Mercurial > repos > enios > nc_rna
view cytoscape.xml @ 15:97abe4dc3ee3 draft
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author | enios |
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date | Sat, 22 May 2021 07:30:24 +0000 |
parents | 9ad10a3a5759 |
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<tool id="Cytoscape" name="Cytoscape" version="1.0.0"> <!-- [REQUIRED] Tool description displayed after the tool name --> <description>Visualize interaction networks from JSON file</description> <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> <requirements> <!--requirement type="binary">perl</requirement--> <container type="docker" >bianca7/lncrna:cytoscape</container> </requirements> <!-- [STRONGLY RECOMMANDED] Exit code rules --> <stdio> <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> <exit_code range="1:" level="fatal" /> </stdio> <!-- [REQUIRED] The command to execute --> <command> perl /code/Cytoscape.sh $input $cytoscape_html $filelog </command> <!-- [REQUIRED] Input files and tool parameters --> <inputs> <param name="input" type="data" format="json" optional="false" label="Cytoscape JSON file" /> </inputs> <!-- [REQUIRED] Output files --> <outputs> <data name="cytoscape_html" format="html" label="Cytoscape network" /> <data name="filelog" format="txt" label="Logfile" /> </outputs> <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> <tests> <!-- [HELP] Test files have to be in the ~/test-data directory --> <test> <param name="input" value="input.json" /> <output name="cytoscape_html" file="network.html"/> </test> </tests> <!-- [OPTIONAL] Help displayed in Galaxy --> <help><![CDATA[ .. class:: infomark **Authors** Max Franz : Cytoscape.js_ .. _Cytoscape.js: http://js.cytoscape.org/ .. class:: infomark **Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA) .. class:: infomark **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr --------------------------------------------------- ================ Cytoscape ================ ----------- Description ----------- | Create a Cytoscape network from Cytoscape JSON file ---------- Input file ---------- JSON file for Cytoscape ------------ Output files ------------ Cytoscape network Log file --------------------------------------------------- --------------- Working example --------------- Input file ========== input.json ---------------------------- :: {"elements": {"nodes": [{ "data": { "id": "MV1", "width": 0.1} }, { "data": { "id": "MV2", "width": 0.1} }, { "data": { "id": "MV3", "width": 0.1} }, { "data": { "id": "haplo1", "width": 1.2000000000000002 } }, { "data": { "id": "haplo2", "width": 0.8 } }, { "data": { "id": "haplo3", "width": 5.0 } }, { "data": { "id": "haplo4", "width": 0.8 } }, { "data": { "id": "haplo5", "width": 0.8 } }, { "data": { "id": "haplo6", "width": 0.8 } }, { "data": { "id": "haplo7", "width": 0.8 } }, { "data": { "id": "haplo8", "width": 0.8 } }], "edges": [ { "data": { "id": "haplo4MV1", "weight": 1, "source": "haplo4", "target": "MV1"} }, { "data": { "id": "haplo3haplo4", "weight": 1, "source": "haplo3", "target": "haplo4"} }, { "data": { "id": "haplo4haplo6", "weight": 1, "source": "haplo4", "target": "haplo6"} }, { "data": { "id": "haplo1MV1", "weight": 1, "source": "haplo1", "target": "MV1"} }, { "data": { "id": "haplo1haplo2", "weight": 1, "source": "haplo1", "target": "haplo2"} }, { "data": { "id": "haplo7MV2", "weight": 1, "source": "haplo7", "target": "MV2"} }, { "data": { "id": "MV2MV3", "weight": 1, "source": "MV2", "target": "MV3"} }, { "data": { "id": "haplo5MV3", "weight": 1, "source": "haplo5", "target": "MV3"} }, { "data": { "id": "MV1MV2", "weight": 1, "source": "MV1", "target": "MV2"} }, { "data": { "id": "haplo8MV3", "weight": 1, "source": "haplo8", "target": "MV3"} }]}} Output file =========== Cytoscape network ---------------------------- .. image:: $PATH_TO_IMAGES/network.png :width: 500 px ]]></help> </tool>