Mercurial > repos > peterjc > predictnls

changeset 3:b1ac9b1dfb38 draft

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planemo upload for https://github.com/peterjc/pico_galaxy/tools/predictnls/71036f58c388735edcec557322b97d7e43775687
author peterjc
date Tue, 12 May 2015 12:01:16 -0400
parents 4e850852fc4f
children ff3221dc06a7
files tools/predictnls/README.rst tools/predictnls/predictnls.py tools/predictnls/predictnls.xml
diffstat 3 files changed, 35 insertions(+), 20 deletions(-) [+]
line wrap: on
line diff
--- a/tools/predictnls/README.rst	Fri Nov 21 07:00:03 2014 -0500
+++ b/tools/predictnls/README.rst	Tue May 12 12:01:16 2015 -0400
@@ -1,7 +1,7 @@
 Python re-implementation of predictNLS with Galaxy wrapper
 ==========================================================
 
-This Galaxy tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute
+This Galaxy tool is copyright 2011-2015 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below.
 
@@ -64,6 +64,8 @@
         - Updated citation information (Cock et al. 2013).
         - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
 v0.0.7  - Tool definition now embeds citation information.
+v0.0.8  - Reorder XML elements (internal change only).
+        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
 ======= ======================================================================
 
 
@@ -76,17 +78,30 @@
 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
 the following command from the Galaxy root folder::
 
-    $ tar -czf predictnls.tar.gz tools/predictnls/README.rst tools/predictnls/predictnls.xml tools/predictnls/predictnls.py tools/predictnls/My_NLS_list test-data/four_human_proteins.fasta test-data/four_human_proteins.predictnls.tabular
 
-Check this worked::
+For pushing a release to the test or main "Galaxy Tool Shed", use the following
+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_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/predictnls/
+    ...
 
-    $ tar -tzf predictnls.tar.gz
-    tools/predictnls/README.rst
-    tools/predictnls/predictnls.xml
-    tools/predictnls/predictnls.py
-    tools/predictnls/My_NLS_list
+or::
+
+    $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/predictnls/
+    ...
+
+To just build and check the tar ball, use::
+
+    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/predictnls/
+    ...
+    $ tar -tzf shed_upload.tar.gz 
     test-data/four_human_proteins.fasta
     test-data/four_human_proteins.predictnls.tabular
+    tools/predictnls/My_NLS_list
+    tools/predictnls/README.rst
+    tools/predictnls/predictnls.py
+    tools/predictnls/predictnls.xml
 
 
 Licence (GPL)
--- a/tools/predictnls/predictnls.py	Fri Nov 21 07:00:03 2014 -0500
+++ b/tools/predictnls/predictnls.py	Tue May 12 12:01:16 2015 -0400
@@ -53,7 +53,7 @@
 import sys
 import re
 
-def stop_err(msg, return_code=1):
+def sys_exit(msg, return_code=1):
     sys.stderr.write(msg.rstrip() + "\n")
     sys.exit(return_code)
 
@@ -70,13 +70,13 @@
         re_filename = os.path.join(os.path.dirname(os.path.realpath(sys.argv[0])),
                                                    "My_NLS_list")
 else:
-    stop_err("Expect 2 or 3 arguments: input FASTA file, output tabular file, and NLS motif file")
+    sys_exit("Expect 2 or 3 arguments: input FASTA file, output tabular file, and NLS motif file")
 
 if not os.path.isfile(fasta_filename):
-    stop_err("Could not find FASTA input file: %s" % fasta_filename)
+    sys_exit("Could not find FASTA input file: %s" % fasta_filename)
 
 if not os.path.isfile(re_filename):
-    stop_err("Could not find NLS motif file: %s" % re_filename)
+    sys_exit("Could not find NLS motif file: %s" % re_filename)
 
 def load_re(filename):
     """Parse the 5+ column tabular NLS motif file."""
@@ -92,7 +92,7 @@
             regex = re.compile(regex)
             p_count = int(p_count)
         except ValueError:
-            stop_err("Bad data in line: %s" % line)
+            sys_exit("Bad data in line: %s" % line)
         if 6 <= len(parts):
             proteins = parts[5]
             assert p_count == len(proteins.split(",")), line
--- a/tools/predictnls/predictnls.xml	Fri Nov 21 07:00:03 2014 -0500
+++ b/tools/predictnls/predictnls.xml	Tue May 12 12:01:16 2015 -0400
@@ -1,13 +1,16 @@
-<tool id="predictnls" name="PredictNLS" version="0.0.7">
+<tool id="predictnls" name="PredictNLS" version="0.0.8">
     <description>Find nuclear localization signals (NLSs) in protein sequences</description>
-    <command interpreter="python">
-      predictnls.py $fasta_file $tabular_file
-    </command>
+    <requirements>
+        <requirement type="binary">predictnls</requirement>
+    </requirements>
     <stdio>
         <!-- Assume anything other than zero is an error -->
         <exit_code range="1:" />
         <exit_code range=":-1" />
     </stdio>
+    <command interpreter="python">
+      predictnls.py $fasta_file $tabular_file
+    </command>
     <inputs>
         <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> 
     </inputs>
@@ -20,9 +23,6 @@
              <output name="tabular_file" file="four_human_proteins.predictnls.tabular"/>
         </test>
     </tests>
-    <requirements>
-        <requirement type="binary">predictnls</requirement>
-    </requirements>
     <help>
     
 **What it does**