Mercurial > repos > iuc > gemini

diff gemini_pathways.xml @ 4:ca4449689d61 draft

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Uploaded
author iuc
date Mon, 25 Aug 2014 03:19:30 -0400
parents e6512af21622
children 6ab82d8ca805
line wrap: on
line diff
--- a/gemini_pathways.xml	Sun Aug 24 17:50:00 2014 -0400
+++ b/gemini_pathways.xml	Mon Aug 25 03:19:30 2014 -0400
@@ -8,7 +8,9 @@
     </macros>
     <command>
 <![CDATA[
-        gemini @BINARY@
+        gemini 
+            --annotation-dir ${annotation_databases}
+            @BINARY@
             -v $ensembl
             $lof
             "${ infile }"
@@ -26,7 +28,7 @@
 
         <param name="lof" type="boolean" truevalue="--lof" falsevalue="" checked="False" 
             label="Report only pathways with loss-of-function variants" help="(--lof)"/>
-
+        <expand macro="annotation_dir" />
     </inputs>
     <outputs>
         <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />