diff vcfannotate.xml @ 0:87d916fbb7c4 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcfannotate.xml	Thu Mar 19 12:39:51 2015 -0400
@@ -0,0 +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" size="20" 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>