Mercurial > repos > peterjc > mira_assembler

diff tools/mira3/mira.xml @ 23:83a94a5038a7 draft

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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira3/ commit fd979d17340cde155de176604744831d9597c6b6
author peterjc
date Thu, 18 May 2017 13:35:41 -0400
parents f74bc0420db4
children 56dede4f0735
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--- a/tools/mira3/mira.xml	Wed Feb 10 09:07:29 2016 -0500
+++ b/tools/mira3/mira.xml	Thu May 18 13:35:41 2017 -0400
@@ -1,11 +1,13 @@
-<tool id="mira_assembler" name="Assemble with MIRA v3.4" version="0.0.11">
+<tool id="mira_assembler" name="Assemble with MIRA v3.4" version="0.0.12">
     <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description>
     <requirements>
-        <requirement type="binary">mira</requirement>
         <requirement type="package" version="3.4.1.1">MIRA</requirement>
     </requirements>
-    <version_command interpreter="python">mira.py -v</version_command>
-    <command interpreter="python">mira.py mira $out_fasta $out_qual $out_ace $out_caf $out_wig $out_log
+    <version_command>
+python $__tool_directory__/mira.py -v
+    </version_command>
+    <command detect_errors="aggressive">
+python $__tool_directory__/mira.py mira '$out_fasta' '$out_qual' '$out_ace' '$out_caf' '$out_wig' '$out_log'
 ##Give the wrapper script list of output filenames, then the mira command...
 mira --job=$job_method,$job_type,$job_quality