| Next changeset 1:0e43c52e2449 (2021-06-09) |
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Commit message:
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f |
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added:
Cytoscape.pl Cytoscape.sh Cytoscape.xml static/images/network.png test-data/input.json test-data/network.html |
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| diff -r 000000000000 -r e3beb33f88f0 Cytoscape.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Cytoscape.pl Tue Aug 14 08:02:10 2018 -0400 |
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| @@ -0,0 +1,115 @@ +#!/usr/bin/perl + +use strict; +#use Switch; +use Getopt::Long; +use Bio::SeqIO; + +use Cwd; +my $dir = getcwd; + + +my $usage = qq~Usage:$0 <args> [<opts>] +where <args> are: + -i, --input <input> + -h, --html <html_output> +~; +$usage .= "\n"; + +my ($infile,$htmlout); + + +GetOptions( + "input=s" => \$infile, + "html=s" => \$htmlout, +); + + +die $usage + if ( !$infile); + + +my $datain = ""; +open(I,$infile); +while(<I>){ + my $line = $_; + $datain.=$line; +} +close(I); +chomp($datain);chomp($datain); +# remove brackets at the beginning and end of JSON +my $new_datain = substr($datain,1,length($datain)-2); +$datain = $new_datain; + +my @colors = ("#ed292a","#ed292a","#82ABA0","#2255a6","#6ebe43","#e76599","#662e91","#c180ff","#ea8b2f","#fff100","#666666","#01ffff","#bfbfbf","#2ac966","#666666"); + + +my $pie_block = ""; +for (my $i = 0; $i <= scalar @colors; $i++){ + $pie_block .= "'pie-$i-background-color': '$colors[$i]',\n"; + $pie_block .= "'pie-$i-background-size': 'mapData(group$i, 0, 10, 0, 100)',\n"; +} + +open(HTML_CYTOSCAPE,">$htmlout"); + my $html = qq~<!DOCTYPE html> +<html><head> +<meta http-equiv="content-type" content="text/html; charset=UTF-8"> +<link href="http://sniplay.southgreen.fr/cytoscape/Pie_style/style.css" rel="stylesheet"> +<meta charset="utf-8"> +<meta name="viewport" content="user-scalable=no, initial-scale=1.0, minimum-scale=1.0, maximum-scale=1.0, minimal-ui"> +<title>Pie style</title> +<script src="http://sniplay.southgreen.fr/cytoscape/Pie_style/jquery.js"></script> +<script src="http://sniplay.southgreen.fr/cytoscape/Pie_style/cytoscape.js"></script> +<script type="text/javascript"> +\$(function(){ // on dom ready + +\$('#cy').cytoscape({ + + style: cytoscape.stylesheet() + .selector(':selected') + .css({ + 'background-color': 'black', + 'line-color': 'black', + 'opacity': 1 + }) + .selector('.faded') + .css({ + 'opacity': 0.25, + 'text-opacity': 0 + }) + .selector('edge') + .css({ + 'width': 1, + 'line-color': 'black', + }) + .selector('node') + .css({ + 'width': 'mapData(width, 0, 10, 0, 100)', + 'height': 'mapData(width, 0, 10, 0, 100)', + 'content': 'data(id)', + 'pie-size': '98%', + $pie_block + }), +$datain + , +layout: { + name: 'cose', + padding: 10 + }, + + ready: function(){ + window.cy = this; + } +}); + +}); + +</script> +</head> +<body> +<div id="cy"> +</div> +~; +print HTML_CYTOSCAPE $html; +close(HTML_CYTOSCAPE); + |
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| diff -r 000000000000 -r e3beb33f88f0 Cytoscape.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Cytoscape.sh Tue Aug 14 08:02:10 2018 -0400 |
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| @@ -0,0 +1,13 @@ +#!/bin/bash + +tool_path=$(dirname $0) + +filein=$1 +cytoscape_html=$2 +logfile=$3 + +perl $tool_path/Cytoscape.pl --input $filein --html $cytoscape_html >>$logfile 2>&1 + + + + |
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| diff -r 000000000000 -r e3beb33f88f0 Cytoscape.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Cytoscape.xml Tue Aug 14 08:02:10 2018 -0400 |
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| @@ -0,0 +1,134 @@ +<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> + <requirement type="package" version="1.6.924">perl-bioperl</requirement> + </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 interpreter="perl"> + 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> |
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| diff -r 000000000000 -r e3beb33f88f0 static/images/network.png |
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| Binary file static/images/network.png has changed |
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| diff -r 000000000000 -r e3beb33f88f0 test-data/input.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.json Tue Aug 14 08:02:10 2018 -0400 |
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| @@ -0,0 +1,22 @@ +{"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"} }]}} \ No newline at end of file |
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| diff -r 000000000000 -r e3beb33f88f0 test-data/network.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/network.html Tue Aug 14 08:02:10 2018 -0400 |
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| @@ -0,0 +1,111 @@ +<!DOCTYPE html> +<html><head> +<meta http-equiv="content-type" content="text/html; charset=UTF-8"> +<link href="http://sniplay.southgreen.fr/cytoscape/Pie_style/style.css" rel="stylesheet"> +<meta charset="utf-8"> +<meta name="viewport" content="user-scalable=no, initial-scale=1.0, minimum-scale=1.0, maximum-scale=1.0, minimal-ui"> +<title>Pie style</title> +<script src="http://sniplay.southgreen.fr/cytoscape/Pie_style/jquery.js"></script> +<script src="http://sniplay.southgreen.fr/cytoscape/Pie_style/cytoscape.js"></script> +<script type="text/javascript"> +$(function(){ // on dom ready + +$('#cy').cytoscape({ + + style: cytoscape.stylesheet() + .selector(':selected') + .css({ + 'background-color': 'black', + 'line-color': 'black', + 'opacity': 1 + }) + .selector('.faded') + .css({ + 'opacity': 0.25, + 'text-opacity': 0 + }) + .selector('edge') + .css({ + 'width': 1, + 'line-color': 'black', + }) + .selector('node') + .css({ + 'width': 'mapData(width, 0, 10, 0, 100)', + 'height': 'mapData(width, 0, 10, 0, 100)', + 'content': 'data(id)', + 'pie-size': '98%', + 'pie-0-background-color': '#ed292a', +'pie-0-background-size': 'mapData(group0, 0, 10, 0, 100)', +'pie-1-background-color': '#ed292a', +'pie-1-background-size': 'mapData(group1, 0, 10, 0, 100)', +'pie-2-background-color': '#82ABA0', +'pie-2-background-size': 'mapData(group2, 0, 10, 0, 100)', +'pie-3-background-color': '#2255a6', +'pie-3-background-size': 'mapData(group3, 0, 10, 0, 100)', +'pie-4-background-color': '#6ebe43', +'pie-4-background-size': 'mapData(group4, 0, 10, 0, 100)', +'pie-5-background-color': '#e76599', +'pie-5-background-size': 'mapData(group5, 0, 10, 0, 100)', +'pie-6-background-color': '#662e91', +'pie-6-background-size': 'mapData(group6, 0, 10, 0, 100)', +'pie-7-background-color': '#c180ff', +'pie-7-background-size': 'mapData(group7, 0, 10, 0, 100)', +'pie-8-background-color': '#ea8b2f', +'pie-8-background-size': 'mapData(group8, 0, 10, 0, 100)', +'pie-9-background-color': '#fff100', +'pie-9-background-size': 'mapData(group9, 0, 10, 0, 100)', +'pie-10-background-color': '#666666', +'pie-10-background-size': 'mapData(group10, 0, 10, 0, 100)', +'pie-11-background-color': '#01ffff', +'pie-11-background-size': 'mapData(group11, 0, 10, 0, 100)', +'pie-12-background-color': '#bfbfbf', +'pie-12-background-size': 'mapData(group12, 0, 10, 0, 100)', +'pie-13-background-color': '#2ac966', +'pie-13-background-size': 'mapData(group13, 0, 10, 0, 100)', +'pie-14-background-color': '#666666', +'pie-14-background-size': 'mapData(group14, 0, 10, 0, 100)', +'pie-15-background-color': '', +'pie-15-background-size': 'mapData(group15, 0, 10, 0, 100)', + + }), +"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"} }]} + , +layout: { + name: 'cose', + padding: 10 + }, + + ready: function(){ + window.cy = this; + } +}); + +}); + +</script> +</head> +<body> +<div id="cy"> +</div> |
