--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ranger_wrapper.py	Mon Jan 21 14:00:26 2013 -0500
@@ -0,0 +1,185 @@
+#purpose: python wrapper to run peak ranger
+#author: Ziru Zhou
+#Date: November 2012
+
+import sys, subprocess, tempfile, shutil, glob, os, os.path, gzip
+from galaxy import eggs
+import pkg_resources
+pkg_resources.require( "simplejson" )
+import simplejson
+import glob
+import datetime
+
+CHUNK_SIZE = 1024
+
+def main():
+    options = simplejson.load( open( sys.argv[1] ) )
+    outputs = simplejson.load( open( sys.argv[2] ) )
+    script_path = sys.argv[3]
+
+
+    #sets experiment name and sets the chip/input files
+    #========================================================================================    
+    experiment_name = '_'.join( options['experiment_name'].split() ) #save experiment name
+
+    #cmdline = "bash /mnt/galaxyTools/galaxy-central/tools/modENCODE_DCC_tools/peakranger/peakranger %s -d %s --format bam" % ( options['action'], options['chip_file'] )
+    cmdline = "peakranger %s -d %s" % ( options['action'], options['chip_file'] )
+    if 'input_file' in options:
+        cmdline = "%s -c %s" % ( cmdline, options['input_file'] )
+
+    #set additional options
+    #========================================================================================
+    if (options['action'] == "nr"):
+	output_ranger_file = outputs['output_ranger_file']
+
+	cmdline = "%s --format bam -l %s --verbose > default_output.txt" % ( cmdline, options['extension'] ) 
+    elif (options['action'] == "lc"):
+	output_ranger_file = outputs['output_ranger_file']
+
+	cmdline = "%s --verbose > default_output.txt" % ( cmdline )
+    elif (options['action'] == "wig"):
+	output_wigzip_file = outputs['output_wigzip_file']
+
+	cmdline = "%s --format bam -l %s %s %s %s -o ranger_wig" % ( cmdline, options['extension'], options['split'], options['strand'], options['gzip'] ) 
+    elif (options['action'] == "wigpe"):
+	output_wigzip_file = outputs['output_wigzip_file']
+
+	cmdline = "%s -l %s %s %s %s -o ranger_wig" % ( cmdline, options['extension'], options['split'], options['strand'], options['gzip'] ) 
+    elif (options['action'] == "ranger"):
+	output_summit_file = outputs['output_summit_file']
+	output_region_file = outputs['output_region_file']
+	output_details_file = outputs['output_details_file']
+	output_report_file = outputs['output_report_file']
+
+	if (options['gene_annotate_file'] != "None"):
+		gene_annotate_file = "--gene_annot_file %s/gene_annotation_files/%s" % ( script_path, options['gene_annotate_file'] )
+		report = "--report"
+	elif (options['gene_annotate_file'] == "Upload"):
+		gene_annotate_file = options['usr_annot_file']
+		report = "--report"
+	else:
+		gene_annotate_file = ""
+		report = ""
+
+	cmdline = "%s -t %s --format bam %s --plot_region %s -l %s -p %s -q %s -r %s -b %s %s %s -o ranger_peak" % ( cmdline, options['threads'], gene_annotate_file, options['plot_region'], options['extension'], options['pvalue'], options['fdr'], options['delta'], options['bandwith'], options['pad'], report )
+    elif (options['action'] == "ccat"):
+	output_summit_file = outputs['output_summit_file']
+	output_region_file = outputs['output_region_file']
+	output_details_file = outputs['output_details_file']
+	output_report_file = outputs['output_report_file']
+	output_ranger_file = outputs['output_ranger_file']
+	
+	if (options['gene_annotate_file'] != "None"):
+		gene_annotate_file = "--gene_annot_file %s/gene_annotation_files/%s" % ( script_path, options['gene_annotate_file'] )
+		report = "--report"
+	elif (options['gene_annotate_file'] == "Upload"):
+		gene_annotate_file = options['usr_annot_file']
+		report = "--report"
+	else:
+		gene_annotate_file = ""
+		report = ""
+
+	cmdline = "%s --format bam %s --plot_region %s -l %s -q %s --win_size %s --win_step %s --min_count %s --min_score %s %s -o ranger_peak > default_output.txt" % ( cmdline, gene_annotate_file, options['plot_region'], options['extension'], options['fdr'], options['winsize'], options['winstep'], options['mincount'], options['minscore'], report )
+
+    #run cmdline
+    #========================================================================================
+    tmp_dir = tempfile.mkdtemp()
+    stderr_name = tempfile.NamedTemporaryFile().name
+    proc = subprocess.Popen( args=cmdline, shell=True, cwd=tmp_dir, stderr=open( stderr_name, 'wb' ) )
+    proc.wait()
+
+    #Do not terminate if error code, allow dataset (e.g. log) creation and cleanup
+    #========================================================================================
+    if proc.returncode:
+        stderr_f = open( stderr_name )
+        while True:
+            chunk = stderr_f.read( CHUNK_SIZE )
+            if not chunk:
+                stderr_f.close()
+                break
+            sys.stderr.write( chunk )
+
+
+    #determine if the outputs are there, copy them to the appropriate dir and filename
+    #========================================================================================
+    if(options['action'] == "nr" or options['action'] == "lc" or options['action'] == "ccat"):
+	created_ranger_file =  os.path.join( tmp_dir, "default_output.txt" )
+        if os.path.exists( created_ranger_file ):
+        	shutil.move( created_ranger_file, output_ranger_file )
+
+    if(options['action'] == "wig" or options['action'] == "wigpe"):
+	if(options['split'] == "-s" or options['strand'] == "-x"):
+		if(options['gzip'] == "-z"):
+			files = str( glob.glob('%s/*.wig.gz' % tmp_dir) )
+			files = files.replace("[", "")
+			files = files.replace("]", "")
+			files = files.replace(",", "")
+			files = files.replace("'", "")
+			cmd = "zip -j %s/ranger_wig.zip %s > /dev/null" % (tmp_dir, files)
+			#cmd = "tar -czvf %s/ranger_wig.tar %s > /dev/null" % (tmp_dir, files)
+			os.system(cmd)
+			created_wigzip_file =  os.path.join( tmp_dir, "ranger_wig.zip" )
+		else:
+			files = str( glob.glob('%s/*.wig' % tmp_dir) )
+			files = files.replace("[", "")
+			files = files.replace("]", "")
+			files = files.replace(",", "")
+			files = files.replace("'", "")
+			cmd = "zip -j %s/ranger_wig.zip %s > /dev/null" % (tmp_dir, files)
+			#cmd = "tar -czvf %s/ranger_wig.tar %s > /dev/null" % (tmp_dir, files)
+			os.system(cmd)
+			created_wigzip_file =  os.path.join( tmp_dir, "ranger_wig.zip" )
+	else:
+		if(options['gzip'] == "-z"):
+			created_wigzip_file =  os.path.join( tmp_dir, "ranger_wig.wig.gz" )
+		else:
+			created_wigzip_file =  os.path.join( tmp_dir, "ranger_wig.wig" )
+ 
+	if os.path.exists( created_wigzip_file ):
+        	shutil.move( created_wigzip_file, output_wigzip_file )
+ 
+    if(options['action'] == "ranger" or options['action'] == "ccat"):	
+	created_summit_file =  os.path.join( tmp_dir, "ranger_peak_summit.bed"  )
+	if os.path.exists( created_summit_file ):
+        	shutil.move( created_summit_file, output_summit_file )
+
+	created_region_file =  os.path.join( tmp_dir, "ranger_peak_region.bed"  )
+	if os.path.exists( created_region_file ):
+        	shutil.move( created_region_file, output_region_file )
+
+	created_details_file =  os.path.join( tmp_dir, "ranger_peak_details"  )
+	if os.path.exists( created_details_file ):
+        	shutil.move( created_details_file, output_details_file )
+
+	#zips the html report and puts it in history, whole report is too big and display in galaxy is very unformatted 
+	filename = os.path.splitext(os.path.basename(options['chip_file']))[0]
+	filename = filename.upper()
+	extension = os.path.splitext(options['chip_file'])[1]
+	extension = extension.replace(".", "")
+	extension = extension.upper()
+	now = datetime.datetime.now()
+	date = now.strftime("%Y-%m-%d")
+	foldername = "%s_%s_REPORT_%s" % (filename, extension, date)
+
+	created_report_file = os.path.join( tmp_dir, foldername )
+	if os.path.exists ( created_report_file ):
+		#os.system("cp -rf %s %s" % (created_report_file, "/mnt/galaxyData/files/000/"))
+		os.system("cp -rf %s ." % created_report_file)
+		os.system("zip -r created_report.zip %s > /dev/null" % foldername)
+		#os.system("zip -r created_report.zip /mnt/galaxyData/files/000/%s > /dev/null" % foldername)
+		shutil.move( "created_report.zip", output_report_file)
+
+
+		#os.system("ln -fs %s/index.html %s" %( foldername, output_report_file ))
+		#datafoldername = os.path.splitext(os.path.basename(output_report_file))
+		#datafolder = os.path.join ("/mnt/galaxyData/files/000/" datafoldername)
+		#print "datafolder %s" % datafolder
+		#if os.path.exists( datafolder )
+		#	os.system("rm -rf %s" % datafolder)
+		#	os.system("cp -rf %s/%s/imgs /mnt/galaxyData/files/000/%s" % (tmp_dir, foldername, datafolder))
+		#	os.system("cp -rf %s/%s/scripts /mnt/galaxyData/files/000/%s" % (tmp_dir, foldername, datafolder))
+
+    os.unlink( stderr_name )
+    shutil.rmtree( tmp_dir )
+
+if __name__ == "__main__": main()