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comparison cytoexport.xml @ 0:a13b9fcbc0ee

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author pieter.lukasse@wur.nl
date Wed, 08 Jan 2014 12:44:02 +0100
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1 <tool name="CytoExport" id="cytoexport1" version="1.0.2">
2 <description>Exports CSV files to visually rich Cytoscape networks</description>
3 <!--
4 For remote debugging start you listener on port 8000 and use the following as command interpreter:
5 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000
6 //////////////////////////
7 This part is a WORKAROUND for the Cytoscape X11 dependency problem, even when running 'headless' (assuming Xfvb is installed/enabled):
8 export DISPLAY=:995;
9 ...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)
10 ...check how other tools do this
11 -->
12 <command interpreter="export DISPLAY=:995; java -jar ">
13 CytoExport.jar
14 -networkName "$csvDataFile.metadata.base_name"
15 -csvDataFile $csvDataFile
16 -configInputMode $configInputMode.type
17 -vizMapPropsFile $configInputMode.vizMapPropsFile
18 -vizStyleName $vizStyleName
19 -alternativeTableImportJsonFile $configInputMode.alternativeTableImportJsonFile
20 -cysOutFile $cysOutFile
21 -htmlReportFile $htmlReportFile
22 -picturesPath $htmlReportFile.files_path
23 -logFile $logFile
24 </command>
25
26 <inputs>
27 <!-- TODO make possible to have multiple networks in same .cys
28 <param name="networkName" type="text" size="30" value="" label="Network name" />-->
29 <param name="csvDataFile" type="data" format="csv,tabular" label="Network data file" />
30
31
32 <conditional name="configInputMode">
33 <param name="type" type="select" label="Configuration input">
34 <option value="customConfig" selected="true">Use custom configuration files</option>
35 <option value="existingTemplate">Use one of the existing templates</option>
36 </param>
37 <when value="existingTemplate">
38 <param name="alternativeTableImportJsonFile" type="select" label="Select import template">
39 <option value="/com/pri/cytoexport/resources/simple_xtandem_out.json" >Config for X!Tandem .csv</option>
40 <option value="/com/pri/cytoexport/resources/quantifere_network_config.json" >Config for Quantifere .csv (force-directed layout)</option>
41 <option value="/com/pri/cytoexport/resources/quantifere_network_config_no_layout.json" >Config for Quantifere .csv (no layout)</option>
42 </param>
43 <param name="vizMapPropsFile" type="select" label="Select vizualization template">
44 <option value="/com/pri/cytoexport/resources/simple_xtandem_viz.props" >Plain1 for X!Tandem .csv</option>
45 <option value="/com/pri/cytoexport/resources/quantifere_network_layout.props" >Plain1 for Quantifere .csv</option>
46 </param>
47 </when>
48 <when value="customConfig">
49 <param name="alternativeTableImportJsonFile" type="data" format="json" label="Alternative TableImport configuration file" help="The configuration file generated by the 'AlternativeTableImport' plugin"/>
50 <param name="vizMapPropsFile" type="data" format="any" label="VizMap file" />
51 </when>
52 </conditional>
53
54 <param name="vizStyleName" type="text" size="30" value="default" label="VizMap style to apply"
55 help="In which file to display the network"/>
56
57 </inputs>
58 <outputs>
59 <data name="htmlReportFile" format="html" label="${csvDataFile.metadata.base_name} - ${tool.name} on ${on_string}: preview" metadata_source="csvDataFile"/>
60 <data name="cysOutFile" format="cys" label="${csvDataFile.metadata.base_name} - ${tool.name} on ${on_string}: Cytoscape .CYS" metadata_source="csvDataFile"/>
61 <data name="logFile" format="txt" label="${csvDataFile.metadata.base_name} - ${tool.name} on ${on_string}: logfile" metadata_source="csvDataFile"/>
62 </outputs>
63 <tests>
64 </tests>
65 <help>
66
67 .. class:: infomark
68
69 This tool takes in the CSV file and transforms it into a Cytoscape network according to the
70 configurations found in the 'Alternative TableImport configuration file'.
71
72 It provides pipeline automation for generating a visually rich Cytoscape network, which can
73 also be achieved manually by using the `AlternativeTableImport plugin`_ for Cytoscape.
74
75
76 -----
77
78 **Output details**
79
80 `See AlternativeTableImport for more details...`__
81
82
83 .. __: 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')
84 .. _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')
85
86
87
88
89 </help>
90 </tool>