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comparison OPPL/oppl.xml @ 10:3f31c0eb7539

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Interface improved
author Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Thu, 12 Jan 2012 10:20:00 +0100
parents 14bfd77f8520
children 6ca67b155e32
comparison
equal deleted inserted replaced
9:14bfd77f8520 10:3f31c0eb7539
1 <tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.6"> 1 <tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.7">
2 <description>It executes an OPPL script against the input ontology and generates a new ontology with the changes described in the OPPL script</description> 2 <description>It executes an OPPL script against the input ontology and generates a new ontology with the changes described in the OPPL script</description>
3 3
4 <!-- The command execution of the conditional is tacky, I think, but it works! -->
5 <!-- 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 --> 4 <!-- 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 -->
6 <!-- More info on the stderr issue: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr --> 5 <!-- More info on the stderr issue: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr -->
7 6
8 7
9 <!-- For big ontologies I use -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 If that's too much for your machine simply delete or modify at will --> 8 <!-- For big ontologies I use -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 If that's too much for your machine simply delete or modify at will -->
10 9
11 <command> 10 <!--<command>
12 #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 11 #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
13 #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 12 #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
14 #end if 13 #end if
15 </command> 14 </command>-->
15
16
17 <command>
18 #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
19 #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
20 #end if
21 </command>
16 22
17 23
18 <!-- 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, ...... --> 24 <!-- 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, ...... -->
19 <!-- 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 --> 25 <!-- 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 -->
20 26
24 #end if 30 #end if
25 </command>--> 31 </command>-->
26 32
27 33
28 <!-- 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 --> 34 <!-- 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 -->
35 <!-- Testing with wrapper.sh but no success so far -->
29 36
30 <!--<command> 37 <!--<command>
31 #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 38 #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
32 #else #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports $reasoner $merged > $output 39 #else #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports $reasoner $merged > $output
33 #end if 40 #end if
34 </command>--> 41 </command>-->
35 42
36 43
44 #end if 51 #end if
45 #end if 52 #end if
46 </command>--> 53 </command>-->
47 54
48 <inputs> 55 <inputs>
56 <param format="text" name="input" type="data" label="Input ontology file"/>
49 <conditional name="import_opts"> 57 <conditional name="import_opts">
50 <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 <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"/>
51 59
52 <!-- EXPERIMENTS AND HOUSE KEEPING--> 60 <!-- EXPERIMENTS AND HOUSE KEEPING-->
53 <!--<when value="imports_no"/> --> 61 <!--<when value="imports_no"/> -->
56 </when>--> 64 </when>-->
57 65
58 <when value="imports_yes"> 66 <when value="imports_yes">
59 67
60 <param format="text" name="imports" type="data" label="OWL imports URI mapping file"/> 68 <param format="text" name="imports" type="data" label="OWL imports URI mapping file"/>
61 69 <conditional name="merge_opts">
62 <!-- EXPERIMENTS AND HOUSE KEEPING-->
63 <!--<conditional name="merge_opts">
64 <param name="merge_select" type="boolean" value="False" truevalue="merge_yes" falsevalue="merge_no" label="Tick the box to merge ontologies"/> 70 <param name="merge_select" type="boolean" value="False" truevalue="merge_yes" falsevalue="merge_no" label="Tick the box to merge ontologies"/>
65 <when value="merge_yes"> 71 <when value="merge_yes">
66 <param name="merged" type="text" size="100" value="http://oppl-galaxy/merged" label="Type an URI or use the default URI" /> 72 <param name="merged" type="text" size="100" value="http://oppl-galaxy/merged" label="Type an URI or use the default URI" />
67 </when> 73 </when>
68 </conditional>--> 74 </conditional>
69 <!--<param format="text" name="merged" type="data" label="OWL "/>-->
70
71 </when> 75 </when>
72 </conditional> 76 </conditional>
73 <param format="text" name="input" type="data" label="Input ontology file"/>
74 <param format="text" name="OPPL" type="data" label="OPPL file"/> 77 <param format="text" name="OPPL" type="data" label="OPPL file"/>
75 <param name="format" type="select" label="Choose ontology output format"> 78 <param name="format" type="select" label="Choose ontology output format">
76 <option value="OWL" selected="true">OWL</option> 79 <option value="OWL" selected="true">OWL</option>
77 <option value="OBO">OBO</option> 80 <option value="OBO">OBO</option>
78 </param> 81 </param>
79 <param name="inferred" type="boolean" value="False" truevalue="AddInferred" falsevalue="Gora_ni" label="Add inferred subsumption axioms to output ontology"/> 82 <param name="inferred" type="boolean" value="False" truevalue="AddInferred" falsevalue="Gora_ni" label="Add inferred subsumption axioms to output ontology"/>
80 <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)" /> 83 <!-- <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)" /> -->
81 <param name="reasoner" type="select" label="Choose reasoner"> 84 <param name="reasoner" type="select" label="Choose reasoner">
82 <option value="Pellet" selected="true">Pellet</option> 85 <option value="Pellet" selected="true">Pellet</option>
83 <option value="HermiT">HermiT</option> 86 <option value="HermiT">HermiT</option>
84 <option value="FaCTPlusPlus">FaCT++</option> 87 <option value="FaCTPlusPlus">FaCT++</option>
85 </param> 88 </param>
130 133
131 If OWL imports are used, all the ontologies (Main one and imported ones) can be merged in a single ontology for the output. 134 If OWL imports are used, all the ontologies (Main one and imported ones) can be merged in a single ontology for the output.
132 135
133 **More information** 136 **More information**
134 137
138 http://miuras.inf.um.es/OPPL-Galaxy/
139
135 http://oppl.sf.net/ 140 http://oppl.sf.net/
136 141
137 http://owlapi.sourceforge.net/ 142 http://owlapi.sourceforge.net/
138 143
139 http://www.w3.org/TR/owl2-manchester-syntax/ 144 http://www.w3.org/TR/owl2-manchester-syntax/
141 http://clarkparsia.com/pellet 146 http://clarkparsia.com/pellet
142 147
143 http://hermit-reasoner.com/ 148 http://hermit-reasoner.com/
144 149
145 http://code.google.com/p/factplusplus/ 150 http://code.google.com/p/factplusplus/
151
152 **Citation**
153
154 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).
146 155
147 **Contact** 156 **Contact**
148 157
149 Please send any request or comment to mikel.egana.aranguren@gmail.com. 158 Please send any request or comment to mikel.egana.aranguren@gmail.com.
150 159