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comparison OPPL/oppl.xml @ 9:14bfd77f8520

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Interface improved (Imports first) and proper handling of import/merge options added
author Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Tue, 18 Oct 2011 10:30:16 +0200
parents 40adbcb2a7cc
children 3f31c0eb7539
comparison
equal deleted inserted replaced
8:40adbcb2a7cc 9:14bfd77f8520
1 <tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.5"> 1 <tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.6">
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! --> 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 --> 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 -->
6 <!-- More info on the stderr issue: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr --> 6 <!-- More info on the stderr issue: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr -->
44 #end if 44 #end if
45 #end if 45 #end if
46 </command>--> 46 </command>-->
47 47
48 <inputs> 48 <inputs>
49 <param format="text" name="input" type="data" label="Input ontology file"/>
50 <param format="text" name="OPPL" type="data" label="OPPL file"/>
51 <conditional name="import_opts"> 49 <conditional name="import_opts">
52 <param name="imports_select" type="boolean" value="False" truevalue="imports_yes" falsevalue="imports_no" label="Tick the box if the loaded ontology includes OWL imports"/> 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"/>
53 51
54 <!-- EXPERIMENTS AND HOUSE KEEPING--> 52 <!-- EXPERIMENTS AND HOUSE KEEPING-->
55 <!--<when value="imports_no"/> --> 53 <!--<when value="imports_no"/> -->
56 <!--<when value="imports_no"> 54 <!--<when value="imports_no">
57 <param type="hidden" name="merged" value="no_merge"/> 55 <param type="hidden" name="merged" value="no_merge"/>
70 </conditional>--> 68 </conditional>-->
71 <!--<param format="text" name="merged" type="data" label="OWL "/>--> 69 <!--<param format="text" name="merged" type="data" label="OWL "/>-->
72 70
73 </when> 71 </when>
74 </conditional> 72 </conditional>
73 <param format="text" name="input" type="data" label="Input ontology file"/>
74 <param format="text" name="OPPL" type="data" label="OPPL file"/>
75 <param name="format" type="select" label="Choose ontology output format"> 75 <param name="format" type="select" label="Choose ontology output format">
76 <option value="OWL" selected="true">OWL</option> 76 <option value="OWL" selected="true">OWL</option>
77 <option value="OBO">OBO</option> 77 <option value="OBO">OBO</option>
78 </param> 78 </param>
79 <param name="inferred" type="boolean" value="False" truevalue="AddInferred" falsevalue="Gora_ni" label="Add inferred subsumption axioms to output ontology"/> 79 <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 the ontologies, type an URI for the new ontology (Leave NoMerge for not merging)" /> 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)" />
81 <param name="reasoner" type="select" label="Choose reasoner"> 81 <param name="reasoner" type="select" label="Choose reasoner">
82 <option value="Pellet" selected="true">Pellet</option> 82 <option value="Pellet" selected="true">Pellet</option>
83 <option value="HermiT">HermiT</option> 83 <option value="HermiT">HermiT</option>
84 <option value="FaCTPlusPlus">FaCT++</option> 84 <option value="FaCTPlusPlus">FaCT++</option>
85 </param> 85 </param>
141 http://clarkparsia.com/pellet 141 http://clarkparsia.com/pellet
142 142
143 http://hermit-reasoner.com/ 143 http://hermit-reasoner.com/
144 144
145 http://code.google.com/p/factplusplus/ 145 http://code.google.com/p/factplusplus/
146
147 http://code.google.com/p/oboformat/
148 146
149 **Contact** 147 **Contact**
150 148
151 Please send any request or comment to mikel.egana.aranguren@gmail.com. 149 Please send any request or comment to mikel.egana.aranguren@gmail.com.
152 150