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changeset 1:815622f17a3d draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 0b9b6512272b82637c2f1e831367e89aed77ae79
author devteam
date Thu, 15 Sep 2016 16:03:56 -0400
parents 77ae7fbde89a
children c51b43f8098f
files macros.xml test-data/vcfdistance-test1.vcf tool_dependencies.xml vcfdistance.xml
diffstat 4 files changed, 40 insertions(+), 42 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Mon Nov 09 12:31:21 2015 -0500
+++ b/macros.xml	Thu Sep 15 16:03:56 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/vcfdistance-test1.vcf	Mon Nov 09 12:31:21 2015 -0500
+++ b/test-data/vcfdistance-test1.vcf	Thu Sep 15 16:03:56 2016 -0400
@@ -23,7 +23,10 @@
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
 19	111	.	A	C	9.6	.	BasesToClosestVariant=1	GT:HQ	0|0:10,10	0|0:10,10	0/1:3,3
 19	112	.	A	G	10	.	BasesToClosestVariant=1	GT:HQ	0|0:10,10	0|0:10,10	0/1:3,3
-20	17330	.	T	A	3	q10	AF=0.017;BasesToClosestVariant=1093366;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	14370	rs6054257	G	A	29	PASS	AF=0.5;BasesToClosestVariant=2960;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;BasesToClosestVariant=2960;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,T	67	PASS	AA=T;AF=0.333,0.667;BasesToClosestVariant=119541;DP=10;NS=2;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;BasesToClosestVariant=4330;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;AN=6;BasesToClosestVariant=670;DP=9;NS=3	GT:GQ:DP	0/1:.:4	0/2:17:2	1/1:40:3
+20	1235237	.	T	.	0	.	BasesToClosestVariant=670	GT	0/0	0|0	./.
+X	10	rsTest	AC	A,ATG	10	PASS	.	GT	0	0/1	0|2
--- a/tool_dependencies.xml	Mon Nov 09 12:31:21 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/vcfdistance.xml	Mon Nov 09 12:31:21 2015 -0500
+++ b/vcfdistance.xml	Thu Sep 15 16:03:56 2016 -0400
@@ -1,34 +1,34 @@
-<tool id="vcfdistance" name="VCFdistance:" version="0.0.3">
-  <description>Calculate distance to the nearest variant</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"></expand>
-  <expand macro="stdio" />
-  <command>cat "${input1}" | vcfdistance > "${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="vcfdistance-test1.vcf"/>
-    </test>
-    </tests>
-  <help>
-
-Adds a value to each VCF record indicating the distance to the nearest variant in the file.
-
-.. class:: infomark
-
-The dataset used as input to this tool must be coordinate sorted. This can be achieved by either using the VCFsort utility or Galaxy's general purpose sort tool (in this case sort on the first and the second column in ascending order).
-
-----
-
-Vcfdistance @IS_PART_OF_VCFLIB@
-</help>
-  <expand macro="citations" />
-</tool>
+<tool id="vcfdistance" name="VCFdistance:" version="@WRAPPER_VERSION@.0">
+  <description>Calculate distance to the nearest variant</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio" />
+  <command>cat "${input1}" | vcfdistance > "${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="vcfdistance-test1.vcf"/>
+    </test>
+    </tests>
+  <help>
+
+Adds a value to each VCF record indicating the distance to the nearest variant in the file.
+
+.. class:: infomark
+
+The dataset used as input to this tool must be coordinate sorted. This can be achieved by either using the VCFsort utility or Galaxy's general purpose sort tool (in this case sort on the first and the second column in ascending order).
+
+----
+
+Vcfdistance @IS_PART_OF_VCFLIB@
+</help>
+  <expand macro="citations" />
+</tool>