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diff duplex.xml @ 8:e504cc1d5a76 draft

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planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
author nick
date Mon, 23 Nov 2015 19:11:52 -0500
parents 9d46c9ca7ceb
children f6f61b363467
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line diff
--- a/duplex.xml	Mon Nov 23 19:05:48 2015 -0500
+++ b/duplex.xml	Mon Nov 23 19:11:52 2015 -0500
@@ -3,15 +3,16 @@
   <description>from duplex sequencing data</description>
   <requirements>
     <requirement type="package" version="0.1">duplex</requirement>
+    <requirement type="set_environment">DUPLEX_DIR</requirement>
   </requirements>
   <command interpreter="python" detect_errors="exit_code"><![CDATA[
-    duplex.py -r $min_reads -q $qual_thres -F $qual_format $input
+    \$DUPLEX_DIR/duplex.py -r $min_reads -q $qual_thres -F $qual_format $input
     #if $keep_sscs:
       --sscs-file $sscs
     #end if
     > duplex.fa
-    && awk -f $__tool_directory__/utils/outconv.awk -v target=1 duplex.fa > $output1
-    && awk -f $__tool_directory__/utils/outconv.awk -v target=2 duplex.fa > $output2
+    && awk -f \$DUPLEX_DIR/utils/outconv.awk -v target=1 duplex.fa > $output1
+    && awk -f \$DUPLEX_DIR/utils/outconv.awk -v target=2 duplex.fa > $output2
   ]]>
   </command>
   <inputs>