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changeset 1:a7253d23c34d draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbreakcreatemulti commit 0b9b6512272b82637c2f1e831367e89aed77ae79
author devteam
date Thu, 15 Sep 2016 16:03:01 -0400
parents cf27d58e1a99
children 596a7f6ef564
files macros.xml test-data/vcfbreakcreatemulti-test1.vcf tool_dependencies.xml vcfbreakcreatemulti.xml
diffstat 4 files changed, 55 insertions(+), 65 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Mon Nov 09 12:30:13 2015 -0500
+++ b/macros.xml	Thu Sep 15 16:03:01 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">
--- a/test-data/vcfbreakcreatemulti-test1.vcf	Mon Nov 09 12:30:13 2015 -0500
+++ b/test-data/vcfbreakcreatemulti-test1.vcf	Thu Sep 15 16:03:01 2016 -0400
@@ -24,11 +24,11 @@
 19	112	.	A	G	10	.	.	GT:HQ	0|0:10,10	0|0:10,10	0/1:3,3
 20	14370	rs6054257	G	A	29	PASS	AF=0.5;DP=14;NS=3;DB;H2	GT:GQ:DP:HQ	0|0:48:1:51,51	1|0:48:8:51,51	1/1:43:5:.,.
 20	17330	.	T	A	3	q10	AF=0.017;DP=11;NS=3	GT:GQ:DP:HQ	0|0:49:3:58,50	0|1:3:5:65,3	0/0:41:3:.,.
-20	1110696	rs6040355	A	G	67	PASS	AA=T;AF=0.333,0.667;DP=10;NS=2;DB	GT:GQ:DP:HQ	./1:21:6:23,27	./1:2:0:18,2	./.:35:4:.,.
-20	1110696	rs6040355	A	T	67	PASS	AA=T;AF=0.333,0.667;DP=10;NS=2;DB	GT:GQ:DP:HQ	./1:21:6:23,27	./1:2:0:18,2	1/1:35:4:.,.
+20	1110696	rs6040355	A	G	67	PASS	AA=T;AF=0.333,0.667;DP=10;NS=2;DB	GT:GQ:DP:HQ	1|.:21:6:23,27	.|1:2:0:18,2	./.:35:4:.,.
+20	1110696	rs6040355	A	T	67	PASS	AA=T;AF=0.333,0.667;DP=10;NS=2;DB	GT:GQ:DP:HQ	.|1:21:6:23,27	1|.:2:0:18,2	1/1:35:4:.,.
 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	50	PASS	AA=G;AC=3,1;AN=6;DP=9;NS=3	GT:GQ:DP	0/1:.:4	./0:17:2	1/1:40:3
 20	1234567	microsat1	G	GAC	50	PASS	AA=G;AC=3,1;AN=6;DP=9;NS=3	GT:GQ:DP	./0:.:4	0/1:17:2	./.:40:3
-20	1235237	.	T	.	0	.	.	GT	0/0	0|0	.
-X	10	rsTest	AC	A	10	PASS	.	GT	0	0/1	./0
-X	10	rsTest	AC	ATG	10	PASS	.	GT	0	./0	0/1
+20	1235237	.	T	.	0	.	.	GT	0/0	0|0	./.
+X	10	rsTest	AC	A	10	PASS	.	GT	0	0/1	0|.
+X	10	rsTest	AC	ATG	10	PASS	.	GT	0	./0	0|1
--- a/tool_dependencies.xml	Mon Nov 09 12:30:13 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>
--- a/vcfbreakcreatemulti.xml	Mon Nov 09 12:30:13 2015 -0500
+++ b/vcfbreakcreatemulti.xml	Thu Sep 15 16:03:01 2016 -0400
@@ -1,53 +1,48 @@
-<tool id="vcfbreakcreatemulti" name="VCFbreakCreateMulti:" version="0.0.3">
-  <description>Break multiple alleles into multiple records, or combine overallpoing alleles into a single record</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"></expand>
-  <expand macro="stdio" />
-  <command>
-
-   #if str($break_or_create) == "break":
-       vcfbreakmulti "${input1}" > "${out_file1}"
-   #elif str($break_or_create) == "create": 
-       vcfcreatemulti "${input1}" > "${out_file1}"
-   #end if
-
-</command>
-
-  <inputs>
-    <param format="vcf" name="input1" type="data" label="Select VCF dataset"/>
-    <param name="break_or_create" type="select" display="radio" label="Break or Create?">
-      <option value="break">Break</option>
-      <option value="create">Create</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data format="vcf" name="out_file1" />
-  </outputs>
-  <tests>
-    <test>
-      <param name="break_or_create" value="break"/>
-      <param name="input1" value="vcflib.vcf"/>
-      <output name="out_file1" file="vcfbreakcreatemulti-test1.vcf"/>
-    </test>
-    <test>
-      <param name="break_or_create" value="create"/>
-      <param name="input1" value="vcfbreakcreatemulti-test2-input.vcf"/>
-      <output name="out_file1" file="vcfbreakcreatemulti-test2.vcf"/>
-    </test>
-  </tests>
-  <help>
-
-This tool breaks or creates multiallelic VCF records based on user selection (**Break** or **Create**, respectively):
-
- - **Break** = If multiple alleles are specified in a single record, break the record into multiple lines, preserving allele-specific INFO fields.
- - **Create** = If overlapping alleles are represented across multiple records, merge them into a single record.
-
-----
-
-This tools is based on vcfbreakmulti and vcfcreatemulti utilities from the VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).                                                                                                                                 
-
-</help>
-  <expand macro="citations" />
-</tool>
+<tool id="vcfbreakcreatemulti" name="VCFbreakCreateMulti:" version="@WRAPPER_VERSION@.0">
+    <description>Break multiple alleles into multiple records, or combine overallpoing alleles into a single record</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio" />
+    <command>
+        #if str($break_or_create) == "break":
+            vcfbreakmulti "${input1}" > "${out_file1}"
+        #elif str($break_or_create) == "create":
+            vcfcreatemulti "${input1}" > "${out_file1}"
+        #end if
+    </command>
+    <inputs>
+        <param format="vcf" name="input1" type="data" label="Select VCF dataset"/>
+        <param name="break_or_create" type="select" display="radio" label="Break or Create?">
+            <option value="break">Break</option>
+            <option value="create">Create</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="vcf" name="out_file1" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="break_or_create" value="break"/>
+            <param name="input1" value="vcflib.vcf"/>
+            <output name="out_file1" file="vcfbreakcreatemulti-test1.vcf"/>
+        </test>
+        <test>
+            <param name="break_or_create" value="create"/>
+            <param name="input1" value="vcfbreakcreatemulti-test2-input.vcf"/>
+            <output name="out_file1" file="vcfbreakcreatemulti-test2.vcf"/>
+        </test>
+    </tests>
+    <help>
+This tool breaks or creates multiallelic VCF records based on user selection (**Break** or **Create**, respectively):
+
+ - **Break** = If multiple alleles are specified in a single record, break the record into multiple lines, preserving allele-specific INFO fields.
+ - **Create** = If overlapping alleles are represented across multiple records, merge them into a single record.
+
+----
+
+This tools is based on vcfbreakmulti and vcfcreatemulti utilities from the VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
+    </help>
+    <expand macro="citations" />
+</tool>