# HG changeset patch
# User devteam
# Date 1473969806 14400
# Node ID 0b93ada8f718ee593cac6aaf40e49cf36bd7e10a
# Parent  a9ce47a1d6534e982de5cc6cbcf7423cd2ca51f6
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfcombine commit 0b9b6512272b82637c2f1e831367e89aed77ae79

diff -r a9ce47a1d653 -r 0b93ada8f718 macros.xml
--- a/macros.xml	Mon Nov 09 12:30:48 2015 -0500
+++ b/macros.xml	Thu Sep 15 16:03:26 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 a9ce47a1d653 -r 0b93ada8f718 test-data/vcfcombine-test1.vcf
--- a/test-data/vcfcombine-test1.vcf	Mon Nov 09 12:30:48 2015 -0500
+++ b/test-data/vcfcombine-test1.vcf	Thu Sep 15 16:03:26 2016 -0400
@@ -27,5 +27,5 @@
 20	1110696	rs6040355	A	G,T	67	PASS	AA=T;AF=0.333,0.667;DP=10;NS=2	GT:GQ:DP:HQ	1|2:21:6:23,27	2|1:2:0:18,2	2/2:35:4:.,.
 20	1230237	.	T	.	47	PASS	AA=T;DP=13;NS=3	GT:GQ:DP:HQ	0|0:54:.:56,60	0|0:48:4:51,51	0/0:61:2:.,.
 20	1234567	microsat1	G	GA,GAC	50	PASS	AA=G;AC=3,1;AN=6;DP=9;NS=3	GT:GQ:DP	0/1:.:4	0/2:17:2	1/1:40:3
-20	1235237	.	T	.	0	.	.	GT	0/0	0|0	.
+20	1235237	.	T	.	0	.	.	GT	0/0	0|0	./.
 X	10	rsTest	AC	A,ATG	10	PASS	.	GT	0	0/1	0|2
diff -r a9ce47a1d653 -r 0b93ada8f718 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Nov 09 12:30:48 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="3ac0905f7b7c" name="package_vcflib_8a5602bf07" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>
diff -r a9ce47a1d653 -r 0b93ada8f718 vcfcombine.xml
--- a/vcfcombine.xml	Mon Nov 09 12:30:48 2015 -0500
+++ b/vcfcombine.xml	Thu Sep 15 16:03:26 2016 -0400
@@ -1,40 +1,39 @@
-<tool id="vcfcombine" name="VCFcombine:" version="0.0.4">
-  <description>Combine multiple VCF datasets</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"></expand>
-  <expand macro="stdio" />
-  <command>
-
-   vcfcombine
-
-   #for $input_vcf in $input_vcfs:
-        "${input_vcf}"
-   #end for
-
-   > "${out_file1}"
-
-  </command>
-  <inputs>
-    <param name="input_vcfs" type="data" format="vcf" label="Select VCF Datasets" min="2" multiple="True"/>
-  </inputs>
-  <outputs>
-    <data format="vcf" name="out_file1" />
-  </outputs>
-  <tests>
-    <test>
-      <param name="input_vcfs" value="vcflib.vcf"/>
-      <output name="out_file1" file="vcfcombine-test1.vcf"/>
-    </test>
-    </tests>
-  <help>
-
-Combines VCF files positionally, combining samples when sites and alleles are identical. Any number of VCF files may be combined. The INFO field and other columns are taken from one of the files, which are combined when records in multiple files match. Alleles must have identical ordering to be combined into one record. If they do not, multiple records will be emitted.
-
------
-
-Vcfcombine @IS_PART_OF_VCFLIB@
-</help>
-  <expand macro="citations" />
-</tool>
+<tool id="vcfcombine" name="VCFcombine:" version="@WRAPPER_VERSION@.0">
+    <description>Combine multiple VCF datasets</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio" />
+    <command>
+        vcfcombine
+
+        #for $input_vcf in $input_vcfs:
+            "${input_vcf}"
+        #end for
+
+        > "${out_file1}"
+
+    </command>
+    <inputs>
+        <param name="input_vcfs" type="data" format="vcf" label="Select VCF Datasets" min="2" multiple="True"/>
+    </inputs>
+    <outputs>
+        <data format="vcf" name="out_file1" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_vcfs" value="vcflib.vcf,vcflib.vcf" ftype="vcf"/>
+            <output name="out_file1" file="vcfcombine-test1.vcf"/>
+        </test>
+        </tests>
+    <help>
+
+Combines VCF files positionally, combining samples when sites and alleles are identical. Any number of VCF files may be combined. The INFO field and other columns are taken from one of the files, which are combined when records in multiple files match. Alleles must have identical ordering to be combined into one record. If they do not, multiple records will be emitted.
+
+-----
+
+Vcfcombine @IS_PART_OF_VCFLIB@
+    </help>
+    <expand macro="citations" />
+</tool>