# HG changeset patch
# User peterjc
# Date 1312283173 14400
# Node ID e607c342312f9206e3b861238b9bb9cce1819152
# Parent  43436379876f564d050cd1e42402d7be20e0fcfc
Wrapper v0.0.8, includes effectiveT3.loc.sample file

diff -r 43436379876f -r e607c342312f tool-data/effectiveT3.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/effectiveT3.loc.sample	Tue Aug 02 07:06:13 2011 -0400
@@ -0,0 +1,26 @@
+# This is a three column tab separated file to define the modules (models)
+# for the Effective T3 prediction tool.
+#
+# Column 1 - Module ID, string that Galaxy will save in its database
+# Column 2 - Human readable name, Galaxy will show this in the UI
+# Column 3 - Filename, Galaxy will use this when calling the tool
+#
+#NOTE: In EffectiveT3 v1.0.1, the modules are given as their filename
+#(with the JAR extension) but without any path. They are expected to
+#be located in a subdirectory called module under the working directory.
+#For the galaxy wrapper, we assume this means under the folder where the
+#main JAR file is, TTSS_GUI-1.0.1.jar
+#
+#e.g.
+#
+# /opt/EffectiveT3/TTSS_GUI-1.0.1.jar
+# /opt/EffectiveT3/module/TTSS_STD-1.0.1.jar
+# /opt/EffectiveT3/module/TTSS_ANIMAL-1.0.1.jar
+# /opt/EffectiveT3/module/TTSS_PLANT-1.0.1.jar
+#
+#See files ../tools/protein_analysis/effectiveT3.* for more details,
+#and http://effectors.org
+#
+standard	Type III Effector prediction with standard set	TTSS_STD-1.0.1.jar
+animal	Type III Effector prediction with animal set	TTSS_ANIMAL-1.0.1.jar
+plant	Type III Effector prediction with plant set	TTSS_PLANT-1.0.1.jar
diff -r 43436379876f -r e607c342312f tools/protein_analysis/effectiveT3.txt
--- a/tools/protein_analysis/effectiveT3.txt	Tue Jun 07 17:21:30 2011 -0400
+++ b/tools/protein_analysis/effectiveT3.txt	Tue Aug 02 07:06:13 2011 -0400
@@ -19,6 +19,10 @@
 
 http://effectors.org/
 
+
+Installation
+===========
+
 You can change the path by editing the definition near the start of the Python
 script effectiveT3.py, but by default it expects the following files to be
 installed at these locations:
@@ -35,6 +39,9 @@
 * 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:
@@ -48,6 +55,7 @@
 =======
 
 v0.0.7 - Initial public release
+v0.0.8 - Include effectiveT3.loc.sample in Tool Shed
 
 
 Developers
@@ -59,7 +67,7 @@
 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
 the following command from the Galaxy root folder:
 
-$ tar -czf effectiveT3.tar.gz tools/protein_analysis/effectiveT3.xml tools/protein_analysis/effectiveT3.py tools/protein_analysis/effectiveT3.txt
+$ tar -czf effectiveT3.tar.gz tools/protein_analysis/effectiveT3.xml tools/protein_analysis/effectiveT3.py tools/protein_analysis/effectiveT3.txt tool-data/effectiveT3.loc.sample
 
 Check this worked:
 
@@ -67,7 +75,7 @@
 tools/protein_analysis/effectiveT3.xml
 tools/protein_analysis/effectiveT3.py
 tools/protein_analysis/effectiveT3.txt
-
+tool-data/effectiveT3.loc.sample
 
 Licence (MIT/BSD style)
 =======================
@@ -90,5 +98,5 @@
 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. NLStradamus
-is available and licenced separately.
+NOTE: This is the licence for the Galaxy Wrapper only.
+EffectiveT3 is available and licenced separately.
diff -r 43436379876f -r e607c342312f tools/protein_analysis/effectiveT3.xml
--- a/tools/protein_analysis/effectiveT3.xml	Tue Jun 07 17:21:30 2011 -0400
+++ b/tools/protein_analysis/effectiveT3.xml	Tue Aug 02 07:06:13 2011 -0400
@@ -1,4 +1,4 @@
-<tool id="effectiveT3" name="Effective T3" version="0.0.7">
+<tool id="effectiveT3" name="Effective T3" version="0.0.8">
     <description>Find bacterial effectors in protein sequences</description>
     <command interpreter="python">
 effectiveT3.py $module.fields.path