# 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 @@
+
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diff -r 000000000000 -r 5bc82cf5439b NOTICE
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NOTICE Fri May 02 15:36:43 2014 +0200
@@ -0,0 +1,16 @@
+PRIMO-multi-omics toolset & Galaxy wrappers
+===========================================
+
+Tools and wrappers for the 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
\ 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).
+
+
+