Mercurial > repos > pieterlukasse > primv_visualization
changeset 0:cb11ee34d92f
Initial Toolshed commit
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Mon, 30 Dec 2013 15:33:01 +0100 |
| parents | |
| children | cec65381447b |
| files | CytoExport.jar LICENSE NOTICE README.rst cytoexport.xml datatypes_conf.xml static/images/tood.png |
| diffstat | 7 files changed, 383 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NOTICE Mon Dec 30 15:33:01 2013 +0100 @@ -0,0 +1,16 @@ +PRIMV-visualization toolset & Galaxy wrappers +========================================== + +Tools and wrappers for the PRIMV visualization toolset. +Suite of tools that generate multi-purpose views to assist in the visualization +and interpretation of large and complex datasets. + +Can be used a.o. in combination with PRIMS-MASSCOMB (prims_masscomb package) and +PRIMS-proteomics (prims_proteomics package). + +Copyright 2010-2013 by Pieter Lukasse, Plant Research International (PRI), +Wageningen, The Netherlands. All rights reserved. See the license text below. + +Galaxy wrappers and installation are available from the Galaxy Tool Shed at: +http://toolshed.g2.bx.psu.edu/view/pieterlukasse/primv_visualization +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Mon Dec 30 15:33:01 2013 +0100 @@ -0,0 +1,67 @@ +PRIMV-visualization toolset & Galaxy wrappers +============================================= + +Visualization module of Plant Research International's Multi-purpose Views (PRIMV) toolsuite. + +This toolset consists of tools that generate multi-purpose views to assist in the visualization +and interpretation of large and complex datasets. + +Can be used a.o. in combination with PRIMS-MASSCOMB (prims_masscomb package) and +PRIMS-proteomics (prims_proteomics package). + +Copyright 2010-2013 by Pieter Lukasse, Plant Research International (PRI), +Wageningen, The Netherlands. All rights reserved. See the license text below. + +Galaxy wrappers and installation are available from the Galaxy Tool Shed at: +http://toolshed.g2.bx.psu.edu/view/pieterlukasse/primv_visualization + +History +======= + +============== ======================================================================== +Date Changes +-------------- ------------------------------------------------------------------------ +January 2014 -first release via Tool Shed +November 2013 -cytoexport tool used internally at PRI +October 2012 -first tool for generating visually rich Cytoscape networks (cytoexport) +============== ======================================================================== + +Tool Versioning +=============== + +PRIMS tools will have versions of the form X.Y.Z. Versions +differing only after the second decimal should be completely +compatible with each other. Breaking changes should result in an +increment of the number before and/or after the first decimal. All +tools of version less than 1.0.0 should be considered beta. + + +Bug Reports & other questions +============================= + +For the time being issues can be reported via the contact form at +http://www.wageningenur.nl/en/Persons/PNJ-Pieter-Lukasse.htm + +Developers, Contributions & Collaborations +========================================== + +If you wish to join forces and collaborate on some of the +tools do not hesitate to contact Pieter Lukasse via the contact form above. + +License (Apache, Version 2.0) +============================= + +Copyright 2013 Pieter Lukasse, Plant Research International (PRI). + +Licensed under the Apache License, Version 2.0 (the "License"); +you may not use this software except in compliance with the License. +You may obtain a copy of the License at + +http://www.apache.org/licenses/LICENSE-2.0 + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. + \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cytoexport.xml Mon Dec 30 15:33:01 2013 +0100 @@ -0,0 +1,88 @@ +<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 $logFile + </command> + + <inputs> + <!-- TODO make possible to have multiple networks in same .cys + <param name="networkName" type="text" size="30" value="" label="Network name" />--> + <param name="csvDataFile" type="data" format="csv,tabular" label="Network data file" /> + + + <conditional name="configInputMode"> + <param name="type" type="select" label="Configuration input"> + <option value="customConfig" selected="true">Use custom configuration files</option> + <option value="existingTemplate">Use one of the existing templates</option> + </param> + <when value="existingTemplate"> + <param name="alternativeTableImportJsonFile" type="select" label="Select import template"> + <option value="/com/pri/cytoexport/resources/simple_xtandem_out.json" >Config for X!Tandem .csv</option> + <option value="/com/pri/cytoexport/resources/quantifere_network_config.json" >Config for Quantifere .csv</option> + </param> + <param name="vizMapPropsFile" type="select" label="Select vizualization template"> + <option value="/com/pri/cytoexport/resources/simple_xtandem_viz.props" >Plain1 for X!Tandem .csv</option> + <option value="/com/pri/cytoexport/resources/quantifere_network_layout.props" >Plain1 for Quantifere .csv</option> + </param> + </when> + <when value="customConfig"> + <param name="alternativeTableImportJsonFile" type="data" format="json" label="Alternative TableImport configuration file" help="The configuration file generated by the 'AlternativeTableImport' plugin"/> + <param name="vizMapPropsFile" type="data" format="any" label="VizMap file" /> + </when> + </conditional> + + <param name="vizStyleName" type="text" size="30" value="default" label="VizMap style to apply" + help="In which file to display the network"/> + + </inputs> + <outputs> + <data name="htmlReportFile" format="html" label="${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=700,width=800,left=10,top=10,resizable=yes,scrollbars=yes,toolbar=yes,menubar=no,location=no,directories=no,status=yes') + + + + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes_conf.xml Mon Dec 30 15:33:01 2013 +0100 @@ -0,0 +1,10 @@ +<?xml version="1.0"?> +<datatypes> + <datatype_files> + </datatype_files> + <registration display_path="display_applications"> + <!-- type for the cytoscape export tool output --> + <datatype extension="cys" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream" + display_in_upload="true" subclass="true"/> + </registration> +</datatypes> \ No newline at end of file