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comparison Cytoscape.xml @ 0:e3beb33f88f0 draft

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planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
author dereeper
date Tue, 14 Aug 2018 08:02:10 -0400
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1 <tool id="Cytoscape" name="Cytoscape" version="1.0.0">
2
3 <!-- [REQUIRED] Tool description displayed after the tool name -->
4 <description>Visualize interaction networks from JSON file</description>
5
6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
7 <requirements>
8 <requirement type="binary">perl</requirement>
9 <requirement type="package" version="1.6.924">perl-bioperl</requirement>
10 </requirements>
11
12
13 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
14 <stdio>
15 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
16 <exit_code range="1:" level="fatal" />
17 </stdio>
18
19 <!-- [REQUIRED] The command to execute -->
20 <command interpreter="perl">
21 Cytoscape.sh $input $cytoscape_html $filelog
22 </command>
23 <!-- [REQUIRED] Input files and tool parameters -->
24 <inputs>
25 <param name="input" type="data" format="json" optional="false" label="Cytoscape JSON file" />
26 </inputs>
27
28 <!-- [REQUIRED] Output files -->
29 <outputs>
30 <data name="cytoscape_html" format="html" label="Cytoscape network" />
31 <data name="filelog" format="txt" label="Logfile" />
32 </outputs>
33
34 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
35 <tests>
36 <!-- [HELP] Test files have to be in the ~/test-data directory -->
37 <test>
38 <param name="input" value="input.json" />
39 <output name="cytoscape_html" file="network.html"/>
40 </test>
41 </tests>
42
43 <!-- [OPTIONAL] Help displayed in Galaxy -->
44 <help><![CDATA[
45
46 .. class:: infomark
47
48 **Authors** Max Franz : Cytoscape.js_
49
50 .. _Cytoscape.js: http://js.cytoscape.org/
51
52 .. class:: infomark
53
54 **Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)
55
56 .. class:: infomark
57
58 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
59
60 ---------------------------------------------------
61
62 ================
63 Cytoscape
64 ================
65
66 -----------
67 Description
68 -----------
69
70 | Create a Cytoscape network from Cytoscape JSON file
71
72 ----------
73 Input file
74 ----------
75
76 JSON file for Cytoscape
77
78 ------------
79 Output files
80 ------------
81
82 Cytoscape network
83
84 Log file
85
86 ---------------------------------------------------
87
88 ---------------
89 Working example
90 ---------------
91
92 Input file
93 ==========
94
95 input.json
96 ----------------------------
97
98 ::
99
100 {"elements": {"nodes": [{ "data": { "id": "MV1", "width": 0.1} },
101 { "data": { "id": "MV2", "width": 0.1} },
102 { "data": { "id": "MV3", "width": 0.1} },
103 { "data": { "id": "haplo1", "width": 1.2000000000000002 } },
104 { "data": { "id": "haplo2", "width": 0.8 } },
105 { "data": { "id": "haplo3", "width": 5.0 } },
106 { "data": { "id": "haplo4", "width": 0.8 } },
107 { "data": { "id": "haplo5", "width": 0.8 } },
108 { "data": { "id": "haplo6", "width": 0.8 } },
109 { "data": { "id": "haplo7", "width": 0.8 } },
110 { "data": { "id": "haplo8", "width": 0.8 } }],
111 "edges": [
112 { "data": { "id": "haplo4MV1", "weight": 1, "source": "haplo4", "target": "MV1"} },
113 { "data": { "id": "haplo3haplo4", "weight": 1, "source": "haplo3", "target": "haplo4"} },
114 { "data": { "id": "haplo4haplo6", "weight": 1, "source": "haplo4", "target": "haplo6"} },
115 { "data": { "id": "haplo1MV1", "weight": 1, "source": "haplo1", "target": "MV1"} },
116 { "data": { "id": "haplo1haplo2", "weight": 1, "source": "haplo1", "target": "haplo2"} },
117 { "data": { "id": "haplo7MV2", "weight": 1, "source": "haplo7", "target": "MV2"} },
118 { "data": { "id": "MV2MV3", "weight": 1, "source": "MV2", "target": "MV3"} },
119 { "data": { "id": "haplo5MV3", "weight": 1, "source": "haplo5", "target": "MV3"} },
120 { "data": { "id": "MV1MV2", "weight": 1, "source": "MV1", "target": "MV2"} },
121 { "data": { "id": "haplo8MV3", "weight": 1, "source": "haplo8", "target": "MV3"} }]}}
122
123 Output file
124 ===========
125
126 Cytoscape network
127 ----------------------------
128
129 .. image:: $PATH_TO_IMAGES/network.png
130 :width: 500 px
131
132 ]]></help>
133
134 </tool>