Mercurial > repos > mikel-egana-aranguren > oppl

diff OPPL/oppl.xml @ 11:6ca67b155e32

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Imports simplified, new tool for inference added
author Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Fri, 09 Mar 2012 16:15:27 +0100
parents 3f31c0eb7539
children d0722148cb59
line wrap: on
line diff
--- a/OPPL/oppl.xml	Thu Jan 12 10:20:00 2012 +0100
+++ b/OPPL/oppl.xml	Fri Mar 09 16:15:27 2012 +0100
@@ -1,92 +1,57 @@
-<tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.7">
+<tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.8">
 	<description>It executes an OPPL script against the input ontology and generates a new ontology with the changes described in the OPPL script</description>
 
 	<!-- 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 -->
+	<!-- Testing with wrapper.sh but no success so far -->
 	
-
-	<!-- For big ontologies I use -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 If that's too much for your machine simply delete or modify at will -->
-
-	<!--<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>-->
+	
 	
+	<!-- DEFAULT SETTINGS -->
+	
+	<!-- For big ontologies I use -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 If that's too much for your machine simply delete or modify at will, but since Galaxy is usually used in a server setting it makes sense to use a big chunk of memory -->
 
 	<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
+		java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output 2>/dev/null
 	</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, ...... -->
+	
+	<!-- FACT++ -->
+	
+	<!-- If you are planning to use FaCT++ you have to uncomment bellow (And comment the default settings 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, ...... -->
 	<!-- Using this setting doesn't upset the rest of the reasoners so you may as well leave it on if you plan to switch between FaCT++, Pellet and HermiT -->
 	
 	<!--<command>
-		#if $import_opts.imports_select==False #java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred NoImports $reasoner NoMerge > $output 2>/dev/null
-		#else #java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports $reasoner $merged > $output 2>/dev/null
-		#end if
-	</command>-->
+		java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output 2>/dev/null
+	</commadn>-->
+
+	
 	
 	
-	<!-- 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 #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>-->
+	<!-- DEBUGGING -->
 	
-		
-	<!-- EXPERIMENTS AND HOUSE KEEPING-->
-	<!--<command>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</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 
-		  #if $merge_opts.merge_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
-		#end if
-	</command>-->
+	<!-- For debugging simply remove 2>/dev/null Or uncomment bellow (And comment the default settings above). It will fail always (Due to OPPL messages) but at least it will be informative -->
+
+	<command>
+		java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output
+	</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"/>
-
-			<!-- EXPERIMENTS AND HOUSE KEEPING-->
-			<!--<when value="imports_no"/> -->
-			<!--<when value="imports_no">
-				<param type="hidden" name="merged" value="no_merge"/>
-	    		</when>-->
-			
-			<when value="imports_yes">
-				       		
-				<param format="text" name="imports" type="data" label="OWL imports URI mapping file"/>
-				<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>  
-            		</when>
-		</conditional>
+		<param name="reasoner" type="select" label="Choose reasoner">
+			<option value="Pellet" selected="true">Pellet</option>
+			<option value="HermiT">HermiT</option>
+			<option value="FaCTPlusPlus">FaCT++</option>
+		</param>
 		<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="reasoner" type="select" label="Choose reasoner">
-			<option value="Pellet" selected="true">Pellet</option>
-			<option value="HermiT">HermiT</option>
-			<option value="FaCTPlusPlus">FaCT++</option>
-		</param>
-
 	</inputs>
 	<outputs>
 		<data format="text" name="output" />
@@ -95,11 +60,8 @@
 		<test>
 			<param name="input" value="test.owl"/>
 			<param name="OPPL" value="test.oppl"/>
-			<param name="imports" value="NoImports"/>
 			<param name="format" value="OWL"/>
-			<param name="inferred" value="False"/>
 			<param name="reasoner" value="Pellet"/>
-			<param name="merged" value="no_merge"/>
 			<output name="out_file" file="test_new.owl"/>	
 		</test>
 	</tests>
@@ -115,27 +77,33 @@
 
 **Usage**
 
-  An ontology and an OPPL file are needed (test.owl and test.oppl can be used as samples, both available in the bundle). Load both with Get Data >> Upload File from your computer. 
+  An ontology and an OPPL file are needed (test.owl and test.oppl can be used as samples, both available in the bundle). Load both with Get Data >> Upload File from your computer, or redirect from another Galaxy tool.
 
   Then execute the OPPL file against the OWL file with Ontology Pre Processor Language >> Execute an OPPL file against an OWL file. A new output ontology will be generated.
 
-  In case the loaded ontology includes OWL imports, a file that maps the imported ontologies' URIs to actual physical URIs is needed. The file (See the file test_URI_mappings provided in the bundle) follows the convention URI-tab-physical URI:
-  
-  http://purl.obolibrary.org/obo/CHEBI_ONTOLOGY_chebi_ontology	/home/pik/UPM/OPPL_galaxy/oppl/OPPL/chebi.owl
-
-  http://purl.obolibrary.org/obo/UBERON_uberon	/home/pik/UPM/OPPL_galaxy/oppl/OPPL/cell.owl
+  In case the loaded ontology includes OWL imports, OPPL-Galaxy will try to resolve them. 
 
   The output ontology can be OBO or OWL (RDF/XML).
- 
-  The inferred subsumption axioms can be added to the output ontology as asserted axioms. 
-
+   
   The reasoner can be Pellet, HermiT FaCT++. Sometimes, if an execution fails it can be fixed by using a different reasoner. 
 
-  If OWL imports are used, all the ontologies (Main one and imported ones) can be merged in a single ontology for the output.
-
 **More information**
 
+  Galaxy public instances with OPPL-Galaxy pre-installed:
+  
+  http://sele.inf.um.es:8080/
+  
+  http://linkeddata2.dia.fi.upm.es:8080
+  
+  OPPL-Galaxy Examples: 
+  
   http://miuras.inf.um.es/OPPL-Galaxy/
+  
+  OPPL examples:
+  
+  http://oppl2.sourceforge.net/taggedexamples/
+  
+  Links of interest:
 
   http://oppl.sf.net/
 
@@ -151,7 +119,7 @@
   
 **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).
+  Mikel Egaña Aranguren, Jesualdo Tomás Fernández-Breis and Erick Antezana. OPPL-Galaxy: Enhancing ontology exploitation in Galaxy with OPPL. SWAT4LS 2011.
 
 **Contact**