# HG changeset patch
# User peterjc
# Date 1503311174 14400
# Node ID b27388e5a0bbded63234a8f7fdcfcbe8b9083ee2
# Parent  2c32e8a8990fe28630ce97f800efc3b7d6ec7bbd
v0.0.10 removed unused reference to muscle format

diff -r 2c32e8a8990f -r b27388e5a0bb tools/align_back_trans/README.rst
--- a/tools/align_back_trans/README.rst	Thu May 11 06:13:04 2017 -0400
+++ b/tools/align_back_trans/README.rst	Mon Aug 21 06:26:14 2017 -0400
@@ -45,7 +45,7 @@
 
 You will also need to install Biopython 1.62 or later.
 
-If you wish to run the unit tests, also	move/copy the ``test-data/`` files
+If you wish to run the unit tests, also move/copy the ``test-data/`` files
 under Galaxy's ``test-data/`` folder. Then::
 
     ./run_tests.sh -id align_back_trans
@@ -80,6 +80,8 @@
         - Use ``<command detect_errors="aggressive">`` (internal change only).
         - Single quote command line arguments (internal change only).
 v0.0.9  - Python 3 compatible print function.
+v0.0.10 - Remove unused reference to ``muscle`` format in wrapper, reported by
+          Björn Grüning (internal change only).
 ======= ======================================================================
 
 
diff -r 2c32e8a8990f -r b27388e5a0bb tools/align_back_trans/align_back_trans.py
--- a/tools/align_back_trans/align_back_trans.py	Thu May 11 06:13:04 2017 -0400
+++ b/tools/align_back_trans/align_back_trans.py	Mon Aug 21 06:26:14 2017 -0400
@@ -88,6 +88,7 @@
 
 
 def sequence_back_translate(aligned_protein_record, unaligned_nucleotide_record, gap, table=0):
+    """Back-translate a sequence."""
     # TODO - Separate arguments for protein gap and nucleotide gap?
     if not gap or len(gap) != 1:
         raise ValueError("Please supply a single gap character")
diff -r 2c32e8a8990f -r b27388e5a0bb tools/align_back_trans/align_back_trans.xml
--- a/tools/align_back_trans/align_back_trans.xml	Thu May 11 06:13:04 2017 -0400
+++ b/tools/align_back_trans/align_back_trans.xml	Mon Aug 21 06:26:14 2017 -0400
@@ -1,16 +1,16 @@
-<tool id="align_back_trans" name="Thread nucleotides onto a protein alignment (back-translation)" version="0.0.9">
+<tool id="align_back_trans" name="Thread nucleotides onto a protein alignment (back-translation)" version="0.0.10">
     <description>Gives a codon aware alignment</description>
     <requirements>
         <requirement type="package" version="1.67">biopython</requirement>
     </requirements>
     <version_command>
 python $__tool_directory__/align_back_trans.py --version
-</version_command>
+    </version_command>
     <command detect_errors="aggressive">
 python $__tool_directory__/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." />
+        <param name="prot_align" type="data" format="fasta,clustal" label="Aligned protein file" help="Mutliple sequence file in FASTA, ClustalW or PHYLIP format." />
         <param name="table" type="select" label="Genetic code" help="Tables from the NCBI, these determine the start and stop codons">
             <option value="1">1. Standard</option>
             <option value="2">2. Vertebrate Mitochondrial</option>
diff -r 2c32e8a8990f -r b27388e5a0bb tools/align_back_trans/tool_dependencies.xml
--- a/tools/align_back_trans/tool_dependencies.xml	Thu May 11 06:13:04 2017 -0400
+++ b/tools/align_back_trans/tool_dependencies.xml	Mon Aug 21 06:26:14 2017 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="biopython" version="1.67">
-        <repository changeset_revision="a42f244cce44" name="package_biopython_1_67" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="a12f73c3b116" name="package_biopython_1_67" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>