--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyrocleaner_galaxy_tool_V1.2/pyrocleaner_wrapper.py	Thu Jun 09 06:09:09 2011 -0400
@@ -0,0 +1,88 @@
+#
+# Pyrocleaner wrapper for galaxy
+# Copyright (C) 2009 INRA
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+#
+
+__author__ = 'Plateforme bioinformatique Midi Pyrenees'
+__copyright__ = 'Copyright (C) 2009 INRA'
+__license__ = 'GNU General Public License'
+__version__ = '1.2'
+__email__ = 'support.genopole@toulouse.inra.fr'
+__status__ = 'beta'
+
+import optparse, os, shutil, subprocess, sys, tempfile, re, string
+    
+if __name__ == "__main__":
+    
+    parser = optparse.OptionParser()
+    
+    parser.add_option( '-s', '--options',      dest='options',      help='The pyrocleaner options' )
+    parser.add_option( '-l', '--log',          dest='log',          help='Path to the pyrocleaner log' )
+    parser.add_option( '-f', '--format',       dest='format',       help='The input file format (sff|fastq)' )
+    parser.add_option( '-o', '--output',       dest='output',       help='The output file path' )
+    parser.add_option( '-a', '--out-pe-qual',  dest='out_pe_qual',  help='The output pairends qual file path' )
+    parser.add_option( '-b', '--out-pe-fasta', dest='out_pe_fasta', help='The output pairends fasta file path' )
+    parser.add_option( '-d', '--out-dir',      dest='out_dir',      help='The output dir where to process the data' )
+    
+    (options, args) = parser.parse_args()
+    
+    buffsize = 1048576
+    tmp_dir = tempfile.mkdtemp()
+    
+    try:
+    
+        if options.format == "sff": format = "sff"
+        else : format = "fastq"
+        
+        tmp_stderr_name = tempfile.NamedTemporaryFile( dir=tmp_dir,suffix='.err' ).name
+        tmp_stderr = open( tmp_stderr_name, 'wb' )
+        tmp_stdout_name = tempfile.NamedTemporaryFile( dir=tmp_dir,suffix='.out' ).name
+        tmp_stdout = open( tmp_stdout_name, 'wb' )
+        cmd = 'pyrocleaner --format %s %s --out %s' % (format, options.options, options.out_dir)
+        proc = subprocess.Popen( args=cmd, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno() )
+        returncode = proc.wait()
+        tmp_stderr.close()
+        # get stderr, allowing for case where it's very large
+        tmp_stderr = open( tmp_stderr_name, 'rb' )
+        stderr = ''
+        try:
+            while True:
+                stderr += tmp_stderr.read( buffsize )
+                if not stderr or len( stderr ) % buffsize != 0:
+                    break
+        except OverflowError:
+            pass
+        tmp_stderr.close()
+        if returncode != 0:
+            raise Exception, stderr
+        
+        # Move the log file to the right place
+        shutil.move(os.path.join(options.out_dir, "pyrocleaner.log"), options.log)
+        
+        for file in os.listdir(options.out_dir):
+            # If the file has the input file format and is not a shotgun file
+            if file.endswith(format):
+                shutil.move(os.path.join(options.out_dir, file), options.output)
+            # If it's a quality file from shotgun
+            if file.endswith(".qual") :
+                shutil.move(os.path.join(options.out_dir, file), options.out_pe_qual)
+            # If it's a fasta file from shotgun
+            elif file.endswith(".fasta") :
+                shutil.move(os.path.join(options.out_dir, file), options.out_pe_fasta)
+
+    except Exception:
+        raise Exception, 'Error executing pyrocleaner.'