# HG changeset patch
# User devteam
# Date 1473970086 14400
# Node ID 31a86dbe17c03fcf945cdfb426fc3d7121d528d7
# Parent  834e1f313036a5a72d81b06f0c6943af31661158
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79

diff -r 834e1f313036 -r 31a86dbe17c0 macros.xml
--- a/macros.xml	Wed Nov 11 12:58:07 2015 -0500
+++ b/macros.xml	Thu Sep 15 16:08:06 2016 -0400
@@ -1,7 +1,7 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="8a5602bf07">vcflib</requirement>
+            <requirement type="package" version="1.0.0_rc1">vcflib</requirement>
             <yield/>
         </requirements>
     </xml>
@@ -10,6 +10,7 @@
             <exit_code range="1:" level="fatal" />
         </stdio>
     </xml>
+   <token name="@WRAPPER_VERSION@">1.0.0_rc1</token>
    	<xml name="citations">
    	     <citations>
              <citation type="bibtex">
diff -r 834e1f313036 -r 31a86dbe17c0 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Nov 11 12:58:07 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="vcflib" version="8a5602bf07">
-        <repository changeset_revision="7e67466b033e" name="package_vcflib_8a5602bf07" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>
diff -r 834e1f313036 -r 31a86dbe17c0 vcfbedintersect.xml
--- a/vcfbedintersect.xml	Wed Nov 11 12:58:07 2015 -0500
+++ b/vcfbedintersect.xml	Thu Sep 15 16:08:06 2016 -0400
@@ -1,62 +1,59 @@
-<tool id="vcfbedintersect" name="VCF-BEDintersect:" version="0.0.3">
-  <description>Intersect VCF and BED datasets</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"></expand>
-  <expand macro="stdio" />
-  <command>
-    #if str($bed_vs_interval.bed_vs_interval_selector) == "bed":
-        vcfintersect -b "${bed_vs_interval.bed_input}" ${invert} "${vcf_input}" > "${out_file1}"
-   #else:
-        vcfintersect -R "${bed_vs_interval.int_input}" ${invert} "${vcf_input}" > "${out_file1}"
-   #end if
-
-  </command>
-  <inputs>
-    <!-- selecting refernce source -->
-    <param name="vcf_input" type="data" format="vcf" label="Select VCF dataset" />
-     <conditional name="bed_vs_interval">
-       <param name="bed_vs_interval_selector" type="select" label="BED dataset or an interval to intersect with">
-	 <option value="bed">BED</option>
-	 <option value="interval">Interval</option>
-       </param>
-       <when value="bed">
-	 <param name="bed_input" type="data" format="bed" label="Select BED dataset" />
-       </when>
-       <when value="interval">
-	 <param name="int_input" type="text" value="chr20:1-30" label="Enter interval string" help="use chr:start-end format" />
-       </when>
-     </conditional>
-     <param name="invert" type="boolean" truevalue="-v" falsevalue="" label="Invert selection?" help="-v, --invert. Print entries that DO NOT intersect." />
-  </inputs>
-  <outputs>
-    <data format="vcf" name="out_file1" />
-  </outputs>
-  <tests>
-    <test>
-      <param name="bed_vs_interval_selector" value="bed" />
-      <param name="bed_input" value="vcfannotate.bed" />
-      <param name="invert" value="False" />
-      <param name="vcf_input" value="vcflib.vcf"/>
-      <output name="out_file1" file="vcfbedintersect-test1.vcf"/>
-    </test>
-    <test>
-      <param name="bed_vs_interval_selector" value="interval" />
-      <param name="int_input" value="20:1-30000" />
-      <param name="invert" value="False" />
-      <param name="vcf_input" value="vcflib.vcf"/>
-      <output name="out_file1" file="vcfbedintersect-test2.vcf"/>
-    </test>
-    </tests>
-
-  <help>
-
-Computes intersection between a VCF dataset and a set of genomic intervals defined as either a BED dataset (http://genome.ucsc.edu/FAQ/FAQformat.html#format1) or a manually typed interval (in the form of chr:start-end).
-
-----                                                                                                                                                                              
-
-VCFBEDintersect is based on vcfintersect utility of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).     
-</help>
-  <expand macro="citations" />
-</tool>
+<tool id="vcfbedintersect" name="VCF-BEDintersect:" version="@WRAPPER_VERSION@.0">
+    <description>Intersect VCF and BED datasets</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio" />
+    <command>
+        #if str($bed_vs_interval.bed_vs_interval_selector) == "bed":
+            vcfintersect -b "${bed_vs_interval.bed_input}" ${invert} "${vcf_input}" > "${out_file1}"
+        #else:
+            vcfintersect -R "${bed_vs_interval.int_input}" ${invert} "${vcf_input}" > "${out_file1}"
+        #end if
+    </command>
+    <inputs>
+        <!-- selecting refernce source -->
+        <param name="vcf_input" type="data" format="vcf" label="Select VCF dataset" />
+        <conditional name="bed_vs_interval">
+            <param name="bed_vs_interval_selector" type="select" label="BED dataset or an interval to intersect with">
+                <option value="bed">BED</option>
+                <option value="interval">Interval</option>
+            </param>
+            <when value="bed">
+                <param name="bed_input" type="data" format="bed" label="Select BED dataset" />
+            </when>
+            <when value="interval">
+                <param name="int_input" type="text" value="chr20:1-30" label="Enter interval string" help="use chr:start-end format" />
+            </when>
+        </conditional>
+        <param name="invert" type="boolean" truevalue="-v" falsevalue="" label="Invert selection?" help="-v, --invert. Print entries that DO NOT intersect." />
+    </inputs>
+    <outputs>
+        <data format="vcf" name="out_file1" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="bed_vs_interval_selector" value="bed" />
+            <param name="bed_input" value="vcfannotate.bed" ftype="bed" />
+            <param name="invert" value="False" />
+            <param name="vcf_input" value="vcflib.vcf"/>
+            <output name="out_file1" file="vcfbedintersect-test1.vcf"/>
+        </test>
+        <test>
+            <param name="bed_vs_interval_selector" value="interval" />
+            <param name="int_input" value="20:1-30000" />
+            <param name="invert" value="False" />
+            <param name="vcf_input" value="vcflib.vcf"/>
+            <output name="out_file1" file="vcfbedintersect-test2.vcf"/>
+        </test>
+    </tests>
+    <help>
+Computes intersection between a VCF dataset and a set of genomic intervals defined as either a BED dataset (http://genome.ucsc.edu/FAQ/FAQformat.html#format1) or a manually typed interval (in the form of chr:start-end).
+
+----
+
+VCFBEDintersect is based on vcfintersect utility of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
+    </help>
+    <expand macro="citations" />
+</tool>