| Previous changeset 6:8fa07f40d2eb (2014-08-01) Next changeset 8:97e10319d86f (2015-03-23) |
|
Commit message:
renamed to TermMapper |
|
modified:
LICENSE README.rst |
|
added:
TermMapperTool.jar term_mapper.xml |
|
removed:
Results2O.jar results2o.xml |
| b |
| diff -r 8fa07f40d2eb -r ce9228263148 LICENSE --- a/LICENSE Fri Aug 01 17:21:30 2014 +0200 +++ b/LICENSE Mon Mar 23 21:02:01 2015 +0100 |
| b |
| @@ -1,7 +1,7 @@ Apache License Version 2.0, January 2004 - http://www.apache.org/licenses/ + http://www.apache.org/licenses/ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION |
| b |
| diff -r 8fa07f40d2eb -r ce9228263148 README.rst --- a/README.rst Fri Aug 01 17:21:30 2014 +0200 +++ b/README.rst Mon Mar 23 21:02:01 2015 +0100 |
| b |
| @@ -20,6 +20,7 @@ ============== ====================================================================== Date Changes -------------- ---------------------------------------------------------------------- +August 2014 * improvements release May 2014 * first release via Tool Shed ============== ====================================================================== |
| b |
| diff -r 8fa07f40d2eb -r ce9228263148 Results2O.jar |
| b |
| Binary file Results2O.jar has changed |
| b |
| diff -r 8fa07f40d2eb -r ce9228263148 TermMapperTool.jar |
| b |
| Binary file TermMapperTool.jar has changed |
| b |
| diff -r 8fa07f40d2eb -r ce9228263148 results2o.xml --- a/results2o.xml Fri Aug 01 17:21:30 2014 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,107 +0,0 @@ -<tool name="Results2O" id="results2o1" version="0.0.1"> - <description>use ontology mapping to annotate results (e.g. annotate protein identifications with Gene Ontology[GO] terms)</description> - <!-- - For remote debugging start you listener on port 8000 and use the following as command interpreter: - java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000 - --> - <!-- similar to "join two datasets" tool http://galaxy.wur.nl/galaxy_production/root?tool_id=join1 - but this one is probably having more powerful features like supporting multiple ';' codes in key fields - and the feature in ontologyTermColName(s) supporting direct hierarchy like annotation --> - <command interpreter="java -jar "> - Results2O.jar - -inputFileName $inputFileName - -inputIdColumnName "$inputIdColumnName" - -inputIdPrefix "$inputIdPrefix" - -quantifColumn "$quantifColumn" - - -ontologyMappingFileName $ontologyMappingFileName - -mappingFileIdColName "$mappingFileIdColName" - -mappingIdPrefix "$mappingIdPrefix" - -mappingFileOntologyTermColName "$mappingFileOntologyTermColName" - -removeWhiteSpacesFromOterms $removeWhiteSpacesFromOterms - - -outputFileName $outputFileName - -outputObservationsFileName $outputObservationsFileName - - </command> - - <inputs> - - <param name="inputFileName" type="data" format="tabular,csv" label="Input file (TSV/CSV)" /> - <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)"/> - <param name="inputIdPrefix" type="text" size="50" value="" label="(Optional) Prefix in ID column" - help="Fill in if any prefix is found in the ID column values (e.g. in some - files the value is preceded by a fixed value like for example 'lipidmaps:LMFA00000007' instead of just 'LMFA00000007' - in this - example one would fill in 'lipidmaps:' as prefix)"/> - <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)"/> - - <!-- =================== ONTOLOGY part ============== --> - <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."/> - <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)"/> - <param name="mappingIdPrefix" type="text" size="50" value="" label="(Optional) Prefix in mapping ID column" - help="Fill in if any prefix is found in the ID column values (e.g. in some - files the value is preceded by a fixed value like for example 'lipidmaps:LMFA00000007' instead of just 'LMFA00000007' - in this - example one would fill in 'lipidmaps:' as prefix)"/> - - <param name="mappingFileOntologyTermColName" type="text" size="50" value="" label="Ontology term column name(s)" - 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). - 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 - found it will try the second one, and so forth. "/> - - <param name="removeWhiteSpacesFromOterms" type="boolean" checked="false" - label="Remove white spaces from ontology terms" - help="This could be needed for some ontologies, like the current custom one for Lipidmaps."/> - - </inputs> - <outputs> - #if isinstance( $inputFileName.datatype, $__app__.datatypes_registry.get_datatype_by_extension('tabular').__class__): - <data name="outputFileName" format="tabular" label="${tool.name} on ${on_string}: annotated file " ></data> - #else: - <data name="outputFileName" format="csv" label="${tool.name} on ${on_string}: annotated file " ></data> - #end if - - <data name="outputObservationsFileName" format="tabular" label="${tool.name} on ${on_string}: ontology observations file (TSV)"></data> - </outputs> - <tests> - <!-- find out how to use --> - <test> - </test> - </tests> - <help> - -.. class:: infomark - -This tool is responsible for annotating quantifications result file -with the ontology terms given in a mapping file. This mapping file links the items found in the result file -(e.g. protein identifications coded in common protein coding formats such as UniProt ) -to their respective ontology terms (e.g. GO terms). It enables users to use the cross-reference -information now available in different repositories (like uniprot and KEGG - see for example -http://www.uniprot.org/taxonomy/ or http://www.genome.jp/linkdb/ ) -to map their results to other useful coding schemes such as ontologies for functional annotations. - -As an example for transcripts and proteins, users can check http://www.uniprot.org/taxonomy/ to -see if their organism has been mapped to GO terms by Uniprot. For example the link -http://www.uniprot.org/uniprot/?query=taxonomy:2850 will show the Uniprot repository and cross-references -for the taxonomy 2850. -When the organism being studied is not available, then other strategies -could be tried (like Blast2GO for example). - - -Despite the specific examples above, this class is generic and can be used to map any -results file to an Ontology according to a given mapping file. One example would be mapping metabolomics -identifications to the CheBI ontology. - - ------ - -**Output** - -This method will read in the given input file and for each line it will add a new column -containing the Ontology terms found for the ID in that line. So the output file is the same as the -input file + extra Ontology terms column (separated by ; ). - -A second summarized "ontology observations" file is also generated which can be used for visualizing the results -in an ontology viewer (e.g. see OntologyAndObservationsViewer). - - </help> -</tool> |
| b |
| diff -r 8fa07f40d2eb -r ce9228263148 term_mapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/term_mapper.xml Mon Mar 23 21:02:01 2015 +0100 |
| [ |
| b'@@ -0,0 +1,207 @@\n+<tool name="TermMapperTool" id="TermMapperTool1" version="0.0.2">\r\n+\t<description>use cross-reference lookup tables to annotate results</description>\r\n+\t<!-- \r\n+\t For remote debugging start you listener on port 8000 and use the following as command interpreter:\r\n+\t java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000 \r\n+\t -->\r\n+\t <!-- similar to "join two datasets" tool http://galaxy.wur.nl/galaxy_production/root?tool_id=join1 \r\n+\t but this one is probably having more powerful features like supporting multiple \';\' codes in key fields \r\n+\t and the feature in termColName(s) supporting direct hierarchy like annotation -->\r\n+\t<command interpreter="java -jar ">\r\n+\t TermMapperTool.jar \r\n+\t\t-inputFileName $inputFileName\r\n+ \t\t-inputIdColumnName "$inputIdColumnName"\r\n+ \t\t#if $inputIdCol.inputIdHasPrefix == True\r\n+ \t\t\t-inputIdPrefix "$inputIdCol.inputIdPrefix" \r\n+ \t\t#end if\r\n+\t\t\r\n+\t\t-mappingFileName $mappingFileName\r\n+\t\t-mappingFileIdColName "$mappingFileIdColName" \r\n+\t\t\r\n+\t\t#if $mappingIdCol.mappingIdHasPrefix == True\r\n+ \t\t\t-mappingIdPrefix "$mappingIdCol.mappingIdPrefix" \r\n+ \t\t#end if\r\n+\t\t\r\n+\t\t-mappingFileTermColName "$mappingFileTermColName"\r\n+\r\n+\t\t-outputFileName $outputFileName\r\n+\t\t\r\n+\t\t#if $genObservations.genObservationsFile == True\r\n+\t\t\t-outputObservationsFileName $outputObservationsFileName\r\n+ \t-quantifColumn "$genObservations.quantifColumn" \r\n+ \t\t#end if\r\n+\t\t\r\n+\t\t-mappedTermsColName $mappedTermsColName\r\n+ \t \r\n+\t</command>\r\n+\t\r\n+\t<inputs>\r\n+\t \t\r\n+ \t\t<param name="inputFileName" type="data" format="tabular,csv" label="Target file (TSV/CSV)" />\r\n+ \t\t\r\n+ \t\t<param name="inputIdColumnName" type="text" size="50" value="" label="ID column name" \r\n+ \t\t\thelp="Name of the column containing the identification codes (in the given input file)"/>\r\n+ \t\t\r\n+ \t\t<conditional name="inputIdCol">\r\n+ \t\t<param name="inputIdHasPrefix" type="boolean" truevalue="Yes" falsevalue="No" checked="false" \r\n+ \t\t\tlabel="ID values have a prefix"/>\r\n+ \t\t<when value="Yes">\r\n+ \t\t\t\t<param name="inputIdPrefix" type="text" size="50" value="" label="Prefix in ID column" \r\n+ \t\t\t\t\thelp="Fill in if any prefix is found in the ID column values (e.g. in some \r\n+\t\t\t\t\t\t files the value is preceded by a fixed value like for example \'lipidmaps:LMFA00000007\' instead of just \'LMFA00000007\' - in this \r\n+\t\t\t\t\t\t example one would fill in \'lipidmaps:\' as prefix)"/>\r\n+\t\t\t</when>\r\n+\t\t\t<when value="No">\r\n+\t\t\t</when>\r\n+\t\t</conditional>\r\n+ \t\t\r\n+ \t\t<!-- =================== cross-reference part ============== -->\r\n+ \t\t<param name="mappingFileName" type="data" format="tabular,csv" label="Lookup table (TSV/CSV)" help="Simple mapping file between the coding scheme used to another scheme"/>\r\n+ \t\t<param name="mappingFileIdColName" type="text" size="50" value="" label="ID column name (in lookup table)" help="Name of the ID column for the lookup"/>\r\n+ \t\t\r\n+ \t\t<conditional name="mappingIdCol">\r\n+ \t\t<param name="mappingIdHasPrefix" type="boolean" truevalue="Yes" falsevalue="No" checked="false" \r\n+ \t\t\tlabel="ID values have a prefix"/>\r\n+ \t\t<when value="Yes">\r\n+ \t\t\t\t<param name="mappingIdPrefix" type="text" size="50" value="" label="Prefix in ID column" \r\n+ \t\t\t\t\thelp="Fill in if any prefix is found in the ID column values (e.g. in some \r\n+\t\t\t\t\t\tfiles the value is preceded by a fixed value like for example \'lipidmaps:LMFA00000007\' instead of just \'LMFA00000007\' - in this \r\n+\t\t\t\t\t \texample one would fill in \'lipidmaps:\' as prefix)"/>\r\n+\t\t\t</when>\r\n+\t\t\t<when value="No">\r\n+\t\t\t</when>\r\n+\t\t</conditional>\r\n+\r\n+ \t\t<param name="mappingFileTermColName" type="text" size="50" value="" label="Term column name(s) or number(s)" \r\n+ \t\t help="Name(s) or number(s) of the column(s) containing the term(s) in the lookup table (and which will be transfered to the target file based on ID match in \'ID column name\'). \r\n+ \t\t For using multiple term column names, set'..b'lues (in the given input file)"/>\r\n+ \t\t</when>\r\n+ \t\t<when value="No">\r\n+\t\t\t</when>\r\n+\t\t</conditional>\r\n+ \t\r\n+\t</inputs>\r\n+\t<outputs>\r\n+\t\t#if isinstance( $inputFileName.datatype, $__app__.datatypes_registry.get_datatype_by_extension(\'tabular\').__class__):\r\n+\t\t\t<data name="outputFileName" format="tabular" label="${tool.name} on ${on_string}: annotated file " ></data>\r\n+\t\t#else:\r\n+ \t\t<data name="outputFileName" format="csv" label="${tool.name} on ${on_string}: annotated file " ></data>\r\n+ \t\t#end if\r\n+\t \r\n+\t <data name="outputObservationsFileName" format="tabular" label="${tool.name} on ${on_string}: term observations file (TSV)">\r\n+\t \t<!-- If the expression is false, the file is not created -->\r\n+\t \t<filter>( genObservations.genObservationsFile == True )</filter>\r\n+\t </data>\r\n+\t</outputs>\r\n+\t<tests>\r\n+\t <!-- find out how to use -->\r\n+\t <test>\r\n+\t </test>\r\n+\t</tests>\r\n+ <help>\r\n+ \r\n+.. class:: infomark\r\n+\r\n+ \r\n+This tool is responsible for annotating the given target file \r\n+with the terms given in a lookup table. This lookup table maps the items found in the target file\r\n+(e.g. protein identifications coded in common protein coding formats such as UniProt )\r\n+to their respective terms (e.g. GO terms). It enables users to use the cross-reference \r\n+information now available from different repositories (like uniprot and KEGG - see for example\r\n+http://www.uniprot.org/taxonomy/ or http://www.genome.jp/linkdb/ )\r\n+to map their data to other useful coding schemes or to ontologies and functional annotations. \r\n+\r\n+.. class:: infomark\r\n+\r\n+**NB:** Currently the tool will do "smart parsing" of hierarchy based fields in the target file ID column. \r\n+ This means that if the colum contains a ".", the trailing part of the ID after the "." is ignored if the full\r\n+ ID does not get a match in the lookup table while the part before the "." does. \r\n+ \r\n+.. class:: infomark\r\n+\r\n+Examples of usage:\r\n+\r\n+ annotate protein identifications with Gene Ontology[GO] terms\r\n+ \r\n+ annotate metabolite CAS identifications with chebi codes\r\n+ \r\n+ add KEGG gene codes to a file containing UNIPROT codes\r\n+ \r\n+ add KEGG compound codes to a file containing chebi codes\r\n+ \r\n+ etc\r\n+ \r\n+As an example for transcripts and proteins, users can check http://www.uniprot.org/taxonomy/ to\r\n+see if their organism has been mapped to GO terms by Uniprot. For example the link \r\n+http://www.uniprot.org/uniprot/?query=taxonomy:2850 will show the Uniprot repository and cross-references\r\n+for the taxonomy 2850.\r\n+When the organism being studied is not available, then other strategies \r\n+could be tried (like Blast2GO for example).\r\n+\r\n+Despite the specific examples above, this class is generic and can be used to map any \r\n+values to new terms according to a given lookup table. \r\n+ \r\n+.. class:: infomark\r\n+\r\n+*Omics cross-reference resources on the web:*\r\n+\r\n+LinkDB: http://www.genome.jp/linkdb/\r\n+\r\n+*Ready to use metabolomics links:*\r\n+\r\n+http://rest.genome.jp/link/compound/chebi\r\n+\r\n+http://rest.genome.jp/link/compound/lipidmaps\r\n+\r\n+http://rest.genome.jp/link/compound/lipidbank\r\n+\r\n+http://rest.genome.jp/link/compound/hmdb\r\n+\r\n+\r\n+*Ready to use proteomics links:*\r\n+\r\n+http://rest.genome.jp/link/uniprot/pti (Phaeodactylum Tri.)\r\n+\r\n+http://rest.genome.jp/link/uniprot/hsa (Homo Sapiens)\r\n+\r\n+(for organism code list see: )\r\n+\r\n+\r\n+Uniprot to GO\r\n+\r\n+http://www.uniprot.org/taxonomy/\r\n+\r\n+\r\n+-----\r\n+\r\n+**Output**\r\n+\r\n+This method will read in the given input file and for each line it will add a new column \r\n+containing the terms found for the ID in that line. So the output file is the same as the \r\n+input file + extra terms column (separated by ; ).\r\n+\r\n+-----\r\n+\r\n+**Link to ontology viewer**\r\n+\r\n+A second summarized "terms observations" file can also be generated.\r\n+In case the terms are ontology terms, this file can be used for visualizing the results\r\n+in the ontology viewer "OntologyAndObservationsViewer". \r\n+\r\n+ </help>\r\n+</tool>\r\n' |