# HG changeset patch
# User anton
# Date 1410807248 14400
# Node ID 89c1efc31618ee5731a6a87094c9156e9a9aad48
# Parent  b8ab4ef85a5b5ac0d5a8f38d1f730b7673601c78
Uploaded

diff -r b8ab4ef85a5b -r 89c1efc31618 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Jun 25 16:51:34 2014 -0400
+++ b/tool_dependencies.xml	Mon Sep 15 14:54:08 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 b8ab4ef85a5b -r 89c1efc31618 vcfvcfintersect.xml
--- a/vcfvcfintersect.xml	Wed Jun 25 16:51:34 2014 -0400
+++ b/vcfvcfintersect.xml	Mon Sep 15 14:54:08 2014 -0400
@@ -1,6 +1,6 @@
 <tool id="vcfvcfintersect" name="VCF-VCFintersect:" version="0.0.2">
 <requirements>
-    <requirement type="package" version="86723982aa">vcflib</requirement>
+    <requirement type="package" version="8a5602bf07">vcflib</requirement>
     <!-- <requirement type="package" version="0.1.18">samtools</requirement> -->
 </requirements>
   <description>Intersect two VCF datasets</description>
@@ -78,7 +78,7 @@
       <param name="reference_source_selector" value="history" />
       <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" />
       <param name="vcf_input2" value="vcfvcfintersect-input2.vcf" />
-      <param name="isect_union" value="Intersect" />
+      <param name="isect_union" value="-i" />
       <param name="invert" value="False" />
       <param name="loci" value="False" />
       <patam name="adv_options" value="False" />
@@ -90,7 +90,7 @@
       <param name="reference_source_selector" value="history" />
       <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" />
       <param name="vcf_input2" value="vcfvcfintersect-input2.vcf" />
-      <param name="isect_union" value="Union" />
+      <param name="isect_union" value="-u" />
       <param name="invert" value="False" />
       <param name="loci" value="False" />
       <patam name="adv_options" value="False" />
@@ -109,7 +109,6 @@
     -i, --intersect-vcf FILE  use this VCF for set intersection generation
     -u, --union-vcf FILE      use this VCF for set union generation
     -w, --window-size N       compare records up to this many bp away (default 30)
-    -r, --reference FILE      FASTA reference file, required with -i and -u
     -l, --loci                output whole loci when one alternate allele matches
     -m, --ref-match           intersect on the basis of record REF string
     -t, --tag TAG             attach TAG to each record's info field if it would intersect