# HG changeset patch
# User devteam
# Date 1473969920 14400
# Node ID c58ebedf1159b04423e0b82bb69dad0618b5f445
# Parent  bbf46057ef480552060d20daf3250ba5a848e0ad
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 0b9b6512272b82637c2f1e831367e89aed77ae79

diff -r bbf46057ef48 -r c58ebedf1159 macros.xml
--- a/macros.xml	Mon Nov 09 12:29:05 2015 -0500
+++ b/macros.xml	Thu Sep 15 16:05:20 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 bbf46057ef48 -r c58ebedf1159 test-data/vcfallelicprimitives-test1.vcf
--- a/test-data/vcfallelicprimitives-test1.vcf	Mon Nov 09 12:29:05 2015 -0500
+++ b/test-data/vcfallelicprimitives-test1.vcf	Thu Sep 15 16:05:20 2016 -0400
@@ -30,6 +30,6 @@
 20	1110696	.	A	G,T	67	PASS	AF=0.333,0.667;LEN=1,1;TYPE=snp,snp;Split primitives	GT	1|2	2|1	2|2
 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	.	G	GA,GAC	50	PASS	AC=3,1;LEN=1,2;TYPE=ins,ins;Split primitives	GT	0|1	0|2	1|1
-20	1235237	.	T	.	0	.	.	GT	0/0	0|0	.
+20	1235237	.	T	.	0	.	.	GT	0/0	0|0	./.
 X	10	.	AC	ATC,A	10	PASS	LEN=1,1;TYPE=ins,del;Split primitives	GT	0	0|2	0|1
 X	11	.	C	G	10	PASS	LEN=1;TYPE=snp;Split primitives	GT	0	0|0	0|1
diff -r bbf46057ef48 -r c58ebedf1159 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Nov 09 12:29:05 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 bbf46057ef48 -r c58ebedf1159 vcfallelicprimitives.xml
--- a/vcfallelicprimitives.xml	Mon Nov 09 12:29:05 2015 -0500
+++ b/vcfallelicprimitives.xml	Thu Sep 15 16:05:20 2016 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="vcfallelicprimitives" name="VcfAllelicPrimitives:" version="0.0.3">
+<tool id="vcfallelicprimitives" name="VcfAllelicPrimitives:" version="@WRAPPER_VERSION@.0">
     <description>Split alleleic primitives (gaps or mismatches) into multiple VCF lines</description>
     <macros>
         <import>macros.xml</import>
@@ -10,7 +10,7 @@
         cat "${input}" | vcfallelicprimitives 
             ${m_option} 
             -t "${t_option}"
-	    -L "${max_length}" 
+            -L "${max_length}" 
             $keep_info 
             $keep_geno > "${out_file1}"
     </command>
@@ -18,7 +18,7 @@
         <param format="vcf" name="input" type="data" label="Select VCF dataset"/>
         <param name="m_option" type="boolean" checked="false" truevalue="--use-mnps" falsevalue="" label="Retain MNPs as separate events" help="--use-mnps option"/>
         <param name="t_option" type="text" value="Split primitives" label="Tag records which are split apart of a complex allele with this flag. " help="--tag-parsed option"/>
-	<param name="max_length" type="integer" value="200" label="Do not manipulate records in which either the ALT or REF is longer than (bp)" help="--max-length option"/>
+        <param name="max_length" type="integer" value="200" label="Do not manipulate records in which either the ALT or REF is longer than (bp)" help="--max-length option"/>
         <param name="keep_info" type="boolean" truevalue="--keep-info" falsevalue="" checked="False" 
             label="Maintain site and allele-level annotations when decomposing" 
             help="Note that in many cases, such as multisample VCFs, these won't be valid post-decomposition.  For biallelic loci in single-sample VCFs, they should be usable with caution. (--keep-info)"/>