Mercurial > repos > bebatut > qiime

annotate beta_diversity_through_plots_wrapper.py @ 0:c1bd0c560018 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
author bebatut
date Tue, 02 Feb 2016 05:50:37 -0500
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c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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1 #!/usr/bin/env python
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2
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3 # create a html output for beta_diverity_through_plots.py
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4 # to replace beta_diversity_through_plot_html.py in qiime 1.8
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5 # Leroi Laura laura.leroi@ifremer.fr
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7 import optparse
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8 import os
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9 import sys
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10 import subprocess
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11
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12 # Create html template
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13 def html_maker(metrics):
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14
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15 tag=""
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16 plots = metrics.split(',')
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17 for i in range(0, len(plots)):
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18 tag = tag+"""\t\t<option value='%s_emperor_pcoa_plot/index.html'>%s</option>\n""" % (plots[i], plots[i])
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19 template_html= """
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20 <!doctype html>
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21 <html lang="en">
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22 <head>
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23 <meta charset="utf-8">
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24 <script type="text/javascript" src="/galaxy/static/scripts/libs/jquery/jquery.js"></script>
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25 </head>
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26 <body>
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27 <label for="outputs">Select a beta-diversity metric :</label>
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28 <select id="outputs" name="outputs">
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29 %s
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30 </select>
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31 <br/>
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32 <br/>
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33 <iframe id="plot" name="plot" style="position:absolute; width: 90%%; height: 90%%;" src="" frameborder="0"></iframe>
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34 <script>
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35 $(document).ready(function(){
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36 var str = "";
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37 $( "#outputs option:selected" ).each(function() {
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38 str += $( this ).val() + " ";
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39 $("#plot").attr("src", str);
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40 });
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41
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42 });
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43 $( "#outputs" ).change(function () {
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44 var str = "";
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45 $( "#outputs option:selected" ).each(function() {
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46 str += $( this ).val() + " ";
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47 $("#plot").attr("src", str);
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48 });
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49 }).change();
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50 </script>
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51 </body>
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52 </html> """ % (tag)
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53 return template_html
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54
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55
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56 def html_matrix_maker(metrics):
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57
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58 tag=""
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59 plots = metrics.split(',')
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60 for i in range(0, len(plots)):
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61 tag = tag+"""\t\t<a href='%s_dm.txt'>%s_dm</a><br/>\n""" % (plots[i], plots[i])
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62
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63 template_html= """
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64 <!doctype html>
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65 <html lang="en">
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66 <body>
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67 <label>Metrics matrix : </label><br/>
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68 %s
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69 </body>
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70 </html> """ % (tag)
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71 return template_html
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72
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73
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74 def main():
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75
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76 #On importe l environnemnent envqiime
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77 pipe = subprocess.Popen(". /home12/caparmor/bioinfo/GALAXY_DEV/ourenv/envqiime; python -c 'import os; print \"newenv = %r\" % os.environ'", stdout=subprocess.PIPE, shell=True)
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78 exec(pipe.communicate()[0])
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79 os.environ.update(newenv)
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80
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81 #New parser
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82 parser = optparse.OptionParser()
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83 #beta diversity options
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84 parser.add_option('--metrics',dest='metrics')
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85 parser.add_option('--biom',dest='biom')
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86 parser.add_option('--mapping',dest='mapping')
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87 parser.add_option('--tree',dest='tree')
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88 parser.add_option('--depth',dest='depth')
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89 parser.add_option('--masterhtml',dest='masterhtml')
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90 parser.add_option('--outputfolder',dest='outputfolder')
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91 parser.add_option('--matrixhtml',dest='matrixhtml')
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92
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93 (options,args) = parser.parse_args()
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94
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95 #New hmtl template
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96 master = open('./master.html', 'w')
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97 master.write(html_maker(options.metrics))
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98 master.close()
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99 #On lance le fichier avec les options precisees pour l'affichage html
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100 os.system("mv master.html %s" % options.masterhtml)
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101
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102 #parameter file, which specifies changes to the default behavior
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103 parameters = open('./parameters.txt','w')
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104 parameters.write("beta_diversity:metrics %s" % options.metrics)
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105 parameters.close()
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106
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107 if options.depth:
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108 if options.tree :
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109 os.system("beta_diversity_through_plots.py -i %s -m %s -t %s -e %s -o %s -p ./parameters.txt >& file_log.txt" % (options.biom, options.mapping, options.tree, options.depth, options.outputfolder))
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110 else :
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111 os.system("beta_diversity_through_plots.py -i %s -m %s -e %s -o %s -p ./parameters.txt >& file_log.txt" % (options.biom, options.mapping, options.depth, options.outputfolder))
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112 else:
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113 if options.tree :
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114 os.system("beta_diversity_through_plots.py -i %s -m %s -t %s -o %s -p ./parameters.txt >& file_log.txt" % (options.biom, options.mapping, options.tree, options.outputfolder))
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115 else :
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116 os.system("beta_diversity_through_plots.py -i %s -m %s -o %s -p ./parameters.txt >& file_log.txt" % (options.biom, options.mapping, options.outputfolder))
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117
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118 os.system("mkdir %s/txt" % (options.outputfolder))
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119 os.system("mv %s/*_dm.txt %s/txt" %(options.outputfolder,options.outputfolder))
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120 os.system("compress_path.py -i %s/txt -o %s" % (options.outputfolder,options.matrixhtml))
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121
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122 if __name__=="__main__":
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123 main()
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124