Mercurial > repos > pieterlukasse > primv_visualization
diff cytoexport.xml @ 0:a13b9fcbc0ee
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author | pieter.lukasse@wur.nl |
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date | Wed, 08 Jan 2014 12:44:02 +0100 |
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--- /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>