# HG changeset patch
# User devteam
# Date 1473969937 14400
# Node ID 4d7bf62772956202001d36a94ba3569dde493193
# Parent  1de250ea8c1a3cbd815585f83a91e1643bb2ffe5
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfhethom commit 0b9b6512272b82637c2f1e831367e89aed77ae79

diff -r 1de250ea8c1a -r 4d7bf6277295 macros.xml
--- a/macros.xml	Mon Nov 09 12:33:06 2015 -0500
+++ b/macros.xml	Thu Sep 15 16:05:37 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 1de250ea8c1a -r 4d7bf6277295 test-data/vcfhethom-test2.tab
--- a/test-data/vcfhethom-test2.tab	Mon Nov 09 12:33:06 2015 -0500
+++ b/test-data/vcfhethom-test2.tab	Thu Sep 15 16:05:37 2016 -0400
@@ -1,2 +1,2 @@
 NA00001	NA00002	NA00003
-inf	inf	1
+inf	inf	0.75
diff -r 1de250ea8c1a -r 4d7bf6277295 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Nov 09 12:33:06 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 1de250ea8c1a -r 4d7bf6277295 vcfhethom.xml
--- a/vcfhethom.xml	Mon Nov 09 12:33:06 2015 -0500
+++ b/vcfhethom.xml	Thu Sep 15 16:05:37 2016 -0400
@@ -1,62 +1,61 @@
-<tool id="vcfhethom" name="VCFhetHomAlleles:" version="0.0.3">
-  <description>Count the number of heterozygotes and alleles, compute het/hom ratio</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"></expand>
-  <expand macro="stdio" />
-  <command>
-
-   #if str($analysis_type) == "count":
-       vcfhetcount "${vcf_input}" > "${out_file1}"
-   #elif str($analysis_type) == "ratio": 
-       vcfhethomratio "${vcf_input}" > "${out_file1}"
-   #elif str($analysis_type) == "allele_count":
-       vcfcountalleles "${vcf_input}" > "${out_file1}" 
-   #end if
-
-</command>
-
-  <inputs>
-    <param name="analysis_type" type="select" display="radio" label="Select type of calculation:">
-      <option value="count">Compute the number of heterozygotes</option>
-      <option value="ratio">Compute the ratio between heterozygotes and homozygotes</option>
-      <option value="allele_count">Compute the total number of alleles</option>
-    </param>
-    <param format="vcf" name="vcf_input" type="data" label="In this VCF dataset"/>
-  </inputs>
-  <outputs>
-    <data format="tabular" name="out_file1" />
-  </outputs>
-  <tests>
-    <test>
-      <param name="analysis_type" value="count"/>
-      <param name="vcf_input" value="vcflib.vcf"/>
-      <output name="out_file1" file="vcfhethom-test1.tab"/>
-    </test>
-    <test>
-      <param name="analysis_type" value="ratio"/>
-      <param name="vcf_input" value="vcflib.vcf"/>
-      <output name="out_file1" file="vcfhethom-test2.tab"/>
-    </test>
-    <test>
-      <param name="analysis_type" value="allele_count"/>
-      <param name="vcf_input" value="vcflib.vcf"/>
-      <output name="out_file1" file="vcfhethom-test3.tab"/>
-    </test>
-  </tests>
-  <help>
-
-This tool performs three basic calculations: 
-
-(1) Computes the number of heterozygotes
-(2) Computes the ratio between heterozygotes and homozygotes
-(3) Computes the total number of alleles in the input dataset
-
-----
-
-This tools is based on vcfhetcount, vcfhethomratio,and vcfcountalleles utilities from the VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).                                                                                                                                 
-
-</help>
-  <expand macro="citations" />
-</tool>
+<tool id="vcfhethom" name="VCFhetHomAlleles:" version="@WRAPPER_VERSION@.0">
+  <description>Count the number of heterozygotes and alleles, compute het/hom ratio</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio" />
+  <command>
+
+   #if str($analysis_type) == "count":
+       vcfhetcount "${vcf_input}" > "${out_file1}"
+   #elif str($analysis_type) == "ratio": 
+       vcfhethomratio "${vcf_input}" > "${out_file1}"
+   #elif str($analysis_type) == "allele_count":
+       vcfcountalleles "${vcf_input}" > "${out_file1}" 
+   #end if
+
+  </command>
+  <inputs>
+    <param name="analysis_type" type="select" display="radio" label="Select type of calculation:">
+      <option value="count">Compute the number of heterozygotes</option>
+      <option value="ratio">Compute the ratio between heterozygotes and homozygotes</option>
+      <option value="allele_count">Compute the total number of alleles</option>
+    </param>
+    <param format="vcf" name="vcf_input" type="data" label="In this VCF dataset"/>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="analysis_type" value="count"/>
+      <param name="vcf_input" value="vcflib.vcf"/>
+      <output name="out_file1" file="vcfhethom-test1.tab"/>
+    </test>
+    <test>
+      <param name="analysis_type" value="ratio"/>
+      <param name="vcf_input" value="vcflib.vcf"/>
+      <output name="out_file1" file="vcfhethom-test2.tab"/>
+    </test>
+    <test>
+      <param name="analysis_type" value="allele_count"/>
+      <param name="vcf_input" value="vcflib.vcf"/>
+      <output name="out_file1" file="vcfhethom-test3.tab"/>
+    </test>
+  </tests>
+  <help>
+
+This tool performs three basic calculations: 
+
+(1) Computes the number of heterozygotes
+(2) Computes the ratio between heterozygotes and homozygotes
+(3) Computes the total number of alleles in the input dataset
+
+----
+
+This tools is based on vcfhetcount, vcfhethomratio,and vcfcountalleles utilities from the VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).                                                                                                                                 
+
+</help>
+  <expand macro="citations" />
+</tool>