# HG changeset patch
# User Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
# Date 1326360000 -3600
# Node ID 3f31c0eb753991c5760c9a6664bc63f26905cdcd
# Parent  14bfd77f852016015b31a221327f4231845221f6
Interface improved

diff -r 14bfd77f8520 -r 3f31c0eb7539 OPPL/README
--- a/OPPL/README	Tue Oct 18 10:30:16 2011 +0200
+++ b/OPPL/README	Thu Jan 12 10:20:00 2012 +0100
@@ -10,7 +10,7 @@
 INSTALLATION
 ============
 
-1.- Stop galaxy.
+1.- Stop Galaxy.
 
 2.- Copy oppl_galaxy_tool.jar, FaCT++-linux-v1.5.2/ FaCT++-OSX-v1.5.2/ 
 and oppl_galaxy_tool_lib/ to /galaxy-dist/tool-data/shared/jars/
@@ -25,7 +25,7 @@
     <tool file="OPPL/oppl.xml"/>
   </section>
 
-6.- Start galaxy.
+6.- Start Galaxy.
 
 
 
@@ -43,13 +43,16 @@
 Ontology Pre Processor Language
 	>> Execute an OPPL file against an OWL file 
 
-An ontology produced by another galaxy tools can also be used.
+An ontology produced by another galaxy tool can also be used.
 
 Test.oppl and test.owl can be used as examples. More OPPL-Galaxy 
 examples can be obtained at http://miuras.inf.um.es/OPPL-Galaxy/, and 
 general OPPL script that may be useful to use with OPPL-Galaxy can be 
 obtained at http://oppl2.sourceforge.net/taggedexamples/.
 
+A public instance of Galaxy with pre-installed OPPL-Galaxy can be used 
+at http://sele.inf.um.es:8080/.
+
 
 
 FORESEEN FEATURES
@@ -58,7 +61,11 @@
 Choose which inferred axioms to add to the output ontology (Right now 
 only subsumption between named classes is available).
 
-OWLLink support.
+Rendering definition (URI fragment, label, etc).
+
+XML catalog support for imported URIs.
+
+OWLLink and Racer support.
 
 
 
diff -r 14bfd77f8520 -r 3f31c0eb7539 OPPL/oppl.xml
--- a/OPPL/oppl.xml	Tue Oct 18 10:30:16 2011 +0200
+++ b/OPPL/oppl.xml	Thu Jan 12 10:20:00 2012 +0100
@@ -1,18 +1,24 @@
-<tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.6">
+<tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.7">
 	<description>It executes an OPPL script against the input ontology and generates a new ontology with the changes described in the OPPL script</description>
 
-	<!-- The command execution of the conditional is tacky, I think, but it works! -->
 	<!-- Galaxy is not happy with OPPL throwing info into stderr, and I have redirected stderr to /dev/null, which is a bad solution since OPPL galaxy does not inform properly when it fails -->
 	<!-- More info on the stderr issue: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr -->
 	
 
 	<!-- For big ontologies I use -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 If that's too much for your machine simply delete or modify at will -->
 
-	<command>
+	<!--<command>
 		#if $import_opts.imports_select==False #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred NoImports $reasoner NoMerge > $output 2>/dev/null
 		#else #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports $reasoner $merged > $output 2>/dev/null
 		#end if
-	</command> 
+	</command>-->
+	
+
+	<command>
+		#if $import_opts.imports_select==False #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred NoImports $reasoner NoMerge > $output 2>/dev/null
+		#else #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $import_opts.imports $reasoner $import_opts.merge_opts.merged > $output 2>/dev/null
+		#end if
+	</command>
 	
 	
 	<!-- If you are planning to use FaCT++ you have to uncomment bellow (And comment the one above) and replace the -Djava.library.path with the appropiate JNI library path for your platform:FaCT++-linux-v1.5.2/64bit, FaCT++-linux-v1.5.2/32bit, FaCT++-OSX-v1.5.2/64bit, ...... -->
@@ -26,9 +32,10 @@
 	
 	
 	<!-- For debugging simply remove 2>/dev/null Or uncomment bellow. It will fail always (Due to OPPL messages) but at least it will be informative -->
+	<!-- Testing with wrapper.sh but no success so far -->
 	
 	<!--<command>
-		#if $import_opts.imports_select==False #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred NoImports $reasoner no_merge > $output
+		#if $import_opts.imports_select==False #wrapper.sh java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred NoImports $reasoner no_merge > $output
 		#else #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports $reasoner $merged > $output 
 		#end if
 	</command>-->
@@ -46,6 +53,7 @@
 	</command>-->
 
 	<inputs>
+		<param format="text" name="input" type="data" label="Input ontology file"/>
 		<conditional name="import_opts">
 			<param name="imports_select" type="boolean" value="False" truevalue="imports_yes" falsevalue="imports_no" label="Tick the box if the input ontology includes OWL imports"/>
 
@@ -58,26 +66,21 @@
 			<when value="imports_yes">
 				       		
 				<param format="text" name="imports" type="data" label="OWL imports URI mapping file"/>
-				
-				<!-- EXPERIMENTS AND HOUSE KEEPING-->
-				<!--<conditional name="merge_opts">
+				<conditional name="merge_opts">
 				    <param name="merge_select" type="boolean" value="False" truevalue="merge_yes" falsevalue="merge_no" label="Tick the box to merge ontologies"/>
 				    <when value="merge_yes">
 				      <param name="merged" type="text" size="100" value="http://oppl-galaxy/merged" label="Type an URI or use the default URI" />  
 				    </when>
-				</conditional>-->  
-				<!--<param format="text" name="merged" type="data" label="OWL "/>-->
-				
+				</conditional>  
             		</when>
 		</conditional>
-		<param format="text" name="input" type="data" label="Input ontology file"/>
 		<param format="text" name="OPPL" type="data" label="OPPL file"/>
 		<param name="format" type="select" label="Choose ontology output format">
 			<option value="OWL" selected="true">OWL</option>
 			<option value="OBO">OBO</option>
 		</param>
 		<param name="inferred" type="boolean" value="False" truevalue="AddInferred" falsevalue="Gora_ni" label="Add inferred subsumption axioms to output ontology"/>
-		<param name="merged" type="text" size="100" value="NoMerge" label="To merge ontologies (If there are imports), type an URI for the new ontology (Leave NoMerge for not merging)" />
+<!-- 		<param name="merged" type="text" size="100" value="NoMerge" label="To merge ontologies (If there are imports), type an URI for the new ontology (Leave NoMerge for not merging)" /> -->
 		<param name="reasoner" type="select" label="Choose reasoner">
 			<option value="Pellet" selected="true">Pellet</option>
 			<option value="HermiT">HermiT</option>
@@ -132,6 +135,8 @@
 
 **More information**
 
+  http://miuras.inf.um.es/OPPL-Galaxy/
+
   http://oppl.sf.net/
 
   http://owlapi.sourceforge.net/
@@ -143,6 +148,10 @@
   http://hermit-reasoner.com/
   
   http://code.google.com/p/factplusplus/
+  
+**Citation**
+
+  Mikel Egaña Aranguren, Jesualdo Tomás Fernández-Breis and Erick Antezana. OPPL-Galaxy: Enhancing ontology exploitation in Galaxy with OPPL. SWAT4LS 2011 (To appear in ACM proceedings).
 
 **Contact**