# HG changeset patch
# User peterjc
# Date 1541779106 18000
# Node ID 8912199785fa44188da18342f3340d6879a88ded
# Parent  92bb5d75d77ee704ddb8e28afab5da68548e3176
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls commit 3ab3d1a9650dec0533344d710ceb027e482d2b10-dirty

diff -r 92bb5d75d77e -r 8912199785fa tools/predictnls/README.rst
--- a/tools/predictnls/README.rst	Fri Sep 15 10:26:52 2017 -0400
+++ b/tools/predictnls/README.rst	Fri Nov 09 10:58:26 2018 -0500
@@ -13,7 +13,7 @@
 Murat Cokol, Rajesh Nair, and Burkhard Rost.
 Finding nuclear localization signals.
 EMBO reports 1(5), 411–415, 2000
-http://dx.doi.org/10.1093/embo-reports/kvd092
+https://doi.org/10.1093/embo-reports/kvd092
 
 This wrapper is available from the Galaxy Tool Shed at
 http://toolshed.g2.bx.psu.edu/view/peterjc/predictnls
diff -r 92bb5d75d77e -r 8912199785fa tools/predictnls/predictnls.py
--- a/tools/predictnls/predictnls.py	Fri Sep 15 10:26:52 2017 -0400
+++ b/tools/predictnls/predictnls.py	Fri Nov 09 10:58:26 2018 -0500
@@ -9,7 +9,7 @@
 # (nair@rostlab.org) and Burkhard Rost (rost@rostlab.org), Rost Lab,
 # Columbia University http://rostlab.org/
 
-"""Batch mode predictNLS, for finding nuclear localization signals
+"""Batch mode predictNLS, for finding nuclear localization signals.
 
 This is a Python script re-implementing the predictNLS method, originally
 written in Perl, described here:
@@ -18,7 +18,7 @@
 Finding nuclear localization signals.
 EMBO reports 1(5), 411-415, 2000
 
-http://dx.doi.org/10.1093/embo-reports/kvd092
+https://doi.org/10.1093/embo-reports/kvd092
 
 The original Perl script was designed to work on a single sequence at a time,
 but offers quite detailed output, including HTML (webpage).
@@ -114,7 +114,7 @@
 
 
 def fasta_iterator(filename):
-    """Simple FASTA parser yielding tuples of (name, upper case sequence)."""
+    """Parse FASTA file yielding tuples of (name, upper case sequence)."""
     if filename == "-":
         handle = sys.stdin
     else:
diff -r 92bb5d75d77e -r 8912199785fa tools/predictnls/predictnls.xml
--- a/tools/predictnls/predictnls.xml	Fri Sep 15 10:26:52 2017 -0400
+++ b/tools/predictnls/predictnls.xml	Fri Nov 09 10:58:26 2018 -0500
@@ -77,12 +77,12 @@
 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
 
 Murat Cokol, Rajesh Nair, and Burkhard Rost (2000).
 Finding nuclear localization signals.
 EMBO reports 1(5), 411–415
-http://dx.doi.org/10.1093/embo-reports/kvd092
+https://doi.org/10.1093/embo-reports/kvd092
 
 See also http://rostlab.org