# HG changeset patch # User pieter.lukasse@wur.nl # Date 1399037803 -7200 # Node ID 5bc82cf5439bc925d453271aa03d3bedacda7cd7 Initial commit diff -r 000000000000 -r 5bc82cf5439b LICENSE --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LICENSE Fri May 02 15:36:43 2014 +0200 @@ -0,0 +1,202 @@ + + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. 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All rights reserved. See the license text below. + +Galaxy wrappers and installation are available from the Galaxy Tool Shed at: +http://toolshed.g2.bx.psu.edu/view/pieterlukasse/primo_multiomics \ No newline at end of file diff -r 000000000000 -r 5bc82cf5439b README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Fri May 02 15:36:43 2014 +0200 @@ -0,0 +1,65 @@ +PRIMO-multi-omics toolset & Galaxy wrappers +=========================================== + +Multi-omics module of Plant Research International's Mass Spectrometry (PRIMO) toolsuite. +This toolset consists of custom tools to facilitate post processing +and integration of different omics datasets. + +Can be used in combination with PRIMS-proteomics (prims_proteomics package) and +with PRIMS-metabolomics (prims_metabolomics package). + +Copyright 2010-2014 by Pieter Lukasse, Plant Research International (PRI), +Wageningen, The Netherlands. All rights reserved. See the license text below. + +Galaxy wrappers and installation are available from the Galaxy Tool Shed at: +http://toolshed.g2.bx.psu.edu/view/pieterlukasse/primo_multiomics + +History +======= + +============== ====================================================================== +Date Changes +-------------- ---------------------------------------------------------------------- +May 2014 * first release via Tool Shed +============== ====================================================================== + +Tool Versioning +=============== + +PRIMO tools will have versions of the form X.Y.Z. Versions +differing only after the second decimal should be completely +compatible with each other. Breaking changes should result in an +increment of the number before and/or after the first decimal. All +tools of version less than 1.0.0 should be considered beta. + + +Bug Reports & other questions +============================= + +For the time being issues can be reported via the contact form at: +http://www.wageningenur.nl/en/Persons/PNJ-Pieter-Lukasse.htm + +Developers, Contributions & Collaborations +========================================== + +If you wish to join forces and collaborate on some of the +tools do not hesitate to contact Pieter Lukasse via the contact form above. + + +License (Apache, Version 2.0) +============================= + +Copyright 2013 Pieter Lukasse, Plant Research International (PRI). + +Licensed under the Apache License, Version 2.0 (the "License"); +you may not use this software except in compliance with the License. +You may obtain a copy of the License at + +http://www.apache.org/licenses/LICENSE-2.0 + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. + \ No newline at end of file diff -r 000000000000 -r 5bc82cf5439b Results2O.jar Binary file Results2O.jar has changed diff -r 000000000000 -r 5bc82cf5439b datatypes_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes_conf.xml Fri May 02 15:36:43 2014 +0200 @@ -0,0 +1,8 @@ + + + + + + + + \ No newline at end of file diff -r 000000000000 -r 5bc82cf5439b results2o.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/results2o.xml Fri May 02 15:36:43 2014 +0200 @@ -0,0 +1,97 @@ + + use ontology mapping to annotate results (e.g. annotate protein identifications with Gene Ontology[GO] terms) + + + Results2O.jar + -inputFileName $inputFileName + -inputIdColumnName "$inputIdColumnName" + -inputIdPrefix "$inputIdPrefix" + -quantifColumn "$quantifColumn" + + -ontologyMappingFileName $ontologyMappingFileName + -mappingFileIdColName "$mappingFileIdColName" + -mappingIdPrefix "$mappingIdPrefix" + -mappingFileOntologyTermColName "$mappingFileOntologyTermColName" + + -outputFileName $outputFileName + -outputObservationsFileName $outputObservationsFileName + + + + + + + + + + + + + + + + + + + + + #if isinstance( $inputFileName.datatype, $__app__.datatypes_registry.get_datatype_by_extension('tabular').__class__): + + #else: + + #end if + + + + + + + + + + +.. 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). + + +