diff tools/protein_analysis/psortb.xml @ 20:a19b3ded8f33 draft

v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes

--- a/tools/protein_analysis/psortb.xml	Wed Feb 01 09:46:42 2017 -0500
+++ b/tools/protein_analysis/psortb.xml	Thu Sep 21 11:35:20 2017 -0400
@@ -1,22 +1,16 @@
-<tool id="Psortb" name="psortb" version="0.0.7">
+<tool id="Psortb" name="psortb" version="0.0.9">
     <description>Determines sub-cellular localisation of bacterial/archaeal protein sequences</description>
     <!-- If job splitting is enabled, break up the query file into parts -->
     <!-- Using 2000 chunks meaning 4 threads doing 500 each is ideal -->
     <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism>
     <requirements>
-        <requirement type="binary">psort</requirement>
         <requirement type="package">psort</requirement>
     </requirements>
-    <stdio>
-        <!-- Anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
-    <version_command interpreter="python">psortb.py --version</version_command>
-    <command interpreter="python">
-psortb.py "\$GALAXY_SLOTS" "$type" "$long" "$cutoff" "$divergent" "$sequence" "$outfile"
-##If the environment variable isn't set, get "", and python wrapper
-##defaults to four threads.
+    <version_command>
+python $__tool_directory__/psortb.py --version
+    </version_command>
+    <command detect_errors="aggressive">
+python $__tool_directory__/psortb.py "\$GALAXY_SLOTS" '$type' '$long' '$cutoff' '$divergent' '$sequence' '$outfile'
     </command>
     <inputs>
         <param format="fasta" name="sequence" type="data"