# HG changeset patch
# User artbio
# Date 1539464956 14400
# Node ID da08e89abd18a062689204ce3049b4b041ee89e0
# Parent  7c913274e22a5b7ef6a5d9b0e313dfdec2b2118e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit 4767dcb09e8bb26a38ea458b2cf4f9d98a4afb95

diff -r 7c913274e22a -r da08e89abd18 yac.py
--- a/yac.py	Wed Jul 26 17:12:08 2017 -0400
+++ b/yac.py	Sat Oct 13 17:09:16 2018 -0400
@@ -110,7 +110,6 @@
 
 if __name__ == "__main__":
     args = Parser()
-    id = 0
     for inputfile in args.input:
         main(inputfile, args.output, args.output_format,
              args.adapter_to_clip, args.min, args.max, args.Nmode)
diff -r 7c913274e22a -r da08e89abd18 yac.xml
--- a/yac.xml	Wed Jul 26 17:12:08 2017 -0400
+++ b/yac.xml	Sat Oct 13 17:09:16 2018 -0400
@@ -1,13 +1,15 @@
-<tool id="yac" name="Clip adapter" version="2.0.1">
+<tool id="yac" name="Clip adapter" version="2.1.1">
     <description />
-    <command interpreter="python">yac.py --input $input
-                                       --output $output
-                                       --output_format "$out_format"
-                                       --adapter_to_clip $clip_source.clip_sequence
-                                       --min $min
-                                       --max $max
-                                       --Nmode $Nmode
-  </command>
+    <command detect_errors="exit_code"><![CDATA[
+        python $__tool_directory__/yac.py
+            --input $input
+            --output $output
+            --output_format "$out_format"
+            --adapter_to_clip $clip_source.clip_sequence
+            --min $min
+            --max $max
+             --Nmode $Nmode
+    ]]></command>
     <inputs>
         <param format="fastq" label="Source file" name="input" type="data" />
         <param label="min size" name="min" size="4" type="integer" value="15" />
@@ -91,6 +93,6 @@
 
 A fastq or fasta file containing clipped sequences satisfying the selected criteria.
 
-  </help>
-  <citations />
+    </help>
+    <citations />
 </tool>