Mercurial > repos > anton > vcffilter

changeset 1:e5dd21db760b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author anton
date Mon, 12 May 2014 15:53:18 -0400
parents c56b2e440fce
children 77e44d465705
files vcffilter.xml
diffstat 1 files changed, 16 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/vcffilter.xml	Mon Apr 14 10:06:14 2014 -0400
+++ b/vcffilter.xml	Mon May 12 15:53:18 2014 -0400
@@ -3,31 +3,39 @@
     <requirement type="package" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">vcflib</requirement>
 </requirements>
   <description>filter VCF data in a variety of attributes</description>
-  <command>vcffilter ${filterList} "${input}" > "${out_file1}"</command>
+  <command>
+  <!-- This tools depends on tabix functionality, which is currently distributed with Galaxy itself via a pysam egg -->
+    ln -s "${input1}" input1.vcf.gz &amp;&amp;
+    ln -s "${Tabixized_input}" input1.vcf.gz.tbi &amp;&amp;
+    vcffilter ${filterList} input1.vcf.gz  > "${out_file1}"
+  </command>
+  
   <inputs>
     <param name="filterList" size="40" type="text" value="-f &quot;DP &gt; 10&quot;" label="Specify filterting expression" help="See explanation of filtering options below">
       <sanitizer>
         <valid initial="string.printable">
-         <remove value="&apos;"/>
+	  <remove value="&apos;"/>
         </valid>
         <mapping initial="none">
           <add source="&apos;" target="__sq__"/>
         </mapping>
-     </sanitizer>
+      </sanitizer>
     </param>
-    <param format="vcf" name="input" type="data" label="From"/>
+    <param format="vcf_bgzip" name="input1" type="data" label="From">
+      <conversion name="Tabixized_input" type="tabix" />
+    </param>
   </inputs>
   <outputs>
     <data format="vcf" name="out_file1" />
   </outputs>
-<tests>
+ <tests>
     <test>
       <param name="filterList" value="-f &quot;DP &gt; 10&quot;"/>
-      <param name="input" value="vcflib.vcf"/>
+      <param name="input1" value="vcflib.vcf"/>
       <output name="out_file1" file="vcffilter-test1.vcf"/>
     </test>
-</tests>
-  <help>
+</tests> 
+ <help>
 
 VCFfilter is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).