# HG changeset patch
# User peterjc
# Date 1541778603 18000
# Node ID 011cfce866f1d156e69362c76fb04c2b09345bec
# Parent  8db22615d43f00a1ed48c4286df45f25b409bb23
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit 3ab3d1a9650dec0533344d710ceb027e482d2b10-dirty

diff -r 8db22615d43f -r 011cfce866f1 tools/effectiveT3/README.rst
--- 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/
 
diff -r 8db22615d43f -r 011cfce866f1 tools/effectiveT3/effectiveT3.py
--- 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.
diff -r 8db22615d43f -r 011cfce866f1 tools/effectiveT3/effectiveT3.xml
--- 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/