Mercurial > repos > peterjc > align_back_trans
changeset 12:61b4236e0cff draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans commit 6d77d2fbb0d3ea1fd4db369073654b8a920c44bf-dirty
| author | peterjc |
|---|---|
| date | Fri, 21 Apr 2017 11:59:23 -0400 |
| parents | eef06667d973 |
| children | e5834d670ed8 |
| files | tools/align_back_trans/README.rst tools/align_back_trans/align_back_trans.xml tools/align_back_trans/tool_dependencies.xml |
| diffstat | 3 files changed, 12 insertions(+), 13 deletions(-) [+] |
line wrap: on
line diff
--- 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) ======= ======================================================================
--- 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." />
--- 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>