| Previous changeset 8:09a8be9247ca (2016-01-09) Next changeset 10:01b0488d9cfb (2017-05-16) |
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Commit message:
v0.2.1 Adds table 24; Depends on Biopython 1.67 via Tool Shed package or bioconda. |
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modified:
tools/get_orfs_or_cdss/README.rst tools/get_orfs_or_cdss/get_orfs_or_cdss.py tools/get_orfs_or_cdss/get_orfs_or_cdss.xml tools/get_orfs_or_cdss/tool_dependencies.xml |
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| diff -r 09a8be9247ca -r a06ad07431ba tools/get_orfs_or_cdss/README.rst --- a/tools/get_orfs_or_cdss/README.rst Sat Jan 09 23:42:32 2016 -0500 +++ b/tools/get_orfs_or_cdss/README.rst Wed May 10 13:24:46 2017 -0400 |
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| @@ -1,7 +1,7 @@ Galaxy tool to find ORFs or simple CDSs ======================================= -This tool is copyright 2011-2015 by Peter Cock, The James Hutton Institute +This tool is copyright 2011-2017 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. Additions copyright 2015-2016 by Eric Rasche. See the licence text below (MIT licence). @@ -77,6 +77,9 @@ - Added NCBI genetic code table 24, Pterobranchia Mitochondrial. v0.1.1 - Reorder XML elements (internal change only). v0.2.0 - Tool now also outputs GFF3 formatted calls (Eric Rasche). +v0.2.1 - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda. + - Added NCBI genetic code table 24, Candidate Division SR1 and + Gracilibacteria. ======= ====================================================================== @@ -93,17 +96,17 @@ Planemo commands (which requires you have set your Tool Shed access details in ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: - $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/get_orfs_or_cdss/ + $ planemo shed_update -t testtoolshed --check_diff tools/get_orfs_or_cdss/ ... or:: - $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/get_orfs_or_cdss/ + $ planemo shed_update -t toolshed --check_diff tools/get_orfs_or_cdss/ ... To just build and check the tar ball, use:: - $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/get_orfs_or_cdss/ + $ planemo shed_upload --tar_only tools/get_orfs_or_cdss/ ... $ tar -tzf shed_upload.tar.gz test-data/Ssuis.fasta |
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| diff -r 09a8be9247ca -r a06ad07431ba tools/get_orfs_or_cdss/get_orfs_or_cdss.py --- a/tools/get_orfs_or_cdss/get_orfs_or_cdss.py Sat Jan 09 23:42:32 2016 -0500 +++ b/tools/get_orfs_or_cdss/get_orfs_or_cdss.py Wed May 10 13:24:46 2017 -0400 |
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| @@ -17,8 +17,10 @@ See accompanying text file for licence details (MIT licence). """ + +import re import sys -import re + from optparse import OptionParser usage = """Use as follows: @@ -210,6 +212,7 @@ raise StopIteration yield values[0] + if options.mode == "all": get_peptides = get_all_peptides elif options.mode == "top": |
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| diff -r 09a8be9247ca -r a06ad07431ba tools/get_orfs_or_cdss/get_orfs_or_cdss.xml --- a/tools/get_orfs_or_cdss/get_orfs_or_cdss.xml Sat Jan 09 23:42:32 2016 -0500 +++ b/tools/get_orfs_or_cdss/get_orfs_or_cdss.xml Wed May 10 13:24:46 2017 -0400 |
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| @@ -1,8 +1,7 @@ -<tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.2.0"> +<tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.2.1"> <description>e.g. to get peptides from ESTs</description> <requirements> - <requirement type="package" version="1.65">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 --> @@ -34,6 +33,15 @@ <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> + --> </param> <param name="ftype" type="select" value="True" label="Look for ORFs or CDSs"> <option value="ORF">Look for ORFs (check for stop codons only, ignore start codons)</option> |
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| diff -r 09a8be9247ca -r a06ad07431ba tools/get_orfs_or_cdss/tool_dependencies.xml --- a/tools/get_orfs_or_cdss/tool_dependencies.xml Sat Jan 09 23:42:32 2016 -0500 +++ b/tools/get_orfs_or_cdss/tool_dependencies.xml Wed May 10 13:24:46 2017 -0400 |
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| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="biopython" version="1.65"> - <repository changeset_revision="030f1a505d40" name="package_biopython_1_65" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="biopython" version="1.67"> + <repository changeset_revision="a42f244cce44" name="package_biopython_1_67" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |