--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/maaslin_wrapper.py	Tue May 13 22:00:40 2014 -0400
@@ -0,0 +1,223 @@
+#!/usr/bin/env python
+
+"""
+Author: George Weingart
+Description: Wrapper program for maaslin
+"""
+
+#####################################################################################
+#Copyright (C) <2012>
+#
+#Permission is hereby granted, free of charge, to any person obtaining a copy of
+#this software and associated documentation files (the "Software"), to deal in the
+#Software without restriction, including without limitation the rights to use, copy,
+#modify, merge, publish, distribute, sublicense, and/or sell copies of the Software,
+#and to permit persons to whom the Software is furnished to do so, subject to
+#the following conditions:
+#
+#The above copyright notice and this permission notice shall be included in all copies
+#or substantial portions of the Software.
+#
+#THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
+#INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+#PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+#HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+#OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+#SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+#####################################################################################
+
+__author__ = "George Weingart"
+__copyright__ = "Copyright 2012"
+__credits__ = ["George Weingart"]
+__license__ = "MIT"
+__maintainer__ = "George Weingart"
+__email__ = "george.weingart@gmail.com"
+__status__ = "Development"
+
+from cStringIO import StringIO
+import sys,string
+import os
+import tempfile 
+from pprint import pprint
+import argparse
+
+######################################################################################
+#  Parse input parms                                                                 #
+######################################################################################
+def read_params(x):
+	parser = argparse.ArgumentParser(description='MaAsLin Argparser')
+	parser.add_argument('--lastmeta', action="store", dest='lastmeta',nargs='?')
+	parser.add_argument('--input', action="store", dest='input',nargs='?')
+	parser.add_argument('--output', action="store", dest='output',nargs='?')
+	parser.add_argument('--zip_file', action="store", dest='zip_file',nargs='?')
+	parser.add_argument('--alpha', action="store", type=float,default=0.05,dest='alpha',nargs='?')
+	parser.add_argument('--min_abd', action="store", type=float,default=0.0001,dest='min_abd',nargs='?')
+	parser.add_argument('--min_samp', action="store", type=float,default=0.01,dest='min_samp',nargs='?')
+	parser.add_argument('--tool_option1', action="store", dest='tool_option1',nargs='?')
+	return  parser
+
+
+
+######################################################################################
+#  Build read config file                                                            #
+######################################################################################
+def build_read_config_file(strTempDir,results, DSrc, DMaaslin, root_dir):
+	fname = results.input
+	input_file = open(fname)
+	input_lines = input_file.readlines()
+	LenInput = len(input_lines)
+	input_file.close()
+	TopLimit = int(results.lastmeta)
+	ReadConfigFileName = os.path.join(strTempDir,"Test.read.config")
+	Q = "'"
+
+	#WorkingDir = os.getcwd()
+	WorkingDir = root_dir
+	os.chdir(DMaaslin)
+
+	Limit1 = Q + "2-" + str(TopLimit )  + Q 
+	ReadConfigTb1 = [
+ 	os.path.join(DSrc,"CreateReadConfigFile.R"),
+	"-c",
+	Limit1,
+        ReadConfigFileName,
+	"Metadata"
+	">/dev/null",\
+	"2>&1"
+	]
+
+	cmd_config1 = " ".join(ReadConfigTb1)
+
+	os.system(cmd_config1)
+
+	Limit2 = Q + str(TopLimit +1 )  + '-' + Q 
+	ReadConfigTb2 = [
+ 	os.path.join(DSrc,"CreateReadConfigFile.R"),
+	"-a",
+	"-c",
+	Limit2,
+        ReadConfigFileName,
+	"Abundance"
+	">/dev/null",\
+	"2>&1"
+	]
+
+	cmd_config2 = " ".join(ReadConfigTb2)
+	os.system(cmd_config2)
+	os.chdir(WorkingDir)
+	return  ReadConfigFileName
+
+
+######################################################################################
+#   Main  Program                                                                    #
+######################################################################################
+
+# Parse commandline in
+parser = read_params( sys.argv )
+results = parser.parse_args()
+root_dir = os.environ.get('maaslin_SCRIPT_PATH')
+
+
+
+
+
+
+### If option 2 is selected inform user on 2 outputs
+if results.tool_option1 == "2":
+	print "***Please note: 2 output files are  generated: Complete zipped results + Summary  ***"
+
+### Project name
+strProjectName = os.path.splitext(os.path.basename(results.input))[0]
+
+### Define directory locations
+D = os.path.join(root_dir)
+DSrc = os.path.join(root_dir,"src")
+DInput = os.path.join(root_dir,"maaslin","input")
+DMaaslin = os.path.join(root_dir)
+
+DMaaslinGalaxy = os.path.join(root_dir)
+
+
+
+### Make temporary folder to work in
+### Change permissions to make useable 
+strTempDir = tempfile.mkdtemp()
+cmd_chmod = "chmod 755 /" + strTempDir
+os.system(cmd_chmod)
+cmd_mkdir1 = "mkdir -m 755 " +  os.path.join(strTempDir,strProjectName)
+os.system(cmd_mkdir1)
+
+### Transpose the pcl file to a tsv file
+TbCmdTranspose = [\
+	"python",
+	DMaaslinGalaxy  + "/transpose.py<" + str(results.input) +  ">" +  os.path.join(strTempDir,"output.tsv")\
+	]
+cmd_transpose = " ".join(TbCmdTranspose)
+os.system(cmd_transpose)
+
+### Make path for target output file
+OutputFile = os.path.join(strTempDir,strProjectName,strProjectName+".txt")
+
+### Make read config file
+ReadConfigFileName = build_read_config_file(strTempDir,results, DSrc, DMaaslin, root_dir)
+
+### Build MaAsLin comamnd
+CmdsArray = [\
+os.path.join(DSrc,"Maaslin.R"),  \
+"-d", str(results.alpha),\
+"-r", str(results.min_abd),\
+"-p", str(results.min_samp), \
+"-i", \
+ReadConfigFileName, \
+OutputFile, \
+os.path.join(strTempDir,"output.tsv"), \
+"-v",\
+"ERROR",\
+">/dev/null",\
+"2>&1"
+]
+
+invoke_maaslin_cmd = " ".join(CmdsArray)
+
+
+
+
+
+### Write to directory cmd line used for troubleshooting
+#CmdFileName = os.path.join(strTempDir,"cmdfile.txt")
+#OutFile = open(CmdFileName,"w")
+#OutputString = invoke_maaslin_cmd + "\n"
+#OutFile.write(OutputString)
+#OutFile.close()
+
+### Call MaAsLin
+os.system(invoke_maaslin_cmd)
+
+
+### Copy output file to make available to galaxy
+cmd_copy = "cp " + os.path.join(strTempDir,strProjectName+"/output.txt") + " " + results.output
+MsgFileName = os.path.join(strTempDir,strProjectName+"/output.txt") 
+
+if  not os.path.isfile(MsgFileName):
+	cmd_copy = "cp " + os.path.join(strTempDir,strProjectName+"/output.txt") + " " + results.output
+	OutFile = open(MsgFileName,"w")
+	OutputString = "A MaAsLin error has occurred\n"
+	OutputString = OutputString + "It typically happens when incorrect 'Last metadata row' was selected\n"
+	OutputString = OutputString + "For demo data please choose 'Weight'\n"
+	OutFile.write(OutputString)
+	OutFile.close()
+
+os.system(cmd_copy)
+
+### Zip up output folder
+cmd_zip = "zip -jr " + os.path.join(strTempDir,strProjectName+".zip") + " " + os.path.join(strTempDir,strProjectName) + ">/dev/null 2>&1"
+
+os.system(cmd_zip)
+
+### Copy output folder to make available to galaxy
+cmd_copy_zip = "cp " + os.path.join(strTempDir,strProjectName+".zip") + " " + results.zip_file
+os.system(cmd_copy_zip)
+
+### Delete temp directory
+cmd_del_tempdir = "rm -r " + strTempDir
+######os.system(cmd_del_tempdir)