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diff 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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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/beta_diversity_through_plots_wrapper.py	Tue Feb 02 05:50:37 2016 -0500
@@ -0,0 +1,124 @@
+#!/usr/bin/env python
+
+# create a html output for beta_diverity_through_plots.py
+# to replace beta_diversity_through_plot_html.py in qiime 1.8
+# Leroi Laura laura.leroi@ifremer.fr
+
+import optparse
+import os
+import sys
+import subprocess
+
+# Create html template
+def html_maker(metrics):
+
+    tag=""
+    plots = metrics.split(',')
+    for i in range(0, len(plots)):
+        tag = tag+"""\t\t<option value='%s_emperor_pcoa_plot/index.html'>%s</option>\n""" % (plots[i], plots[i])
+    template_html= """
+<!doctype html>
+<html lang="en">
+<head>
+        <meta charset="utf-8">
+        <script  type="text/javascript" src="/galaxy/static/scripts/libs/jquery/jquery.js"></script>
+</head>
+<body>
+    <label for="outputs">Select a beta-diversity metric :</label>
+        <select id="outputs" name="outputs">
+%s
+        </select>
+    <br/>
+    <br/>
+        <iframe id="plot" name="plot" style="position:absolute; width: 90%%; height: 90%%;" src="" frameborder="0"></iframe>
+        <script>
+        $(document).ready(function(){
+                var str = "";
+                $( "#outputs option:selected" ).each(function() {
+                        str += $( this ).val() + " ";
+                        $("#plot").attr("src", str);
+                });
+
+        });
+        $( "#outputs" ).change(function () {
+                var str = "";
+                $( "#outputs option:selected" ).each(function() {
+                        str += $( this ).val() + " ";
+                        $("#plot").attr("src", str);
+                });
+        }).change();
+</script>
+</body>
+</html>    """ % (tag)
+    return template_html
+
+
+def html_matrix_maker(metrics):
+
+    tag=""
+    plots = metrics.split(',')
+    for i in range(0, len(plots)):
+        tag = tag+"""\t\t<a href='%s_dm.txt'>%s_dm</a><br/>\n""" % (plots[i], plots[i])
+
+    template_html= """
+<!doctype html>
+<html lang="en">
+<body>
+        <label>Metrics matrix : </label><br/>
+%s
+</body>
+</html> """ % (tag)
+    return template_html
+
+
+def main():
+
+    #On importe l environnemnent envqiime
+    pipe = subprocess.Popen(". /home12/caparmor/bioinfo/GALAXY_DEV/ourenv/envqiime; python -c 'import os; print \"newenv = %r\" % os.environ'", stdout=subprocess.PIPE, shell=True)
+    exec(pipe.communicate()[0])
+    os.environ.update(newenv)
+
+    #New parser
+    parser = optparse.OptionParser()
+    #beta diversity options
+    parser.add_option('--metrics',dest='metrics')
+    parser.add_option('--biom',dest='biom')
+    parser.add_option('--mapping',dest='mapping')
+    parser.add_option('--tree',dest='tree')
+    parser.add_option('--depth',dest='depth')
+    parser.add_option('--masterhtml',dest='masterhtml')
+    parser.add_option('--outputfolder',dest='outputfolder')
+    parser.add_option('--matrixhtml',dest='matrixhtml')
+
+    (options,args) = parser.parse_args()
+
+    #New hmtl template
+    master = open('./master.html', 'w')
+    master.write(html_maker(options.metrics))
+    master.close()
+    #On lance le fichier avec les options precisees pour l'affichage html
+    os.system("mv master.html %s" % options.masterhtml)
+
+    #parameter file, which specifies changes to the default behavior
+    parameters = open('./parameters.txt','w')
+    parameters.write("beta_diversity:metrics %s" % options.metrics)
+    parameters.close()
+
+    if options.depth:
+        if options.tree :
+            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))
+        else :
+            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))
+    else:
+        if options.tree :
+            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))
+        else :
+            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))
+
+    os.system("mkdir %s/txt" % (options.outputfolder))
+    os.system("mv %s/*_dm.txt %s/txt" %(options.outputfolder,options.outputfolder))
+    os.system("compress_path.py -i %s/txt -o %s" % (options.outputfolder,options.matrixhtml))
+
+if __name__=="__main__":
+    main()
+