Mercurial > repos > peterjc > align_back_trans
changeset 6:b27388e5a0bb draft
v0.0.10 removed unused reference to muscle format
| author | peterjc |
|---|---|
| date | Mon, 21 Aug 2017 06:26:14 -0400 |
| parents | 2c32e8a8990f |
| children | 883842b81796 |
| files | tools/align_back_trans/README.rst tools/align_back_trans/align_back_trans.py tools/align_back_trans/align_back_trans.xml tools/align_back_trans/tool_dependencies.xml |
| diffstat | 4 files changed, 8 insertions(+), 5 deletions(-) [+] |
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--- 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). ======= ======================================================================
--- 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")
--- 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>
--- 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>