Mercurial > repos > devteam > vcfannotategenotypes

changeset 2:c96a7e49150a draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 0b9b6512272b82637c2f1e831367e89aed77ae79
author devteam
date Thu, 15 Sep 2016 16:07:50 -0400
parents ad57b4feaf87
children 70bc6ced57f7
files macros.xml test-data/vcfannotategenotypes-test1.vcf tool_dependencies.xml vcfannotategenotypes.xml
diffstat 4 files changed, 37 insertions(+), 42 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Wed Nov 11 12:57:55 2015 -0500
+++ b/macros.xml	Thu Sep 15 16:07:50 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/vcfannotategenotypes-test1.vcf	Wed Nov 11 12:57:55 2015 -0500
+++ b/test-data/vcfannotategenotypes-test1.vcf	Thu Sep 15 16:07:50 2016 -0400
@@ -29,5 +29,5 @@
 20	1110696	rs6040355	A	G,T	67	PASS	AA=T;AF=0.333,0.667;DP=10;NS=2;DB;added-genotypes.has_variant	GT:GQ:DP:HQ:added-genotypes	1|2:21:6:23,27:1/2	2|1:2:0:18,2:./.	2/2:35:4:.,.:2/2
 20	1230237	.	T	.	47	PASS	AA=T;DP=13;NS=3;added-genotypes.has_variant	GT:GQ:DP:HQ:added-genotypes	0|0:54:.:56,60:0/0	0|0:48:4:51,51:./.	0/0:61:2:.,.:0/0
 20	1234567	microsat1	G	GA,GAC	50	PASS	AA=G;AC=3,1;AN=6;DP=9;NS=3;added-genotypes.has_variant	GT:GQ:DP:added-genotypes	0/1:.:4:0/1	0/2:17:2:./.	1/1:40:3:1/1
-20	1235237	.	T	.	0	.	added-genotypes.has_variant	GT:added-genotypes	0/0:0/0	0|0:./.	.
+20	1235237	.	T	.	0	.	added-genotypes.has_variant	GT:added-genotypes	0/0:0/0	0|0:./.	./.:.
 X	10	rsTest	AC	A,ATG	10	PASS	added-genotypes.has_variant	GT:added-genotypes	0:0	0/1:./.	0|2:0/2
--- a/tool_dependencies.xml	Wed Nov 11 12:57:55 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="7e67466b033e" name="package_vcflib_8a5602bf07" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>
--- a/vcfannotategenotypes.xml	Wed Nov 11 12:57:55 2015 -0500
+++ b/vcfannotategenotypes.xml	Thu Sep 15 16:07:50 2016 -0400
@@ -1,34 +1,34 @@
-<tool id="vcfannotategenotypes" name="VCFannotateGenotypes:" version="0.0.3">
-  <description>Annotate genotypes in a VCF dataset using genotypes from another VCF dataset</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"></expand>
-  <expand macro="stdio" />
-  <command>vcfannotategenotypes "${tag_option}" "${input1}" "${input2}" > "${out_file1}"</command>
-  <inputs>
-    <param format="vcf" name="input1" type="data" label="Annotate genotypes in" help="First VCF dataset"/>
-    <param format="vcf" name="input2" type="data" label="using genotypes from" help="Second VCF dataset"/>
-    <param name="tag_option" type="text" value="added-genotypes" label="Mark genotypes added to the first dataset with this tag" help="Annotation tag"/>
-  </inputs>
-  <outputs>
-    <data format="vcf" name="out_file1" />
-  </outputs>
- <tests>
-    <test>
-      <param name="tag_option" value="added-genotypes"/>
-      <param name="input1" value="vcflib.vcf"/>
-      <param name="input2" value="vcfannotategenotypes-input2.vcf"/>
-      <output name="out_file1" file="vcfannotategenotypes-test1.vcf" />
-    </test>
-    </tests>
-<help>
-
-Annotates genotypes in the **First** dataset with genotypes from the **Second** adding the genotype as another flag to each sample filled in the first file. **Annotation-tag** is the name of the sample flag which is added to store the annotation.  Also adds a 'has\_variant' flag for sites where the second file has a variant.
-
------
-
-Vcfannotate @IS_PART_OF_VCFLIB@
-</help>
-  <expand macro="citations" />
-</tool>
+<tool id="vcfannotategenotypes" name="VCFannotateGenotypes:" version="@WRAPPER_VERSION@.0">
+  <description>Annotate genotypes in a VCF dataset using genotypes from another VCF dataset</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio" />
+  <command>vcfannotategenotypes "${tag_option}" "${input1}" "${input2}" > "${out_file1}"</command>
+  <inputs>
+    <param format="vcf" name="input1" type="data" label="Annotate genotypes in" help="First VCF dataset"/>
+    <param format="vcf" name="input2" type="data" label="using genotypes from" help="Second VCF dataset"/>
+    <param name="tag_option" type="text" value="added-genotypes" label="Mark genotypes added to the first dataset with this tag" help="Annotation tag"/>
+  </inputs>
+  <outputs>
+    <data format="vcf" name="out_file1" />
+  </outputs>
+ <tests>
+    <test>
+      <param name="tag_option" value="added-genotypes"/>
+      <param name="input1" value="vcflib.vcf"/>
+      <param name="input2" value="vcfannotategenotypes-input2.vcf"/>
+      <output name="out_file1" file="vcfannotategenotypes-test1.vcf" />
+    </test>
+    </tests>
+<help>
+
+Annotates genotypes in the **First** dataset with genotypes from the **Second** adding the genotype as another flag to each sample filled in the first file. **Annotation-tag** is the name of the sample flag which is added to store the annotation.  Also adds a 'has\_variant' flag for sites where the second file has a variant.
+
+-----
+
+Vcfannotate @IS_PART_OF_VCFLIB@
+</help>
+  <expand macro="citations" />
+</tool>