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comparison results2o.xml @ 0:5bc82cf5439b

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author pieter.lukasse@wur.nl
date Fri, 02 May 2014 15:36:43 +0200
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1 <tool name="Results2O" id="results2o1" version="0.0.1">
2 <description>use ontology mapping to annotate results (e.g. annotate protein identifications with Gene Ontology[GO] terms)</description>
3 <!--
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
6 -->
7 <command interpreter="java -jar ">
8 Results2O.jar
9 -inputFileName $inputFileName
10 -inputIdColumnName "$inputIdColumnName"
11 -inputIdPrefix "$inputIdPrefix"
12 -quantifColumn "$quantifColumn"
13
14 -ontologyMappingFileName $ontologyMappingFileName
15 -mappingFileIdColName "$mappingFileIdColName"
16 -mappingIdPrefix "$mappingIdPrefix"
17 -mappingFileOntologyTermColName "$mappingFileOntologyTermColName"
18
19 -outputFileName $outputFileName
20 -outputObservationsFileName $outputObservationsFileName
21
22 </command>
23
24 <inputs>
25
26 <param name="inputFileName" type="data" format="tabular,csv" label="Input file (TSV/CSV)" />
27 <param name="inputIdColumnName" type="text" size="50" value="" label="ID column name" help="Name of the column containing the identification codes (in the given input file)"/>
28 <param name="inputIdPrefix" type="text" size="50" value="" label="(Optional) Prefix in ID column"
29 help="Fill in if any prefix is found in the ID column values (e.g. in some
30 files the value is preceded by a fixed value like for example 'lipidmaps:LMFA00000007' instead of just 'LMFA00000007' - in this
31 example one would fill in 'lipidmaps:' as prefix)"/>
32 <param name="quantifColumn" type="text" size="50" value="" label="(Optional) Values column name" help="Name of the column containing the quantification values (in the given input file)"/>
33
34 <!-- =================== ONTOLOGY part ============== -->
35 <param name="ontologyMappingFileName" type="data" format="obo" label="ID to Ontology mapping file (TSV/CSV)" help="Simple file linking the coding scheme used for the identifications in the given input file to one or more ontology terms."/>
36 <param name="mappingFileIdColName" type="text" size="50" value="" label="ID column name (in ontology mapping file)" help="Name of the column containing the identification codes (which will in fact link the input file records to the ontology records)"/>
37 <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
39 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)"/>
41
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)"/>
43
44
45 </inputs>
46 <outputs>
47 #if isinstance( $inputFileName.datatype, $__app__.datatypes_registry.get_datatype_by_extension('tabular').__class__):
48 <data name="outputFileName" format="tabular" label="${tool.name} on ${on_string}: annotated file " ></data>
49 #else:
50 <data name="outputFileName" format="csv" label="${tool.name} on ${on_string}: annotated file " ></data>
51 #end if
52
53 <data name="outputObservationsFileName" format="tabular" label="${tool.name} on ${on_string}: ontology observations file (TSV)"></data>
54 </outputs>
55 <tests>
56 <!-- find out how to use -->
57 <test>
58 </test>
59 </tests>
60 <help>
61
62 .. class:: infomark
63
64 This tool is responsible for annotating quantifications result file
65 with the ontology terms given in a mapping file. This mapping file links the items found in the result file
66 (e.g. protein identifications coded in common protein coding formats such as UniProt )
67 to their respective ontology terms (e.g. GO terms). It enables users to use the cross-reference
68 information now available in different repositories (like uniprot and KEGG - see for example
69 http://www.uniprot.org/taxonomy/ or http://www.genome.jp/linkdb/ )
70 to map their results to other useful coding schemes such as ontologies for functional annotations.
71
72 As an example for transcripts and proteins, users can check http://www.uniprot.org/taxonomy/ to
73 see if their organism has been mapped to GO terms by Uniprot. For example the link
74 http://www.uniprot.org/uniprot/?query=taxonomy:2850 will show the Uniprot repository and cross-references
75 for the taxonomy 2850.
76 When the organism being studied is not available, then other strategies
77 could be tried (like Blast2GO for example).
78
79
80 Despite the specific examples above, this class is generic and can be used to map any
81 results file to an Ontology according to a given mapping file. One example would be mapping metabolomics
82 identifications to the CheBI ontology.
83
84
85 -----
86
87 **Output**
88
89 This method will read in the given input file and for each line it will add a new column
90 containing the Ontology terms found for the ID in that line. So the output file is the same as the
91 input file + extra Ontology terms column (separated by ; ).
92
93 A second summarized "ontology observations" file is also generated which can be used for visualizing the results
94 in an ontology viewer (e.g. see OntologyAndObservationsViewer).
95
96 </help>
97 </tool>