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comparison rgFastQC.py @ 9:3a458e268066 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit 8918618a5ef7bdca55a31cd919efa593044a376e
author devteam
date Wed, 02 Nov 2016 16:12:51 -0400
parents 06819360a9e2
children a00a6402d09a
comparison
equal deleted inserted replaced
8:06819360a9e2 9:3a458e268066
26 import tempfile 26 import tempfile
27 import glob 27 import glob
28 import gzip 28 import gzip
29 import bz2 29 import bz2
30 import zipfile 30 import zipfile
31 import mimetypes
31 32
32 class FastQCRunner(object): 33 class FastQCRunner(object):
33 34
34 def __init__(self,opts=None): 35 def __init__(self,opts=None):
35 ''' 36 '''
50 infname = self.opts.inputfilename 51 infname = self.opts.inputfilename
51 linf = infname.lower() 52 linf = infname.lower()
52 trimext = False 53 trimext = False
53 # decompression at upload currently does NOT remove this now bogus ending - fastqc will barf 54 # decompression at upload currently does NOT remove this now bogus ending - fastqc will barf
54 # patched may 29 2013 until this is fixed properly 55 # patched may 29 2013 until this is fixed properly
55 if ( linf.endswith('.gz') or linf.endswith('.gzip') ): 56 type = mimetypes.guess_type(self.opts.input)
57 if linf.endswith('.gz') or linf.endswith('.gzip') or type[-1] == "gzip":
56 f = gzip.open(self.opts.input) 58 f = gzip.open(self.opts.input)
57 try: 59 try:
58 f.readline() 60 f.readline()
59 except: 61 except:
60 trimext = True 62 trimext = True
93 command_line.append('--contaminants %s' % opts.contaminants) 95 command_line.append('--contaminants %s' % opts.contaminants)
94 if opts.limits != None: 96 if opts.limits != None:
95 command_line.append('--limits %s' % opts.limits) 97 command_line.append('--limits %s' % opts.limits)
96 command_line.append('--quiet') 98 command_line.append('--quiet')
97 command_line.append('--extract') # to access the output text file 99 command_line.append('--extract') # to access the output text file
100 if type[-1] != "gzip":
101 command_line.append('-f %s' % opts.informat)
102 else:
103 self.fastqinfilename += ".gz"
98 command_line.append(self.fastqinfilename) 104 command_line.append(self.fastqinfilename)
99 command_line.append('-f %s' % opts.informat)
100 self.command_line = ' '.join(command_line) 105 self.command_line = ' '.join(command_line)
101 106
102 def copy_output_file_to_dataset(self): 107 def copy_output_file_to_dataset(self):
103 ''' 108 '''
104 Retrieves the output html and text files from the output directory and copies them to the Galaxy output files 109 Retrieves the output html and text files from the output directory and copies them to the Galaxy output files