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