# HG changeset patch
# User peterjc
# Date 1495125835 14400
# Node ID 692366540172f8e88d168188ee86fd12fe491c89
# Parent  b662383a4bdcffc8c8bd72687f0e0235ba8e6edb
planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh commit 21f6d9932d322034e4cea5fee23b24bf0b1e1e85-dirty

diff -r b662383a4bdc -r 692366540172 tools/blast_rbh/README.rst
--- a/tools/blast_rbh/README.rst	Thu May 18 07:39:37 2017 -0400
+++ b/tools/blast_rbh/README.rst	Thu May 18 12:43:55 2017 -0400
@@ -91,6 +91,8 @@
 v0.1.11 - Updated to depend on NCBI BLAST+ 2.5.0 via ToolShed or BioConda.
         - Update Biopython dependency.
         - Tweak Python script to work under Python 2 or Python 3.
+v0.1.12 - Use ``<command detect_errors="aggressive">`` (internal change only).
+        - Single quote command line arguments (internal change only).
 ======= ======================================================================
 
 
diff -r b662383a4bdc -r 692366540172 tools/blast_rbh/blast_rbh.xml
--- a/tools/blast_rbh/blast_rbh.xml	Thu May 18 07:39:37 2017 -0400
+++ b/tools/blast_rbh/blast_rbh.xml	Thu May 18 12:43:55 2017 -0400
@@ -1,19 +1,14 @@
-<tool id="blast_reciprocal_best_hits" name="BLAST Reciprocal Best Hits (RBH)" version="0.1.11">
+<tool id="blast_reciprocal_best_hits" name="BLAST Reciprocal Best Hits (RBH)" version="0.1.12">
     <description>from two FASTA files</description>
     <requirements>
         <requirement type="package" version="1.67">biopython</requirement>
         <requirement type="package" version="2.5.0">blast</requirement>
     </requirements>
-    <stdio>
-        <!-- Anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
-    <version_command interpreter="python">
-blast_rbh.py --version
+    <version_command>
+python $__tool_directory__/blast_rbh.py --version
     </version_command>
-    <command interpreter="python">
-blast_rbh.py "$fasta_a" "$fasta_b"
+    <command detect_errors="aggressive">
+python $__tool_directory__/blast_rbh.py '$fasta_a' '$fasta_b'
 -a $seq.dbtype
 #if $seq.dbtype=="nucl"
 -t $seq.nucl_type
@@ -23,7 +18,7 @@
 $make_nr
 -i $identity
 -c $q_cover
--o "$output"
+-o '$output'
     </command>
     <inputs>
         <!-- Galaxy does not have sub-types for protein vs nucletide FASTA -->