -i and -u
     -w, --window-size N     Merge variants at most this many bp apart (default 30)