changeset 0:a13b9fcbc0ee

Push to main toolshed
author pieter.lukasse@wur.nl
date Wed, 08 Jan 2014 12:44:02 +0100
parents
children 492f92862ab5
files CytoExport.jar LICENSE NOTICE README.rst cytoexport.xml datatypes_conf.xml static/images/tood.png
diffstat 7 files changed, 385 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NOTICE	Wed Jan 08 12:44:02 2014 +0100
@@ -0,0 +1,16 @@
+PRIMV-visualization toolset & Galaxy wrappers
+==========================================
+ 
+Tools and wrappers for the PRIMV visualization toolset.
+Suite of tools that generate multi-purpose views to assist in the visualization
+and interpretation of large and complex datasets. 
+
+Can be used a.o. in combination with PRIMS-MASSCOMB (prims_masscomb package) and
+PRIMS-proteomics (prims_proteomics package).
+
+Copyright 2010-2013 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/primv_visualization
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Wed Jan 08 12:44:02 2014 +0100
@@ -0,0 +1,67 @@
+PRIMV-visualization toolset & Galaxy wrappers
+=============================================
+
+Visualization module of Plant Research International's Multi-purpose Views (PRIMV) toolsuite. 
+
+This toolset consists of tools that generate multi-purpose views to assist in the visualization
+and interpretation of large and complex datasets. 
+
+Can be used a.o. in combination with PRIMS-MASSCOMB (prims_masscomb package) and
+PRIMS-proteomics (prims_proteomics package).
+
+Copyright 2010-2013 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/primv_visualization
+
+History
+=======
+
+============== ========================================================================
+Date            Changes
+-------------- ------------------------------------------------------------------------
+January 2014   -first release via Tool Shed
+November 2013  -cytoexport tool used internally at PRI 
+October 2012   -first tool for generating visually rich Cytoscape networks (cytoexport)
+============== ========================================================================
+
+Tool Versioning
+===============
+
+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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cytoexport.xml	Wed Jan 08 12:44:02 2014 +0100
@@ -0,0 +1,90 @@
+<tool name="CytoExport" id="cytoexport1" version="1.0.2">
+	<description>Exports CSV files to visually rich Cytoscape networks</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 
+	                    //////////////////////////
+	   This part is a WORKAROUND for the Cytoscape X11 dependency problem, even when running 'headless' (assuming Xfvb is installed/enabled):
+	       export DISPLAY=:995;
+	       ...TODO -> this is linux specific...follow issue fix on Cytoscape...perhaps we can add try/catch in python here (see http://www.unix.com/shell-programming-scripting/107334-how-use-catch-try-final-bash-script.html)
+	       ...check how other tools do this  
+	    -->
+	<command interpreter="export DISPLAY=:995; java -jar ">
+	    CytoExport.jar 
+	    -networkName "$csvDataFile.metadata.base_name"
+	    -csvDataFile $csvDataFile
+	    -configInputMode $configInputMode.type
+	    -vizMapPropsFile $configInputMode.vizMapPropsFile
+	    -vizStyleName $vizStyleName
+	    -alternativeTableImportJsonFile $configInputMode.alternativeTableImportJsonFile
+	    -cysOutFile $cysOutFile 
+	    -htmlReportFile $htmlReportFile 
+	    -picturesPath $htmlReportFile.files_path
+	    -logFile $logFile
+	</command>
+	
+	<inputs>
+     	<!-- TODO make possible to have multiple networks in same .cys 
+     	<param name="networkName" type="text" size="30" value="" label="Network name" />-->
+   		<param name="csvDataFile" type="data" format="csv,tabular" label="Network data file" />
+   		
+   		
+   		<conditional name="configInputMode">
+		    <param name="type" type="select" label="Configuration input">
+		      <option value="customConfig" selected="true">Use custom configuration files</option>
+		      <option value="existingTemplate">Use one of the existing templates</option>
+		    </param>
+		    <when value="existingTemplate">
+			    <param name="alternativeTableImportJsonFile" type="select" label="Select import template">
+			      <option value="/com/pri/cytoexport/resources/simple_xtandem_out.json" >Config for X!Tandem .csv</option>
+			      <option value="/com/pri/cytoexport/resources/quantifere_network_config.json" >Config for Quantifere .csv (force-directed layout)</option>
+			      <option value="/com/pri/cytoexport/resources/quantifere_network_config_no_layout.json" >Config for Quantifere .csv (no layout)</option>
+			    </param>
+			    <param name="vizMapPropsFile" type="select" label="Select vizualization template">
+			      <option value="/com/pri/cytoexport/resources/simple_xtandem_viz.props" >Plain1 for X!Tandem .csv</option>
+			      <option value="/com/pri/cytoexport/resources/quantifere_network_layout.props" >Plain1 for Quantifere .csv</option>
+			    </param>
+			</when>
+			<when value="customConfig">
+		   		<param name="alternativeTableImportJsonFile" type="data" format="json" label="Alternative TableImport configuration file" help="The configuration file generated by the 'AlternativeTableImport' plugin"/>
+		   		<param name="vizMapPropsFile" type="data" format="any" label="VizMap file" />
+     		</when>
+     	</conditional>
+     	
+     	<param name="vizStyleName" type="text" size="30" value="default" label="VizMap style to apply" 
+			    help="In which file to display the network"/>
+			    
+	</inputs>
+	<outputs>
+		<data name="htmlReportFile" format="html" label="${csvDataFile.metadata.base_name} - ${tool.name} on ${on_string}: preview" metadata_source="csvDataFile"/>
+		<data name="cysOutFile" format="cys" label="${csvDataFile.metadata.base_name} - ${tool.name} on ${on_string}: Cytoscape .CYS" metadata_source="csvDataFile"/>
+		<data name="logFile" format="txt" label="${csvDataFile.metadata.base_name} - ${tool.name} on ${on_string}: logfile" metadata_source="csvDataFile"/>
+	</outputs>
+	<tests>
+	</tests>
+  <help>
+  
+.. class:: infomark
+  
+This tool takes in the CSV file and transforms it into a Cytoscape network according to the 
+configurations found in the 'Alternative TableImport configuration file'. 
+
+It provides pipeline automation for generating a visually rich Cytoscape network, which can 
+also be achieved manually by using the `AlternativeTableImport plugin`_ for Cytoscape. 
+
+
+-----
+
+**Output details**
+
+`See AlternativeTableImport for more details...`__ 
+
+
+.. __: javascript:window.open('http://apps.cytoscape.org/apps/alternativetableimport','popUpWindow','height=800,width=1000,left=10,top=10,resizable=yes,scrollbars=yes,toolbar=yes,menubar=no,location=no,directories=no,status=yes')
+.. _AlternativeTableImport plugin: javascript:window.open('http://apps.cytoscape.org/apps/alternativetableimport','popUpWindow','height=800,width=1000,left=10,top=10,resizable=yes,scrollbars=yes,toolbar=yes,menubar=no,location=no,directories=no,status=yes')
+
+
+
+
+  </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/datatypes_conf.xml	Wed Jan 08 12:44:02 2014 +0100
@@ -0,0 +1,10 @@
+<?xml version="1.0"?>
+<datatypes>
+  <datatype_files>
+  </datatype_files>
+  <registration display_path="display_applications">
+        <!-- type for the cytoscape export tool output -->
+        <datatype extension="cys"  type="galaxy.datatypes.data:Data" mimetype="application/octet-stream" 
+        display_in_upload="true" subclass="true"/>   
+  </registration>
+</datatypes>
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