Mercurial > repos > peterjc > align_back_trans
changeset 13:e5834d670ed8 draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans commit 7cf7d2e3fc5480fbe1a463e8a876e54c5c858dbe-dirty
| author | peterjc |
|---|---|
| date | Wed, 10 May 2017 11:48:59 -0400 |
| parents | 61b4236e0cff |
| children | 50a40a3db275 |
| files | tools/align_back_trans/README.rst tools/align_back_trans/align_back_trans.xml |
| diffstat | 2 files changed, 16 insertions(+), 3 deletions(-) [+] |
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--- a/tools/align_back_trans/README.rst Fri Apr 21 11:59:23 2017 -0400 +++ b/tools/align_back_trans/README.rst Wed May 10 11:48:59 2017 -0400 @@ -72,6 +72,9 @@ 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. + - Added recent NCBI genetic code tables: + * Table 24. *Pterobranchia Mitochondrial Code* + * Table 25. *Candidate Division SR1 and Gracilibacteria* - 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 Fri Apr 21 11:59:23 2017 -0400 +++ b/tools/align_back_trans/align_back_trans.xml Wed May 10 11:48:59 2017 -0400 @@ -4,10 +4,10 @@ <requirement type="package" version="1.67">biopython</requirement> </requirements> <version_command> -python align_back_trans.py --version +python $__tool_directory__/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 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." /> @@ -29,6 +29,16 @@ <option value="21">21. Trematode Mitochondrial</option> <option value="22">22. Scenedesmus obliquus</option> <option value="23">23. Thraustochytrium Mitochondrial</option> + <option value="24">24. Pterobranchia Mitochondrial</option> + <option value="25">25. Candidate Division SR1 and Gracilibacteria</option> + <!-- TODO, these are not in Biopython 1.67 + <option value="26">26. Pachysolen tannophilus Nuclear</option> + <option value="26">27. Karyorelict Nuclear</option> + <option value="26">28. Condylostoma Nuclear</option> + <option value="26">29. Mesodinium Nuclear</option> + <option value="26">30. Peritrich Nuclear</option> + <option value="26">31. Blastocrithidia Nuclear</option> + --> <option value="0">Don't check the translation</option> </param> <param name="nuc_file" type="data" format="fasta" label="Unaligned nucleotide sequences" help="FASTA format, using same identifiers as your protein alignment" />