--- a/tools/effectiveT3/README.rst	Wed Sep 18 06:11:36 2013 -0400
+++ b/tools/effectiveT3/README.rst	Tue Nov 25 08:28:24 2014 -0500
@@ -33,7 +33,7 @@
 Manual Installation
 ===================
 
-You can change the path by setting the environment variable EFFECTIVET3 to the
+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::
 
@@ -45,23 +45,23 @@
 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)
+* ``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).
+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
+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::
+If you wish to run the unit tests, also move/copy the ``test-data/`` files
+under Galaxy's ``test-data/`` folder. Then::
 
-    $ ./run_functional_tests.sh -id effectiveT3
+    $ ./run_tests.sh -id effectiveT3
 
 That's it.
 
@@ -84,6 +84,9 @@
         - Use reStructuredText for this README file.
         - Updated citation information (Cock et al. 2013).
         - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
+v0.0.13 - Relax unit test to allow for small floating point score difference.
+        - Tool definition now embeds citation information.
+        - Fixed error handling in ``effectiveT3.py``.
 ======= ======================================================================
 
 

--- a/tools/effectiveT3/effectiveT3.py	Wed Sep 18 06:11:36 2013 -0400
+++ b/tools/effectiveT3/effectiveT3.py	Tue Nov 25 08:28:24 2014 -0500
@@ -15,13 +15,13 @@
 import os
 import subprocess
 
-#The Galaxy auto-install via tool_dependencies.xml will set this environment variable
+# The Galaxy auto-install via tool_dependencies.xml will set this environment variable
 effectiveT3_dir = os.environ.get("EFFECTIVET3", "/opt/EffectiveT3/")
 effectiveT3_jar = os.path.join(effectiveT3_dir, "TTSS_GUI-1.0.1.jar")
 
 if "-v" in sys.argv or "--version" in sys.argv:
-    #TODO - Get version of the JAR file dynamically?
-    print "Wrapper v0.0.11, TTSS_GUI-1.0.1.jar"
+    # TODO - Get version of the JAR file dynamically?
+    print("Wrapper v0.0.13, TTSS_GUI-1.0.1.jar")
     sys.exit(0)
 
 def stop_err(msg, error_level=1):
@@ -51,12 +51,12 @@
         or line.startswith("Id; Description; Score;"):
             continue
         assert line.count(";") >= 3, repr(line)
-        #Normally there will just be three semi-colons, however the
-        #original FASTA file's ID or description might have had
-        #semi-colons in it as well, hence the following hackery:
+        # Normally there will just be three semi-colons, however the
+        # original FASTA file's ID or description might have had
+        # semi-colons in it as well, hence the following hackery:
         try:
             id_descr, score, effective = line.rstrip("\r\n").rsplit(";",2)
-            #Cope when there was no FASTA description
+            # Cope when there was no FASTA description
             if "; " not in id_descr and id_descr.endswith(";"):
                 id = id_descr[:-1]
                 descr = ""
@@ -74,20 +74,21 @@
     return count, positive, errors
 
 def run(cmd):
-    #Avoid using shell=True when we call subprocess to ensure if the Python
-    #script is killed, so too is the child process.
+    # Avoid using shell=True when we call subprocess to ensure if the Python
+    # script is killed, so too is the child process.
     try:
         child = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
     except Exception, err:
         stop_err("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
-    #Use .communicate as can get deadlocks with .wait(),
+    # Use .communicate as can get deadlocks with .wait(),
     stdout, stderr = child.communicate()
     return_code = child.returncode
     if return_code:
+        cmd_str= " ".join(cmd)  # doesn't quote spaces etc
         if stderr and stdout:
-            stop_err("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, err, stdout, stderr))
+            stop_err("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, cmd_str, stdout, stderr))
         else:
-            stop_err("Return code %i from command:\n%s\n%s" % (return_code, err, stderr))
+            stop_err("Return code %i from command:\n%s\n%s" % (return_code, cmd_str, stderr))
 
 if not os.path.isdir(effectiveT3_dir):
     stop_err("Effective T3 folder not found: %r" % effectiveT3_dir)
@@ -106,10 +107,10 @@
     sys.stderr.write("Main JAR was found: %r\n" % effectiveT3_jar)
     stop_err("Effective T3 model JAR file not found: %r" % effectiveT3_model)
 
-#We will have write access whereever the output should be,
+# We will have write access whereever the output should be,
 temp_file = os.path.abspath(tabular_file + ".tmp")
 
-#Use absolute paths since will change current directory...
+# Use absolute paths since will change current directory...
 tabular_file = os.path.abspath(tabular_file)
 fasta_file = os.path.abspath(fasta_file)
 
@@ -121,7 +122,7 @@
        "-q"]
 
 try:
-    #Must run from directory above the module subfolder:
+    # Must run from directory above the module subfolder:
     os.chdir(effectiveT3_dir)
 except:
     stop_err("Could not change to Effective T3 folder: %s" % effectiveT3_dir)
@@ -141,11 +142,11 @@
 os.remove(temp_file)
 
 if errors:
-   print "%i sequences, %i positive, %i errors" \
-         % (count, positive, errors)
+   print("%i sequences, %i positive, %i errors"
+         % (count, positive, errors))
 else:
-   print "%i/%i sequences positive" % (positive, count)
+   print("%i/%i sequences positive" % (positive, count))
 
 if count and count==errors:
-   #Galaxy will still  allow them to see the output file
+   # Galaxy will still  allow them to see the output file
    stop_err("All your sequences gave an error code")

--- a/tools/effectiveT3/effectiveT3.xml	Wed Sep 18 06:11:36 2013 -0400
+++ b/tools/effectiveT3/effectiveT3.xml	Tue Nov 25 08:28:24 2014 -0500
@@ -1,4 +1,4 @@
-<tool id="effectiveT3" name="Effective T3" version="0.0.12">
+<tool id="effectiveT3" name="Effective T3" version="0.0.13">
     <description>Find bacterial effectors in protein sequences</description>
     <requirements>
         <requirement type="package" version="1.0.1">effectiveT3</requirement>
@@ -47,12 +47,12 @@
             <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" />
             <param name="module" value="animal" />
             <param name="type" value="selective" />
-            <output name="tabular_file" file="four_human_proteins.effectiveT3.tabular" ftype="tabular" />
+            <output name="tabular_file" file="four_human_proteins.effectiveT3.tabular" ftype="tabular" lines_diff="2"/>
         </test>
         <test>
             <param name="fasta_file" value="empty.fasta" ftype="fasta" />
             <param name="module" value="plant" />
-            <param name="type" value="sensistive" />
+            <param name="type" value="sensitive" />
             <output name="tabular_file" file="empty_effectiveT3.tabular" ftype="tabular" />
         </test>
     </tests>
@@ -99,4 +99,9 @@
 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
     </help>
+    <citations>
+        <citation type="doi">10.7717/peerj.167</citation>
+        <citation type="doi">10.1093/nar/gkq1154</citation>
+        <citation type="doi">10.1371/journal.ppat.1000376</citation>
+    </citations>
 </tool>

--- a/tools/effectiveT3/tool_dependencies.xml	Wed Sep 18 06:11:36 2013 -0400
+++ b/tools/effectiveT3/tool_dependencies.xml	Tue Nov 25 08:28:24 2014 -0500
@@ -9,13 +9,13 @@
                 </action>
                 <!-- Main JAR file -->
                 <action type="shell_command">wget http://effectors.org/download/version/TTSS_GUI-1.0.1.jar</action>
-		<!-- If using action type download_file will need to move the file,
+                <!-- If using action type download_file will need to move the file,
                 <action type="move_file"><source>TTSS_GUI-1.0.1.jar</source><destination>$INSTALL_DIR/</destination></action>
-		-->
+                -->
                 <!-- Three model JAR files -->
                 <action type="make_directory">$INSTALL_DIR/module</action>
                 <action type="shell_command">wget http://effectors.org/download/module/TTSS_ANIMAL-1.0.1.jar</action>
-                <action type="move_file"><source>TTSS_ANIMAL-1.0.1.jar</source><destination>$INSTALL_DIR/module/</destination></action>		
+                <action type="move_file"><source>TTSS_ANIMAL-1.0.1.jar</source><destination>$INSTALL_DIR/module/</destination></action>        
                 <action type="shell_command">wget http://effectors.org/download/module/TTSS_PLANT-1.0.1.jar</action>
                 <action type="move_file"><source>TTSS_PLANT-1.0.1.jar</source><destination>$INSTALL_DIR/module/</destination></action>
                 <action type="shell_command">wget http://effectors.org/download/module/TTSS_STD-1.0.1.jar</action>