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diff vcfannotate.xml @ 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
line wrap: on
line diff
--- 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>