# HG changeset patch
# User devteam
# Date 1473969959 14400
# Node ID 9d7e64e4b9fc210b33d898e32c122e071491a525
# Parent  a03f346b6aaec3e280bd9c960e2195259c6f71b8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 0b9b6512272b82637c2f1e831367e89aed77ae79

diff -r a03f346b6aae -r 9d7e64e4b9fc macros.xml
--- a/macros.xml	Thu Mar 19 14:30:34 2015 -0400
+++ b/macros.xml	Thu Sep 15 16:05:59 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 a03f346b6aae -r 9d7e64e4b9fc test-data/vcffixup-test1.vcf
--- a/test-data/vcffixup-test1.vcf	Thu Mar 19 14:30:34 2015 -0400
+++ b/test-data/vcffixup-test1.vcf	Thu Sep 15 16:05:59 2016 -0400
@@ -27,5 +27,5 @@
 20	1110696	rs6040355	A	G,T	67	PASS	AA=T;AC=2,4;AF=0.333333,0.666667;AN=6;DP=10;NS=3;DB	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;AC=0;AF=0;AN=6;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;AF=0.5,0.166667;AN=6;DP=9;NS=3	GT:GQ:DP	0/1:.:4	0/2:17:2	1/1:40:3
-20	1235237	.	T	.	0	.	AC=0;AF=0;AN=4;NS=2	GT	0/0	0|0	.
+20	1235237	.	T	.	0	.	AC=0;AF=0;AN=4;NS=3	GT	0/0	0|0	./.
 X	10	rsTest	AC	A,ATG	10	PASS	AC=1,1;AF=0.2,0.2;AN=5;NS=3	GT	0	0/1	0|2
diff -r a03f346b6aae -r 9d7e64e4b9fc tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Mar 19 14:30:34 2015 -0400
+++ /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 a03f346b6aae -r 9d7e64e4b9fc vcffixup.xml
--- a/vcffixup.xml	Thu Mar 19 14:30:34 2015 -0400
+++ b/vcffixup.xml	Thu Sep 15 16:05:59 2016 -0400
@@ -1,30 +1,30 @@
-<tool id="vcffixup" name="VCFfixup:" version="0.0.3">
-  <description>Count the allele frequencies across alleles present in each record in the VCF file</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"></expand>
-  <expand macro="stdio" />
-  <command>vcffixup "${input1}" > "${out_file1}"</command>
-  <inputs>
-    <param format="vcf" name="input1" type="data" label="Select VCF dataset"/>
-  </inputs>
-  <outputs>
-    <data format="vcf" name="out_file1" />
-  </outputs>
-  <tests>
-    <test>
-      <param name="input1" value="vcflib.vcf"/>
-      <output name="out_file1" file="vcffixup-test1.vcf"/>
-    </test>
-    </tests>
-  <help>
-
-Uses genotypes from the selected VCF dataset to correct AC (alternate allele count), AF (alternate allele frequency), NS (number of called), in the VCF records.
-
-----
-
-Vcffixup @IS_PART_OF_VCFLIB@
-</help>
-  <expand macro="citations" />
-</tool>
+<tool id="vcffixup" name="VCFfixup:" version="@WRAPPER_VERSION@.0">
+  <description>Count the allele frequencies across alleles present in each record in the VCF file</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio" />
+  <command>vcffixup "${input1}" > "${out_file1}"</command>
+  <inputs>
+    <param format="vcf" name="input1" type="data" label="Select VCF dataset"/>
+  </inputs>
+  <outputs>
+    <data format="vcf" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input1" value="vcflib.vcf"/>
+      <output name="out_file1" file="vcffixup-test1.vcf"/>
+    </test>
+    </tests>
+  <help>
+
+Uses genotypes from the selected VCF dataset to correct AC (alternate allele count), AF (alternate allele frequency), NS (number of called), in the VCF records.
+
+----
+
+Vcffixup @IS_PART_OF_VCFLIB@
+</help>
+  <expand macro="citations" />
+</tool>