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author pieter.lukasse@wur.nl
date Fri, 02 May 2014 15:36:43 +0200
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children e2850ead6f59
files LICENSE NOTICE README.rst Results2O.jar datatypes_conf.xml results2o.xml
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--- /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
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--- /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
Binary file Results2O.jar has changed
--- /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 @@
+<?xml version="1.0"?>
+<datatypes>
+  <datatype_files>
+  </datatype_files>
+  <registration display_path="display_applications">
+        <datatype extension="obo" type="galaxy.datatypes.data:Text" display_in_upload="true" />
+  </registration>
+</datatypes>
\ No newline at end of file
--- /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 @@
+<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 
+	    -->
+	<command interpreter="java -jar ">
+	    Results2O.jar 
+		-inputFileName $inputFileName
+ 		-inputIdColumnName "$inputIdColumnName"
+ 		-inputIdPrefix "$inputIdPrefix"  
+		-quantifColumn "$quantifColumn" 
+		
+		-ontologyMappingFileName $ontologyMappingFileName
+		-mappingFileIdColName "$mappingFileIdColName"  
+		-mappingIdPrefix "$mappingIdPrefix"  
+		-mappingFileOntologyTermColName "$mappingFileOntologyTermColName"
+		
+		-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" help="Name of the column containing the ontology terms in the ontology mapping file (and which will be transfered to the input file)"/>
+  		
+     	
+	</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>