# HG changeset patch
# User anton
# Date 1410807103 14400
# Node ID d6fd217a1f90ced336497bc03882affc890aa885
# Parent  a6cd013745fd30cdc73fdadb37b41fa350534ab5
Uploaded

diff -r a6cd013745fd -r d6fd217a1f90 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Jun 25 16:48:39 2014 -0400
+++ b/tool_dependencies.xml	Mon Sep 15 14:51:43 2014 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="vcflib" version="86723982aa">
-      <repository changeset_revision="a6826babf644" name="vcflib_86723982aa" owner="anton" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="vcflib" version="8a5602bf07">
+        <repository changeset_revision="bffe0495cd92" name="package_vcflib_8a5602bf07" owner="anton" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>
diff -r a6cd013745fd -r d6fd217a1f90 vcfgeno2haplo.xml
--- a/vcfgeno2haplo.xml	Wed Jun 25 16:48:39 2014 -0400
+++ b/vcfgeno2haplo.xml	Mon Sep 15 14:51:43 2014 -0400
@@ -1,6 +1,6 @@
 <tool id="vcfgeno2haplo" name="VCFgenotype-to-haplotype:" version="0.0.2">
 <requirements>
-    <requirement type="package" version="86723982aa">vcflib</requirement>
+    <requirement type="package" version="8a5602bf07">vcflib</requirement>
 </requirements>
   <description>Convert genotype-based phased alleles into haplotype alleles</description>
   <command>
@@ -36,7 +36,7 @@
 	 <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="--window-size option (default = 30)" />
+     <param name="window_size" type="text" size="4" value="30" label="compare records up to this many bp away" help="--window-size option (default = 30)" />
      <param name="output_option" type="boolean" truevalue="-o" falsevalue="" 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>
@@ -64,7 +64,6 @@
 
 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)
     -o, --only-variants     Don't output the entire haplotype, just concatenate
                             REF/ALT strings (delimited by ":")