# HG changeset patch
# User peterjc
# Date 1492790363 14400
# Node ID 61b4236e0cffc6fe68976b5cb4e5f566fa449a75
# Parent  eef06667d973eb951d85c72789073410e1110252
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans commit 6d77d2fbb0d3ea1fd4db369073654b8a920c44bf-dirty

diff -r eef06667d973 -r 61b4236e0cff tools/align_back_trans/README.rst
--- a/tools/align_back_trans/README.rst	Thu Feb 09 11:18:24 2017 -0500
+++ b/tools/align_back_trans/README.rst	Fri Apr 21 11:59:23 2017 -0400
@@ -1,7 +1,7 @@
 Galaxy tool to back-translate a protein alignment to nucleotides
 ================================================================
 
-This tool is copyright 2012-2015 by Peter Cock, The James Hutton Institute
+This tool is copyright 2012-2017 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below (MIT licence).
 
@@ -71,6 +71,9 @@
         - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
 v0.0.7  - Minor Python code style improvements (internal change only).
 v0.0.8  - Python coding style change to avoid lamba (internal change only).
+        - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda.
+        - Use ``<command detect_errors="aggressive">`` (internal change only).
+        - Single quote command line arguments (internal change only)
 ======= ======================================================================
 
 
diff -r eef06667d973 -r 61b4236e0cff tools/align_back_trans/align_back_trans.xml
--- a/tools/align_back_trans/align_back_trans.xml	Thu Feb 09 11:18:24 2017 -0500
+++ b/tools/align_back_trans/align_back_trans.xml	Fri Apr 21 11:59:23 2017 -0400
@@ -1,17 +1,13 @@
 <tool id="align_back_trans" name="Thread nucleotides onto a protein alignment (back-translation)" version="0.0.8">
     <description>Gives a codon aware alignment</description>
     <requirements>
-        <requirement type="package" version="1.63">biopython</requirement>
-        <requirement type="python-module">Bio</requirement>
+        <requirement type="package" version="1.67">biopython</requirement>
     </requirements>
-    <stdio>
-        <!-- Anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
-    <version_command interpreter="python">align_back_trans.py --version</version_command>
-    <command interpreter="python">
-align_back_trans.py $prot_align.ext "$prot_align" "$nuc_file" "$out_nuc_align" "$table"
+    <version_command>
+python align_back_trans.py --version
+</version_command>
+    <command detect_errors="aggresive">
+align_back_trans.py $prot_align.ext '$prot_align' '$nuc_file' '$out_nuc_align' '$table'
     </command>
     <inputs>
         <param name="prot_align" type="data" format="fasta,muscle,clustal" label="Aligned protein file" help="Mutliple sequence file in FASTA, ClustalW or PHYLIP format." />
diff -r eef06667d973 -r 61b4236e0cff tools/align_back_trans/tool_dependencies.xml
--- a/tools/align_back_trans/tool_dependencies.xml	Thu Feb 09 11:18:24 2017 -0500
+++ b/tools/align_back_trans/tool_dependencies.xml	Fri Apr 21 11:59:23 2017 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="biopython" version="1.63">
-        <repository changeset_revision="9cddaed73a91" name="package_biopython_1_63" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="biopython" version="1.67">
+        <repository changeset_revision="fc45a61abc2f" name="package_biopython_1_67" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>