<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>