# HG changeset patch
# User nick
# Date 1448323912 18000
# Node ID e504cc1d5a7654efc1c85779b020b01bb458f944
# Parent  bf7478987a6d698dc4b040673317e53abd47d913
planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty

diff -r bf7478987a6d -r e504cc1d5a76 align_families.xml
--- a/align_families.xml	Mon Nov 23 19:05:48 2015 -0500
+++ b/align_families.xml	Mon Nov 23 19:11:52 2015 -0500
@@ -4,8 +4,9 @@
   <requirements>
     <requirement type="package" version="7.221">mafft</requirement>
     <requirement type="package" version="0.1">duplex</requirement>
+    <requirement type="set_environment">DUPLEX_DIR</requirement>
   </requirements>
-  <command interpreter="python" detect_errors="exit_code">align_families.py $input &gt; $output
+  <command interpreter="python" detect_errors="exit_code">\$DUPLEX_DIR/align_families.py $input &gt; $output
   </command>
   <inputs>
     <param name="input" type="data" format="tabular" label="Input reads" help="with barcodes, grouped by family"/>
diff -r bf7478987a6d -r e504cc1d5a76 duplex.xml
--- 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>