annotate results2o.xml @ 6:8fa07f40d2eb

added more parameters/options and made Ontology observations file optional;
author pieter.lukasse@wur.nl
date Fri, 01 Aug 2014 17:21:30 +0200
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1 <tool name="Results2O" id="results2o1" version="0.0.1">
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2 <description>use ontology mapping to annotate results (e.g. annotate protein identifications with Gene Ontology[GO] terms)</description>
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3 <!--
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4 For remote debugging start you listener on port 8000 and use the following as command interpreter:
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5 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000
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6 -->
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7 <!-- similar to "join two datasets" tool http://galaxy.wur.nl/galaxy_production/root?tool_id=join1
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8 but this one is probably having more powerful features like supporting multiple ';' codes in key fields
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9 and the feature in ontologyTermColName(s) supporting direct hierarchy like annotation -->
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10 <command interpreter="java -jar ">
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11 Results2O.jar
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12 -inputFileName $inputFileName
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13 -inputIdColumnName "$inputIdColumnName"
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14 -inputIdPrefix "$inputIdPrefix"
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15 -quantifColumn "$quantifColumn"
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16
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17 -ontologyMappingFileName $ontologyMappingFileName
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18 -mappingFileIdColName "$mappingFileIdColName"
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19 -mappingIdPrefix "$mappingIdPrefix"
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20 -mappingFileOntologyTermColName "$mappingFileOntologyTermColName"
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21 -removeWhiteSpacesFromOterms $removeWhiteSpacesFromOterms
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22
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23 -outputFileName $outputFileName
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24 -outputObservationsFileName $outputObservationsFileName
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25
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26 </command>
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27
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28 <inputs>
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29
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30 <param name="inputFileName" type="data" format="tabular,csv" label="Input file (TSV/CSV)" />
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31 <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)"/>
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32 <param name="inputIdPrefix" type="text" size="50" value="" label="(Optional) Prefix in ID column"
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33 help="Fill in if any prefix is found in the ID column values (e.g. in some
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34 files the value is preceded by a fixed value like for example 'lipidmaps:LMFA00000007' instead of just 'LMFA00000007' - in this
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35 example one would fill in 'lipidmaps:' as prefix)"/>
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36 <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)"/>
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37
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38 <!-- =================== ONTOLOGY part ============== -->
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39 <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."/>
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40 <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)"/>
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41 <param name="mappingIdPrefix" type="text" size="50" value="" label="(Optional) Prefix in mapping ID column"
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42 help="Fill in if any prefix is found in the ID column values (e.g. in some
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43 files the value is preceded by a fixed value like for example 'lipidmaps:LMFA00000007' instead of just 'LMFA00000007' - in this
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44 example one would fill in 'lipidmaps:' as prefix)"/>
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45
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46 <param name="mappingFileOntologyTermColName" type="text" size="50" value="" label="Ontology term column name(s)"
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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).
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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
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49 found it will try the second one, and so forth. "/>
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50
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51 <param name="removeWhiteSpacesFromOterms" type="boolean" checked="false"
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52 label="Remove white spaces from ontology terms"
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53 help="This could be needed for some ontologies, like the current custom one for Lipidmaps."/>
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54
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55 </inputs>
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56 <outputs>
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57 #if isinstance( $inputFileName.datatype, $__app__.datatypes_registry.get_datatype_by_extension('tabular').__class__):
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58 <data name="outputFileName" format="tabular" label="${tool.name} on ${on_string}: annotated file " ></data>
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59 #else:
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60 <data name="outputFileName" format="csv" label="${tool.name} on ${on_string}: annotated file " ></data>
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61 #end if
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62
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63 <data name="outputObservationsFileName" format="tabular" label="${tool.name} on ${on_string}: ontology observations file (TSV)"></data>
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64 </outputs>
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65 <tests>
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66 <!-- find out how to use -->
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67 <test>
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68 </test>
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69 </tests>
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70 <help>
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71
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72 .. class:: infomark
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73
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74 This tool is responsible for annotating quantifications result file
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75 with the ontology terms given in a mapping file. This mapping file links the items found in the result file
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76 (e.g. protein identifications coded in common protein coding formats such as UniProt )
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77 to their respective ontology terms (e.g. GO terms). It enables users to use the cross-reference
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78 information now available in different repositories (like uniprot and KEGG - see for example
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79 http://www.uniprot.org/taxonomy/ or http://www.genome.jp/linkdb/ )
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80 to map their results to other useful coding schemes such as ontologies for functional annotations.
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81
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82 As an example for transcripts and proteins, users can check http://www.uniprot.org/taxonomy/ to
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83 see if their organism has been mapped to GO terms by Uniprot. For example the link
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84 http://www.uniprot.org/uniprot/?query=taxonomy:2850 will show the Uniprot repository and cross-references
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85 for the taxonomy 2850.
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86 When the organism being studied is not available, then other strategies
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87 could be tried (like Blast2GO for example).
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88
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89
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90 Despite the specific examples above, this class is generic and can be used to map any
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91 results file to an Ontology according to a given mapping file. One example would be mapping metabolomics
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92 identifications to the CheBI ontology.
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93
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94
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95 -----
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96
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97 **Output**
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98
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99 This method will read in the given input file and for each line it will add a new column
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100 containing the Ontology terms found for the ID in that line. So the output file is the same as the
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101 input file + extra Ontology terms column (separated by ; ).
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102
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103 A second summarized "ontology observations" file is also generated which can be used for visualizing the results
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104 in an ontology viewer (e.g. see OntologyAndObservationsViewer).
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105
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106 </help>
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107 </tool>