diff vcfselectsamples.xml @ 0:7278d7b4b1e4 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcfselectsamples.xml	Fri May 09 17:30:38 2014 -0400
@@ -0,0 +1,54 @@
+<tool id="vcfselectsamples" name="VCFselectsamples:" version="0.0.1">
+<requirements>
+    <requirement type="package" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">vcflib</requirement>
+</requirements>
+  <description>Select samples from a VCF dataset</description>
+  <command>vcfkeepsamples "${input1}" ${ ' '.join( map( lambda x:'"%s"' % ( x ), str($vcf_samples ).split(",") ) ) } > "${out_file1}"</command>
+  <inputs>
+    <param format="vcf" name="input1" type="data" label="Select VCF dataset"  />
+    <param name="vcf_samples" type="select" label="Check to keep samples; Uncheck to remove" display="checkboxes" multiple="true">
+      <options>
+        <filter type="data_meta" ref="input1" key="sample_names" />
+      </options>
+</param>
+  </inputs>
+  <outputs>
+    <data format="vcf" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="vcf_samples" value="NA00001,NA00003"/>
+      <param name="input1" value="vcflib.vcf"/>
+      <output name="out_file1" file="vcfselectsamples-test1.vcf"/>
+    </test>
+   </tests>
+  <help>
+
+Allows to keep or remove samples from a VCF file.
+
+-----
+
+.. class:: infomark
+
+
+**Example**:
+
+Selecting *NA00001* and *NA00003* from 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, obviously, remove *NA00002*::
+
+ #CHROM POS     ID        REF ALT QUAL FILTER INFO                              FORMAT      NA00001        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 2/2:35:4:.,.
+
+----
+
+Vcfselectsamples is based on vcfkeepsamples/vcfremovesamples utilities from **VCFlib** toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).                                                                                
+                                                 
+
+
+
+</help>
+</tool>