--- /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>