Mercurial > repos > peterjc > seq_primer_clip

diff tools/seq_primer_clip/seq_primer_clip.xml @ 5:530c8d6fedd8 draft

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v0.0.15 - internal changes
author peterjc
date Wed, 10 May 2017 13:09:52 -0400
parents 9b074c1db68e
children b9dc7c967ee6
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line diff
--- a/tools/seq_primer_clip/seq_primer_clip.xml	Thu Feb 02 11:52:37 2017 -0500
+++ b/tools/seq_primer_clip/seq_primer_clip.xml	Wed May 10 13:09:52 2017 -0400
@@ -1,18 +1,14 @@
-<tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.14">
+<tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.15">
     <description>Trim off 5' or 3' primers</description>
     <requirements>
         <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement>
         <requirement type="package" version="1.67">biopython</requirement>
-        <requirement type="python-module">Bio</requirement>
     </requirements>
-    <stdio>
-        <!-- Anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
-    <version_command interpreter="python">seq_primer_clip.py --version</version_command>   
-    <command interpreter="python">
-seq_primer_clip.py $input_file $input_file.ext $primer_fasta $primer_type $mm $min_len $keep_negatives $output_file
+    <version_command>
+python $__tool_directory__/seq_primer_clip.py --version
+    </version_command>
+    <command detect_errors="aggressive">
+python $__tool_directory__/seq_primer_clip.py $input_file $input_file.ext $primer_fasta $primer_type $mm $min_len $keep_negatives $output_file
     </command>
     <inputs>
         <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to clip" help="FASTA, FASTQ, or SFF format."/>