Mercurial > repos > peterjc > effectivet3
changeset 34:011cfce866f1 draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit 3ab3d1a9650dec0533344d710ceb027e482d2b10-dirty
author | peterjc |
---|---|
date | Fri, 09 Nov 2018 10:50:03 -0500 |
parents | 8db22615d43f |
children | e2711662802b |
files | tools/effectiveT3/README.rst tools/effectiveT3/effectiveT3.py tools/effectiveT3/effectiveT3.xml |
diffstat | 3 files changed, 9 insertions(+), 7 deletions(-) [+] |
line wrap: on
line diff
--- a/tools/effectiveT3/README.rst Fri Sep 15 10:23:15 2017 -0400 +++ b/tools/effectiveT3/README.rst Fri Nov 09 10:50:03 2018 -0500 @@ -10,12 +10,12 @@ Jehl, Arnold and Rattei. Effective - a database of predicted secreted bacterial proteins Nucleic Acids Research, 39(Database issue), D591-5, 2011. -http://dx.doi.org/10.1093/nar/gkq1154 +https://doi.org/10.1093/nar/gkq1154 Arnold, Brandmaier, Kleine, Tischler, Heinz, Behrens, Niinikoski, Mewes, Horn and Rattei. Sequence-based prediction of type III secreted proteins. PLoS Pathog. 5(4):e1000376, 2009. -http://dx.doi.org/10.1371/journal.ppat.1000376 +https://doi.org/10.1371/journal.ppat.1000376 http://effectors.org/
--- a/tools/effectiveT3/effectiveT3.py Fri Sep 15 10:23:15 2017 -0400 +++ b/tools/effectiveT3/effectiveT3.py Fri Nov 09 10:50:03 2018 -0500 @@ -102,14 +102,16 @@ except ImportError: # Likely running on Python 2, use backport: def which(cmd, mode=os.F_OK | os.X_OK, path=None): - """Given a command, mode, and a PATH string, return the path which + """Python implementation of command line tool which. + + Given a command, mode, and a PATH string, return the path which conforms to the given mode on the PATH, or None if there is no such file. + `mode` defaults to os.F_OK | os.X_OK. `path` defaults to the result of os.environ.get("PATH"), or can be overridden with a custom search path. """ - # Check that a given file can be accessed with the correct mode. # Additionally check that `file` is not a directory, as on Windows # directories pass the os.access check.
--- a/tools/effectiveT3/effectiveT3.xml Fri Sep 15 10:23:15 2017 -0400 +++ b/tools/effectiveT3/effectiveT3.xml Fri Nov 09 10:50:03 2018 -0500 @@ -87,17 +87,17 @@ Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology. PeerJ 1:e167 -http://dx.doi.org/10.7717/peerj.167 +https://doi.org/10.7717/peerj.167 Jehl, Arnold and Rattei (2011). Effective - a database of predicted secreted bacterial proteins Nucleic Acids Research, 39(Database issue), D591-5. -http://dx.doi.org/10.1093/nar/gkq1154 +https://doi.org/10.1093/nar/gkq1154 Arnold, Brandmaier, Kleine, Tischler, Heinz, Behrens, Niinikoski, Mewes, Horn and Rattei (2009). Sequence-based prediction of type III secreted proteins. PLoS Pathog. 5(4):e1000376. -http://dx.doi.org/10.1371/journal.ppat.1000376 +https://doi.org/10.1371/journal.ppat.1000376 See also http://effectors.org/