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comparison results2o.xml @ 5:eb0b7889dd08

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added more parameters/options and made Ontology observations file optional;
author pieter.lukasse@wur.nl
date Fri, 01 Aug 2014 17:20:02 +0200
parents 5bc82cf5439b
children
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4:b868e946247a 5:eb0b7889dd08
2 <description>use ontology mapping to annotate results (e.g. annotate protein identifications with Gene Ontology[GO] terms)</description> 2 <description>use ontology mapping to annotate results (e.g. annotate protein identifications with Gene Ontology[GO] terms)</description>
3 <!-- 3 <!--
4 For remote debugging start you listener on port 8000 and use the following as command interpreter: 4 For remote debugging start you listener on port 8000 and use the following as command interpreter:
5 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000 5 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000
6 --> 6 -->
7 <!-- similar to "join two datasets" tool http://galaxy.wur.nl/galaxy_production/root?tool_id=join1
8 but this one is probably having more powerful features like supporting multiple ';' codes in key fields
9 and the feature in ontologyTermColName(s) supporting direct hierarchy like annotation -->
7 <command interpreter="java -jar "> 10 <command interpreter="java -jar ">
8 Results2O.jar 11 Results2O.jar
9 -inputFileName $inputFileName 12 -inputFileName $inputFileName
10 -inputIdColumnName "$inputIdColumnName" 13 -inputIdColumnName "$inputIdColumnName"
11 -inputIdPrefix "$inputIdPrefix" 14 -inputIdPrefix "$inputIdPrefix"
13 16
14 -ontologyMappingFileName $ontologyMappingFileName 17 -ontologyMappingFileName $ontologyMappingFileName
15 -mappingFileIdColName "$mappingFileIdColName" 18 -mappingFileIdColName "$mappingFileIdColName"
16 -mappingIdPrefix "$mappingIdPrefix" 19 -mappingIdPrefix "$mappingIdPrefix"
17 -mappingFileOntologyTermColName "$mappingFileOntologyTermColName" 20 -mappingFileOntologyTermColName "$mappingFileOntologyTermColName"
21 -removeWhiteSpacesFromOterms $removeWhiteSpacesFromOterms
18 22
19 -outputFileName $outputFileName 23 -outputFileName $outputFileName
20 -outputObservationsFileName $outputObservationsFileName 24 -outputObservationsFileName $outputObservationsFileName
21 25
22 </command> 26 </command>
37 <param name="mappingIdPrefix" type="text" size="50" value="" label="(Optional) Prefix in mapping ID column" 41 <param name="mappingIdPrefix" type="text" size="50" value="" label="(Optional) Prefix in mapping ID column"
38 help="Fill in if any prefix is found in the ID column values (e.g. in some 42 help="Fill in if any prefix is found in the ID column values (e.g. in some
39 files the value is preceded by a fixed value like for example 'lipidmaps:LMFA00000007' instead of just 'LMFA00000007' - in this 43 files the value is preceded by a fixed value like for example 'lipidmaps:LMFA00000007' instead of just 'LMFA00000007' - in this
40 example one would fill in 'lipidmaps:' as prefix)"/> 44 example one would fill in 'lipidmaps:' as prefix)"/>
41 45
42 <param name="mappingFileOntologyTermColName" type="text" size="50" value="" label="Ontology term column name" help="Name of the column containing the ontology terms in the ontology mapping file (and which will be transfered to the input file)"/> 46 <param name="mappingFileOntologyTermColName" type="text" size="50" value="" label="Ontology term column name(s)"
47 help="Name(s) of the column(s) containing the ontology terms in the ontology mapping file (and which will be transfered to the input file).
48 For using multiple columns, set the names separated by comma (,). If multiple columns are specified, the algorithm will look for an annotation in the first one, if none
49 found it will try the second one, and so forth. "/>
43 50
51 <param name="removeWhiteSpacesFromOterms" type="boolean" checked="false"
52 label="Remove white spaces from ontology terms"
53 help="This could be needed for some ontologies, like the current custom one for Lipidmaps."/>
44 54
45 </inputs> 55 </inputs>
46 <outputs> 56 <outputs>
47 #if isinstance( $inputFileName.datatype, $__app__.datatypes_registry.get_datatype_by_extension('tabular').__class__): 57 #if isinstance( $inputFileName.datatype, $__app__.datatypes_registry.get_datatype_by_extension('tabular').__class__):
48 <data name="outputFileName" format="tabular" label="${tool.name} on ${on_string}: annotated file " ></data> 58 <data name="outputFileName" format="tabular" label="${tool.name} on ${on_string}: annotated file " ></data>