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1 # This is a wrapper for JAMM to use it in Galaxy
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2 # It will be accompanied with a jamm.xml file, which specifies the interface that Galaxy is showing to the user
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3 # as well as the JAMM software including JAMM.sh, the bash script that is actually called.
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4
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5 # This wrapper does the following things:
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6 # map the files (from Galaxy history) to a directory
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7 # pass the parameters from the GUI to JAMM.sh
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8 # call JAMM.sh
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9 # maybe map the resulting tabular files back to history items, the XML could take care of that if output is fixed
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10
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11 #import optparse
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12 import argparse, os, shutil, subprocess, sys, tempfile
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13 import shlex
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14 # importing some of the modules used, especially for symlinking, dir manipulation and tool calling.
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15 # since python2.7, argparse is preferred over optparse.
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16
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17 # for reference wrappers, see
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18 # https://bitbucket.org/fubar/rossdev/src/4a91f99b5e1953270c9b35d2ca70c325a10fcfcb/rgdev/bwa_wrapper.py?at=default
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19 # https://www.e-biogenouest.org/wiki/WrapperpythonforGalaxy:Asyntaxexample
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20
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21 def main():
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22
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23 #Read command line arguments
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24 parser = argparse.ArgumentParser()
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25 parser.add_argument('-i', dest = 'input', nargs='+')
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26 parser.add_argument('-g', dest = 'gsize')
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27 parser.add_argument('-z', dest = 'peakfile')
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28
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29 parser.add_argument('-m', dest = 'mode')
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30 parser.add_argument('-r', dest = 'resolution')
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31 parser.add_argument('-p', dest = 'processes')
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32 #parser.add_argument('-b', dest = 'binSize')
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33
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34 args = parser.parse_args()
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35
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36 print "\n"
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37 print "Wrapper debugging"
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38 print "Files to be used:"
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39 for j in args.input:
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40 print j
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41
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42 print "output file:"
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43 print args.peakfile
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44
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45 # depracted, can still be found in may of the example wrappers
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46 #parser = optparse.OptionParser()
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47 #parser.add_option( '-i', dest='input', help='input bed files' )
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48 #parser.add_option( '-c', dest='csize', help='chr sizes' )
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49 #(options, args) = parser.parse_args()
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50
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51 # create temp dir
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52 tmp_dir = tempfile.mkdtemp()
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53 os.chdir(tmp_dir)
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54 # symlink creation
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55 for file in args.input:
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56 filen = tmp_dir + "/" + os.path.basename(os.path.splitext(file)[0])+".bed"
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57 os.symlink(file, filen)
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58
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59 # in case temp files should have random names
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60 # ref_file = tempfile.NamedTemporaryFile( dir=tmp_dir )
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61 # ref_file_name = ref_file.name
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62 # ref_file.close()
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63 # os.symlink( file, ref_file_name )
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64
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65 command = ( "/home/cmesser/galaxy/tools/jamm/JAMM.sh -s %s -g %s -o results -m %s -r %s -p %s"
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66 % ( tmp_dir, args.gsize, args.mode, args.resolution, args.processes ) )
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67 print command
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68 # depending on how your programm is called, it may be necessary to use shlex.split on the command string before
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69 # in this case, this was actually harmful. idk why
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70 # command = shlex.split(command)
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71 # Please read the docs for subprocess.Popen. You can't just pass as string as variables need to be extended
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72 # Note that shell = True can be a security hazard.
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73 # proc = subprocess.Popen( command, executable = '/bin/bash', shell=True )
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74 proc = subprocess.Popen( command, shell=True)
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75 returncode = proc.wait()
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76
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77 #mv files to a place where galaxy wrapper can find them
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78 mvcommand = "mv %s/results/peaks/all.peaks.narrowPeak %s" % ( tmp_dir, args.peakfile )
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79 os.system(mvcommand)
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80
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81 # clean up temp dir
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82 if os.path.exists( tmp_dir ):
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83 shutil.rmtree( tmp_dir )
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84
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85
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86 if __name__ == "__main__":
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87 main()
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88
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