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1 <tool id="Cytoscape" name="Cytoscape" version="1.0.0">
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2
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3 <!-- [REQUIRED] Tool description displayed after the tool name -->
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4 <description>Visualize interaction networks from JSON file</description>
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5
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6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
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7 <requirements>
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8 <!--requirement type="binary">perl</requirement-->
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9 <container type="docker" >bianca7/lncrna:cytoscape</container>
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10 </requirements>
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11
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12
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13 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
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14 <stdio>
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15 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
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16 <exit_code range="1:" level="fatal" />
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17 </stdio>
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18
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19 <!-- [REQUIRED] The command to execute -->
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20 <command>
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21 perl /code/Cytoscape.sh $input $cytoscape_html $filelog
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22 </command>
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23 <!-- [REQUIRED] Input files and tool parameters -->
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24 <inputs>
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25 <param name="input" type="data" format="json" optional="false" label="Cytoscape JSON file" />
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26 </inputs>
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27
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28 <!-- [REQUIRED] Output files -->
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29 <outputs>
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30 <data name="cytoscape_html" format="html" label="Cytoscape network" />
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31 <data name="filelog" format="txt" label="Logfile" />
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32 </outputs>
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33
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34 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
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35 <tests>
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36 <!-- [HELP] Test files have to be in the ~/test-data directory -->
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37 <test>
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38 <param name="input" value="input.json" />
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39 <output name="cytoscape_html" file="network.html"/>
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40 </test>
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41 </tests>
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42
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43 <!-- [OPTIONAL] Help displayed in Galaxy -->
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44 <help><![CDATA[
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45
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46 .. class:: infomark
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47
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48 **Authors** Max Franz : Cytoscape.js_
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49
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50 .. _Cytoscape.js: http://js.cytoscape.org/
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51
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52 .. class:: infomark
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53
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54 **Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)
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55
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56 .. class:: infomark
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57
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58 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
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59
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60 ---------------------------------------------------
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61
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62 ================
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63 Cytoscape
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64 ================
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65
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66 -----------
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67 Description
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68 -----------
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69
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70 | Create a Cytoscape network from Cytoscape JSON file
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71
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72 ----------
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73 Input file
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74 ----------
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75
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76 JSON file for Cytoscape
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77
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78 ------------
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79 Output files
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80 ------------
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81
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82 Cytoscape network
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83
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84 Log file
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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 Working example
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90 ---------------
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91
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92 Input file
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93 ==========
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94
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95 input.json
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96 ----------------------------
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97
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98 ::
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99
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100 {"elements": {"nodes": [{ "data": { "id": "MV1", "width": 0.1} },
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101 { "data": { "id": "MV2", "width": 0.1} },
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102 { "data": { "id": "MV3", "width": 0.1} },
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103 { "data": { "id": "haplo1", "width": 1.2000000000000002 } },
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104 { "data": { "id": "haplo2", "width": 0.8 } },
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105 { "data": { "id": "haplo3", "width": 5.0 } },
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106 { "data": { "id": "haplo4", "width": 0.8 } },
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107 { "data": { "id": "haplo5", "width": 0.8 } },
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108 { "data": { "id": "haplo6", "width": 0.8 } },
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109 { "data": { "id": "haplo7", "width": 0.8 } },
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110 { "data": { "id": "haplo8", "width": 0.8 } }],
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111 "edges": [
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112 { "data": { "id": "haplo4MV1", "weight": 1, "source": "haplo4", "target": "MV1"} },
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113 { "data": { "id": "haplo3haplo4", "weight": 1, "source": "haplo3", "target": "haplo4"} },
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114 { "data": { "id": "haplo4haplo6", "weight": 1, "source": "haplo4", "target": "haplo6"} },
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115 { "data": { "id": "haplo1MV1", "weight": 1, "source": "haplo1", "target": "MV1"} },
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116 { "data": { "id": "haplo1haplo2", "weight": 1, "source": "haplo1", "target": "haplo2"} },
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117 { "data": { "id": "haplo7MV2", "weight": 1, "source": "haplo7", "target": "MV2"} },
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118 { "data": { "id": "MV2MV3", "weight": 1, "source": "MV2", "target": "MV3"} },
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119 { "data": { "id": "haplo5MV3", "weight": 1, "source": "haplo5", "target": "MV3"} },
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120 { "data": { "id": "MV1MV2", "weight": 1, "source": "MV1", "target": "MV2"} },
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121 { "data": { "id": "haplo8MV3", "weight": 1, "source": "haplo8", "target": "MV3"} }]}}
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122
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123 Output file
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124 ===========
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125
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126 Cytoscape network
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127 ----------------------------
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128
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129 .. image:: $PATH_TO_IMAGES/network.png
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130 :width: 500 px
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131
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132 ]]></help>
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133
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134 </tool>
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135
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