Mercurial > repos > peterjc > tmhmm_and_signalp
changeset 28:22e71e53f534 draft
Capture version of promoter2
| author | peterjc |
|---|---|
| date | Tue, 01 Sep 2015 08:24:49 -0400 |
| parents | 9e36a1b9302d |
| children | 3cb02adf4326 |
| files | tools/protein_analysis/README.rst tools/protein_analysis/promoter2.py tools/protein_analysis/promoter2.xml |
| diffstat | 3 files changed, 8 insertions(+), 3 deletions(-) [+] |
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--- a/tools/protein_analysis/README.rst Thu May 21 10:57:40 2015 -0400 +++ b/tools/protein_analysis/README.rst Tue Sep 01 08:24:49 2015 -0400 @@ -177,6 +177,7 @@ v0.2.7 - Style cleanup in Python scripts. v0.2.8 - Reorder XML elements (internal change only). - Planemo for Tool Shed upload (``.shed.yml``, internal change only). + - Record version of Promoter 2 via ``<version_command>``. ======= ====================================================================== @@ -195,12 +196,12 @@ 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 --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/protein_analysis/ + $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/protein_analysis/ ... or:: - $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/protein_analysis/ + $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/protein_analysis/ ... To just build and check the tar ball, use::
--- a/tools/protein_analysis/promoter2.py Thu May 21 10:57:40 2015 -0400 +++ b/tools/protein_analysis/promoter2.py Tue Sep 01 08:24:49 2015 -0400 @@ -34,6 +34,9 @@ FASTA_CHUNK = 500 +if "-v" in sys.argv or "--version" in sys.argv: + sys.exit(os.system("promoter -V")) + if len(sys.argv) != 4: sys_exit("Require three arguments, number of threads (int), input DNA FASTA file & output tabular file. " "Got %i arguments." % (len(sys.argv)-1))
--- a/tools/protein_analysis/promoter2.xml Thu May 21 10:57:40 2015 -0400 +++ b/tools/protein_analysis/promoter2.xml Tue Sep 01 08:24:49 2015 -0400 @@ -1,4 +1,4 @@ -<tool id="promoter2" name="Promoter 2.0" version="0.0.9"> +<tool id="promoter2" name="Promoter 2.0" version="0.0.10"> <description>Find eukaryotic PolII promoters in DNA sequences</description> <!-- If job splitting is enabled, break up the query file into parts --> <!-- Using 2000 per chunk so 4 threads each doing 500 is ideal --> @@ -12,6 +12,7 @@ <exit_code range="1:" /> <exit_code range=":-1" /> </stdio> + <version_command interpreter="python">promoter2.py --version</version_command> <command interpreter="python"> promoter2.py "\$GALAXY_SLOTS" "$fasta_file" "$tabular_file" ##If the environment variable isn't set, get "", and the python wrapper