changeset 4:f7ce32e13bc6 draft

Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
author peterjc
date Wed, 18 Sep 2013 06:11:36 -0400
parents b0b927299aee
children 1ea715da1879
files tools/effectiveT3/README.rst tools/effectiveT3/effectiveT3.txt tools/effectiveT3/effectiveT3.xml
diffstat 3 files changed, 156 insertions(+), 136 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/effectiveT3/README.rst	Wed Sep 18 06:11:36 2013 -0400
@@ -0,0 +1,141 @@
+Galaxy wrapper for EffectiveT3 v1.0.1
+=====================================
+
+This wrapper is copyright 2011-2013 by Peter Cock, The James Hutton Institute
+(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
+See the licence text below.
+
+This is a wrapper for the command line Java tool EffectiveT3, v1.0.1,
+
+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
+
+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
+
+http://effectors.org/
+
+This wrapper is available from the Galaxy Tool Shed at:
+http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3
+
+
+Automated Installation
+======================
+
+This should be straightforward, Galaxy should automatically download and install
+the Jar files for effectiveT3 v1.0.1 and the three models (animal, plant and std).
+
+
+Manual Installation
+===================
+
+You can change the path by setting the environment variable EFFECTIVET3 to the
+relevant folder, but by default it expects the following files to be installed
+at these locations::
+
+    /opt/EffectiveT3/TTSS_GUI-1.0.1.jar
+    /opt/EffectiveT3/module/TTSS_ANIMAL-1.0.1.jar
+    /opt/EffectiveT3/module/TTSS_PLANT-1.0.1.jar
+    /opt/EffectiveT3/module/TTSS_STD-1.0.1.jar
+
+To install the wrapper copy or move the following files under the Galaxy tools
+folder, e.g. in a tools/effectiveT3 folder:
+
+* effectiveT3.xml (the Galaxy tool definition)
+* effectiveT3.py (the Python wrapper script)
+* README.rst (this file)
+
+Also copy effectiveT3.loc.sample to effectiveT3.loc in the tool-data folder
+(and edit if appropriate, e.g. to add or remove a model).
+
+You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
+tool. If you are using other protein analysis tools like TMHMM or SignalP, put
+it next to them. Just add the line::
+
+  <tool file="effectiveT3/effectiveT3.xml" />
+
+If you wish to run the unit tests, also add this to tools_conf.xml.sample
+and move/copy the test-data files under Galaxy's test-data folder. Then::
+
+    $ ./run_functional_tests.sh -id effectiveT3
+
+That's it.
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.7  - Initial public release
+v0.0.8  - Include effectiveT3.loc.sample in Tool Shed
+v0.0.9  - Check the return code for errors in the XML
+v0.0.10 - Added unit test
+v0.0.11 - Automated installation
+        - Record version of Python script when called from Galaxy
+        - Link to Tool Shed added to help text and this documentation.
+v0.0.12 - More explicit naming of the output dataset.
+        - Adopt standard MIT licence.
+        - Use reStructuredText for this README file.
+        - Updated citation information (Cock et al. 2013).
+        - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
+======= ======================================================================
+
+
+Developers
+==========
+
+This script and related tools were initially developed on the following hg branch:
+http://bitbucket.org/peterjc/galaxy-central/src/tools
+
+Development has now moved to a dedicated GitHub repository:
+https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3
+
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
+the following command from the Galaxy root folder::
+
+    $ tar -czf effectiveT3.tar.gz tools/effectiveT3/README.rst tools/effectiveT3/effectiveT3.xml tools/effectiveT3/effectiveT3.py tools/effectiveT3/tool_dependencies.xml tool-data/effectiveT3.loc.sample test-data/four_human_proteins.fasta test-data/four_human_proteins.effectiveT3.tabular test-data/empty.fasta test-data/empty_effectiveT3.tabular
+
+
+Check this worked::
+
+    $ tar -tzf effectiveT3.tar.gz
+    tools/effectiveT3/README.rst
+    tools/effectiveT3/effectiveT3.xml
+    tools/effectiveT3/effectiveT3.py
+    tools/effectiveT3/tool_dependencies.xml
+    tool-data/effectiveT3.loc.sample
+    test-data/four_human_proteins.fasta
+    test-data/four_human_proteins.effectiveT3.tabular
+    test-data/empty.fasta
+    test-data/empty_effectiveT3.tabular
+
+
+Licence (MIT)
+=============
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
+
+NOTE: This is the licence for the Galaxy Wrapper only.
+EffectiveT3 is available and licenced separately.
--- a/tools/effectiveT3/effectiveT3.txt	Thu May 16 04:45:41 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,129 +0,0 @@
-Galaxy wrapper for EffectiveT3 v1.0.1
-=====================================
-
-This wrapper is copyright 2011-2013 by Peter Cock, The James Hutton Institute
-(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
-See the licence text below.
-
-This is a wrapper for the command line Java tool EffectiveT3, v1.0.1,
-
-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
-
-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
-
-http://effectors.org/
-
-This wrapper is available from the Galaxy Tool Shed at:
-http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3
-
-
-Automated Installation
-======================
-
-This should be straightforward, Galaxy should automatically download and install
-the Jar files for effectiveT3 v1.0.1 and the three models (animal, plant and std).
-
-
-Manual Installation
-===================
-
-You can change the path by setting the environment variable EFFECTIVET3 to the
-relevant folder, but by default it expects the following files to be installed
-at these locations:
-
-/opt/EffectiveT3/TTSS_GUI-1.0.1.jar
-/opt/EffectiveT3/module/TTSS_ANIMAL-1.0.1.jar
-/opt/EffectiveT3/module/TTSS_PLANT-1.0.1.jar
-/opt/EffectiveT3/module/TTSS_STD-1.0.1.jar
-
-To install the wrapper copy or move the following files under the Galaxy tools
-folder, e.g. in a tools/effectiveT3 folder:
-
-* effectiveT3.xml (the Galaxy tool definition)
-* effectiveT3.py (the Python wrapper script)
-* effectiveT3.txt (this README file)
-
-Also copy effectiveT3.loc.sample to effectiveT3.loc in the tool-data folder
-(and edit if appropriate, e.g. to add or remove a model).
-
-You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
-tool. If you are using other protein analysis tools like TMHMM or SignalP, put
-it next to them. Just add the line:
-
-<tool file="effectiveT3/effectiveT3.xml" />
-
-If you wish to run the unit tests, also add this to tools_conf.xml.sample
-and move/copy the test-data files under Galaxy's test-data folder.
-
-$ ./run_functional_tests.sh -id effectiveT3
-
-That's it.
-
-
-History
-=======
-
-v0.0.7 - Initial public release
-v0.0.8 - Include effectiveT3.loc.sample in Tool Shed
-v0.0.9 - Check the return code for errors in the XML
-v0.0.10- Added unit test
-v0.0.11- Automated installation
-       - Record version of Python script when called from Galaxy
-       - Link to Tool Shed added to help text and this documentation.
-
-
-Developers
-==========
-
-This script and related tools are being developed on the following hg branch:
-http://bitbucket.org/peterjc/galaxy-central/src/tools
-
-For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
-the following command from the Galaxy root folder:
-
-$ tar -czf effectiveT3.tar.gz tools/effectiveT3/effectiveT3.xml tools/effectiveT3/effectiveT3.py tools/effectiveT3/effectiveT3.txt tools/effectiveT3/tool_dependencies.xml tool-data/effectiveT3.loc.sample test-data/four_human_proteins.fasta test-data/four_human_proteins.effectiveT3.tabular test-data/empty.fasta test-data/empty_effectiveT3.tabular
-
-
-Check this worked:
-
-$ tar -tzf effectiveT3.tar.gz
-tools/effectiveT3/effectiveT3.xml
-tools/effectiveT3/effectiveT3.py
-tools/effectiveT3/effectiveT3.txt
-tools/effectiveT3/tool_dependencies.xml
-tool-data/effectiveT3.loc.sample
-test-data/four_human_proteins.fasta
-test-data/four_human_proteins.effectiveT3.tabular
-test-data/empty.fasta
-test-data/empty_effectiveT3.tabular
-
-
-Licence (MIT/BSD style)
-=======================
-
-Permission to use, copy, modify, and distribute this software and its
-documentation with or without modifications and for any purpose and
-without fee is hereby granted, provided that any copyright notices
-appear in all copies and that both those copyright notices and this
-permission notice appear in supporting documentation, and that the
-names of the contributors or copyright holders not be used in
-advertising or publicity pertaining to distribution of the software
-without specific prior permission.
-
-THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
-WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
-CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
-OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
-OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
-OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
-OR PERFORMANCE OF THIS SOFTWARE.
-
-NOTE: This is the licence for the Galaxy Wrapper only.
-EffectiveT3 is available and licenced separately.
--- a/tools/effectiveT3/effectiveT3.xml	Thu May 16 04:45:41 2013 -0400
+++ b/tools/effectiveT3/effectiveT3.xml	Wed Sep 18 06:11:36 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="effectiveT3" name="Effective T3" version="0.0.11">
+<tool id="effectiveT3" name="Effective T3" version="0.0.12">
     <description>Find bacterial effectors in protein sequences</description>
     <requirements>
         <requirement type="package" version="1.0.1">effectiveT3</requirement>
@@ -40,7 +40,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="tabular_file" format="tabular" label="$module.value_label results" />
+        <data name="tabular_file" format="tabular" label="Effective T3 $module.value_label on ${on_string}" />
     </outputs>
     <tests>
         <test>
@@ -76,17 +76,25 @@
 
 **References**
 
-Jehl, Arnold and Rattei.
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following papers:
+
+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
+
+Jehl, Arnold and Rattei (2011).
 Effective - a database of predicted secreted bacterial proteins
-Nucleic Acids Research, 39(Database issue), D591-5, 2011.
+Nucleic Acids Research, 39(Database issue), D591-5.
 http://dx.doi.org/10.1093/nar/gkq1154
 
-Arnold, Brandmaier, Kleine, Tischler, Heinz, Behrens, Niinikoski, Mewes, Horn and Rattei.
+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, 2009.
+PLoS Pathog. 5(4):e1000376.
 http://dx.doi.org/10.1371/journal.ppat.1000376
 
-http://effectors.org/
+See also http://effectors.org/
 
 This wrapper is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3