diff jammwrapper.py @ 0:d42f4d78c85e draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/jammwrapper.py	Wed Dec 17 10:40:23 2014 -0500
@@ -0,0 +1,88 @@
+# This is a wrapper for JAMM to use it in Galaxy
+# It will be accompanied with a jamm.xml file, which specifies the interface that Galaxy is showing to the user
+# as well as the JAMM software including JAMM.sh, the bash script that is actually called.
+
+# This wrapper does the following things:
+# map the files (from Galaxy history) to a directory
+# pass the parameters from the GUI to JAMM.sh
+# call JAMM.sh
+# maybe map the resulting tabular files back to history items, the XML could take care of that if output is fixed
+
+#import optparse
+import argparse, os, shutil, subprocess, sys, tempfile
+import shlex
+# importing some of the modules used, especially for symlinking, dir manipulation and tool calling.
+# since python2.7, argparse is preferred over optparse.
+
+# for reference wrappers, see
+# https://bitbucket.org/fubar/rossdev/src/4a91f99b5e1953270c9b35d2ca70c325a10fcfcb/rgdev/bwa_wrapper.py?at=default
+# https://www.e-biogenouest.org/wiki/WrapperpythonforGalaxy:Asyntaxexample
+
+def main(): 
+
+    #Read command line arguments
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-i', dest = 'input', nargs='+')
+    parser.add_argument('-g', dest = 'gsize')
+    parser.add_argument('-z', dest = 'peakfile')
+    
+    parser.add_argument('-m', dest = 'mode')
+    parser.add_argument('-r', dest = 'resolution')
+    parser.add_argument('-p', dest = 'processes')
+    #parser.add_argument('-b', dest = 'binSize')
+    
+    args = parser.parse_args()
+   
+    print "\n"
+    print "Wrapper debugging" 
+    print "Files to be used:"
+    for j in args.input:
+        print j
+
+    print "output file:"
+    print args.peakfile
+
+    # depracted, can still be found in may of the example wrappers    
+    #parser = optparse.OptionParser()
+    #parser.add_option( '-i',  dest='input', help='input bed files' )
+    #parser.add_option( '-c',  dest='csize', help='chr sizes' )
+    #(options, args) = parser.parse_args()	
+   
+    # create temp dir
+    tmp_dir = tempfile.mkdtemp()
+    os.chdir(tmp_dir)
+    # symlink creation
+    for file in args.input:
+        filen =  tmp_dir + "/" + os.path.basename(os.path.splitext(file)[0])+".bed"
+        os.symlink(file, filen)
+        
+        # in case temp files should have random names
+        # ref_file = tempfile.NamedTemporaryFile( dir=tmp_dir )
+        # ref_file_name = ref_file.name
+        # ref_file.close()
+        # os.symlink( file, ref_file_name )
+    
+    command = ( "/home/cmesser/galaxy/tools/jamm/JAMM.sh -s %s -g %s -o results -m %s -r %s -p %s"
+     % ( tmp_dir, args.gsize, args.mode, args.resolution, args.processes ) ) 
+    print command
+    # depending on how your programm is called, it may be necessary to use shlex.split on the command string before
+    # in this case, this was actually harmful. idk why
+#    command = shlex.split(command)
+    # Please read the docs for subprocess.Popen. You can't just pass as string as variables need to be extended
+    # Note that shell = True can be a security hazard. 
+#    proc = subprocess.Popen( command, executable = '/bin/bash', shell=True )
+    proc = subprocess.Popen( command, shell=True)
+    returncode = proc.wait()
+    
+    #mv files to a place where galaxy wrapper can find them
+    mvcommand = "mv %s/results/peaks/all.peaks.narrowPeak %s" % ( tmp_dir, args.peakfile ) 
+    os.system(mvcommand)
+
+# clean up temp dir
+    if os.path.exists( tmp_dir ):
+        shutil.rmtree( tmp_dir )    
+
+    
+if __name__ == "__main__":
+    main()
+