<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>