Mercurial > repos > devteam > vcfannotate

changeset 2:d64204113938 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
author devteam
date Thu, 15 Sep 2016 16:07:40 -0400
parents 829d46588cf5
children 6faa2c4c71d2
files macros.xml test-data/vcfannotate-test1.vcf tool_dependencies.xml vcfannotate.xml
diffstat 4 files changed, 54 insertions(+), 59 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Wed Nov 11 12:57:42 2015 -0500
+++ b/macros.xml	Thu Sep 15 16:07:40 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/vcfannotate-test1.vcf	Wed Nov 11 12:57:42 2015 -0500
+++ b/test-data/vcfannotate-test1.vcf	Thu Sep 15 16:07:40 2016 -0400
@@ -28,5 +28,5 @@
 20	1110696	rs6040355	A	G,T	67	PASS	AA=T;AF=0.333,0.667;BED-features=uc010zpo.2:uc002wel.4:uc010zpp.2:uc002wen.4;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;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;DP=9;NS=3	GT:GQ:DP	0/1:.:4	0/2:17:2	1/1:40:3
-20	1235237	.	T	.	0	.	.	GT	0/0	0|0	.
+20	1235237	.	T	.	0	.	.	GT	0/0	0|0	./.
 X	10	rsTest	AC	A,ATG	10	PASS	.	GT	0	0/1	0|2
--- a/tool_dependencies.xml	Wed Nov 11 12:57:42 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/vcfannotate.xml	Wed Nov 11 12:57:42 2015 -0500
+++ b/vcfannotate.xml	Thu Sep 15 16:07:40 2016 -0400
@@ -1,51 +1,51 @@
-<tool id="vcfannotate" name="VCFannotate:" version="0.0.3">
-  <description>Intersect VCF records with BED annotations</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"></expand>
-  <expand macro="stdio" />
-  <command>vcfannotate --key "${key_option}" -b "${bed_data}" "${input}" > "${out_file1}"</command>
-  <inputs>        
-    <param format="vcf" name="input" type="data" label="Select VCF dataset"/>
-    <param name="bed_data" type="data" format="bed" label="Select BED dataset to itersect with"/>
-    <param name="key_option" type="text" value="BED-features" label="Intersecting VCF records will be prefixed with this TAG within the INFO field" help="--key option"/>
-  </inputs>
-  <outputs>
-    <data format="vcf" name="out_file1" />
-  </outputs>
-  <tests>
-    <test>
-      <param name="bed_data" value="vcfannotate.bed" ftype="bed"/>
-      <param name="key_option" value="BED-features"/>
-      <param name="input" value="vcflib.vcf"/>
-      <output name="out_file1" file="vcfannotate-test1.vcf" lines_diff="2" />
-    </test>
-    </tests>
-  <help>
-
-Intersect the records in the VCF file with intervals (features) provided in a BED file. Intersections are done on the reference sequences in the VCF file. 
-
------
-
-.. class:: infomark
-
-
-**Example**:
-
-The following VCF line::
-
- #CHROM POS     ID        REF ALT QUAL FILTER INFO                              FORMAT      NA00001        NA00002      NA00003
- 20     1110696 rs6040355 A   G,T 67   PASS   NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,.
-
-will appear as the follwing after intersectuion with BED records uc010zpo.2, uc002wel.4, uc010zpp.2, and uc002wen::
-
- #CHROM POS     ID        REF ALT QUAL FILTER INFO                                                                                       FORMAT      NA00001        NA00002      NA00003                                                  
- 20     1110696 rs6040355 A   G,T 67   PASS   AA=T;AF=0.333,0.667;BED-features=uc010zpo.2:uc002wel.4:uc010zpp.2:uc002wen.4;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:.,.
-
-----
-
-Vcfannotate @IS_PART_OF_VCFLIB@
-    </help>
-    <expand macro="citations" />
-</tool>
+<tool id="vcfannotate" name="VCFannotate:" version="@WRAPPER_VERSION@.0">
+  <description>Intersect VCF records with BED annotations</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio" />
+  <command>vcfannotate --key "${key_option}" -b "${bed_data}" "${input}" > "${out_file1}"</command>
+  <inputs>
+    <param format="vcf" name="input" type="data" label="Select VCF dataset"/>
+    <param name="bed_data" type="data" format="bed" label="Select BED dataset to itersect with"/>
+    <param name="key_option" type="text" value="BED-features" label="Intersecting VCF records will be prefixed with this TAG within the INFO field" help="--key option"/>
+  </inputs>
+  <outputs>
+    <data format="vcf" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="bed_data" value="vcfannotate.bed" ftype="bed"/>
+      <param name="key_option" value="BED-features"/>
+      <param name="input" value="vcflib.vcf"/>
+      <output name="out_file1" file="vcfannotate-test1.vcf" lines_diff="2" />
+    </test>
+    </tests>
+  <help>
+
+Intersect the records in the VCF file with intervals (features) provided in a BED file. Intersections are done on the reference sequences in the VCF file. 
+
+-----
+
+.. class:: infomark
+
+
+**Example**:
+
+The following VCF line::
+
+ #CHROM POS     ID        REF ALT QUAL FILTER INFO                              FORMAT      NA00001        NA00002      NA00003
+ 20     1110696 rs6040355 A   G,T 67   PASS   NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,.
+
+will appear as the follwing after intersectuion with BED records uc010zpo.2, uc002wel.4, uc010zpp.2, and uc002wen::
+
+ #CHROM POS     ID        REF ALT QUAL FILTER INFO                                                                                       FORMAT      NA00001        NA00002      NA00003                                                  
+ 20     1110696 rs6040355 A   G,T 67   PASS   AA=T;AF=0.333,0.667;BED-features=uc010zpo.2:uc002wel.4:uc010zpp.2:uc002wen.4;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:.,.
+
+----
+
+Vcfannotate @IS_PART_OF_VCFLIB@
+    </help>
+    <expand macro="citations" />
+</tool>