fastqc: rgFastQC.py annotate

annotate rgFastQC.py @ 8:5b995cef2fbb draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702

author	iuc
date	Tue, 31 Jan 2017 07:22:22 -0500
parents	ec73b7c83b2c
children	0a7c65540937

rev	line source
0 d5e4121e45ed Imported from capsule None devteam parents: diff changeset	1 """
1 67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	2 Rewrite of rgFastQC.py for Version 0.11.2 of FastQC.
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	3
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	4 Changes implemented from tmcgowan at
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	5 https://testtoolshed.g2.bx.psu.edu/view/tmcgowan/fastqc
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	6 and iuc at https://toolshed.g2.bx.psu.edu/view/iuc/fastqc
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	7 with minor changes and bug fixes
0 d5e4121e45ed Imported from capsule None devteam parents: diff changeset	8
1 67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	9 SYNOPSIS
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	10
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	11 rgFastQC.py -i input_file -j input_file.name -o output_html_file [-d output_directory]
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	12 [-f fastq\|bam\|sam] [-n job_name] [-c contaminant_file] [-e fastqc_executable]
0 d5e4121e45ed Imported from capsule None devteam parents: diff changeset	13
1 67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	14 EXAMPLE (generated by Galaxy)
0 d5e4121e45ed Imported from capsule None devteam parents: diff changeset	15
1 67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	16 rgFastQC.py -i path/dataset_1.dat -j 1000gsample.fastq -o path/dataset_3.dat -d path/job_working_directory/subfolder
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	17 -f fastq -n FastQC -c path/dataset_2.dat -e fastqc
0 d5e4121e45ed Imported from capsule None devteam parents: diff changeset	18 """
8 5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	19 import bz2
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	20 import glob
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	21 import gzip
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	22 import mimetypes
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	23 import optparse
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	24 import os
0 d5e4121e45ed Imported from capsule None devteam parents: diff changeset	25 import re
1 67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	26 import shutil
0 d5e4121e45ed Imported from capsule None devteam parents: diff changeset	27 import subprocess
d5e4121e45ed Imported from capsule None devteam parents: diff changeset	28 import tempfile
d5e4121e45ed Imported from capsule None devteam parents: diff changeset	29 import zipfile
8 5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	30
0 d5e4121e45ed Imported from capsule None devteam parents: diff changeset	31
1 67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	32 class FastQCRunner(object):
8 5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	33 def __init__(self, opts=None):
1 67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	34 '''
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	35 Initializes an object to run FastQC in Galaxy. To start the process, use the function run_fastqc()
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	36 '''
6 e8c90ad3cbf9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8 devteam parents: 4 diff changeset	37
1 67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	38 # Check whether the options are specified and saves them into the object
8 5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	39 assert opts is not None
1 67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	40 self.opts = opts
0 d5e4121e45ed Imported from capsule None devteam parents: diff changeset	41
1 67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	42 def prepare_command_line(self):
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	43 '''
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	44 Develops the Commandline to run FastQC in Galaxy
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	45 '''
6 e8c90ad3cbf9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8 devteam parents: 4 diff changeset	46
1 67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	47 # Check whether a given file compression format is valid
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	48 # This prevents uncompression of already uncompressed files
0 d5e4121e45ed Imported from capsule None devteam parents: diff changeset	49 infname = self.opts.inputfilename
d5e4121e45ed Imported from capsule None devteam parents: diff changeset	50 linf = infname.lower()
d5e4121e45ed Imported from capsule None devteam parents: diff changeset	51 trimext = False
d5e4121e45ed Imported from capsule None devteam parents: diff changeset	52 # decompression at upload currently does NOT remove this now bogus ending - fastqc will barf
d5e4121e45ed Imported from capsule None devteam parents: diff changeset	53 # patched may 29 2013 until this is fixed properly
7 ec73b7c83b2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit 8918618a5ef7bdca55a31cd919efa593044a376e devteam parents: 6 diff changeset	54 type = mimetypes.guess_type(self.opts.input)
ec73b7c83b2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit 8918618a5ef7bdca55a31cd919efa593044a376e devteam parents: 6 diff changeset	55 if linf.endswith('.gz') or linf.endswith('.gzip') or type[-1] == "gzip":
0 d5e4121e45ed Imported from capsule None devteam parents: diff changeset	56 f = gzip.open(self.opts.input)
d5e4121e45ed Imported from capsule None devteam parents: diff changeset	57 try:
1 67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	58 f.readline()
0 d5e4121e45ed Imported from capsule None devteam parents: diff changeset	59 except:
d5e4121e45ed Imported from capsule None devteam parents: diff changeset	60 trimext = True
d5e4121e45ed Imported from capsule None devteam parents: diff changeset	61 f.close()
d5e4121e45ed Imported from capsule None devteam parents: diff changeset	62 elif linf.endswith('bz2'):
8 5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	63 f = bz2.BZ2File(self.opts.input, 'r')
0 d5e4121e45ed Imported from capsule None devteam parents: diff changeset	64 try:
d5e4121e45ed Imported from capsule None devteam parents: diff changeset	65 f.readline()
d5e4121e45ed Imported from capsule None devteam parents: diff changeset	66 except:
d5e4121e45ed Imported from capsule None devteam parents: diff changeset	67 trimext = True
d5e4121e45ed Imported from capsule None devteam parents: diff changeset	68 f.close()
d5e4121e45ed Imported from capsule None devteam parents: diff changeset	69 elif linf.endswith('.zip'):
d5e4121e45ed Imported from capsule None devteam parents: diff changeset	70 if not zipfile.is_zipfile(self.opts.input):
d5e4121e45ed Imported from capsule None devteam parents: diff changeset	71 trimext = True
d5e4121e45ed Imported from capsule None devteam parents: diff changeset	72 if trimext:
8 5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	73 f = open(self.opts.input)
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	74 try:
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	75 f.readline()
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	76 except:
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	77 raise Exception("Input file corruption, could not identify the filetype")
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	78 infname = os.path.splitext(infname)[0]
6 e8c90ad3cbf9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8 devteam parents: 4 diff changeset	79
1 67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	80 # Replace unwanted or problematic charaters in the input file name
8 5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	81 self.fastqinfilename = re.sub(r'[^a-zA-Z0-9_\-\.]', '_', os.path.basename(infname))
4 ca0eb9b89b32 Uploaded devteam parents: 3 diff changeset	82 # check that the symbolic link gets a proper ending, fastqc seems to ignore the given format otherwise
8 5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	83 if 'fastq' in self.opts.informat:
6 e8c90ad3cbf9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8 devteam parents: 4 diff changeset	84 # with fastq the .ext is ignored, but when a format is actually passed it must comply with fastqc's
4 ca0eb9b89b32 Uploaded devteam parents: 3 diff changeset	85 # accepted formats..
8 5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	86 self.opts.informat = 'fastq'
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	87 elif not self.fastqinfilename.endswith(self.opts.informat):
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	88 self.fastqinfilename += '.%s' % self.opts.informat
4 ca0eb9b89b32 Uploaded devteam parents: 3 diff changeset	89
1 67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	90 # Build the Commandline from the given parameters
8 5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	91 command_line = [opts.executable, '--outdir %s' % self.opts.outputdir]
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	92 if self.opts.contaminants is not None:
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	93 command_line.append('--contaminants %s' % self.opts.contaminants)
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	94 if self.opts.limits is not None:
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	95 command_line.append('--limits %s' % self.opts.limits)
1 67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	96 command_line.append('--quiet')
8 5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	97 command_line.append('--extract') # to access the output text file
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	98 if type[-1] != "gzip":
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	99 command_line.append('-f %s' % self.opts.informat)
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	100 else:
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	101 self.fastqinfilename += ".gz"
1 67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	102 command_line.append(self.fastqinfilename)
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	103 self.command_line = ' '.join(command_line)
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	104
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	105 def copy_output_file_to_dataset(self):
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	106 '''
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	107 Retrieves the output html and text files from the output directory and copies them to the Galaxy output files
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	108 '''
6 e8c90ad3cbf9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8 devteam parents: 4 diff changeset	109
1 67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	110 # retrieve html file
8 5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	111 result_file = glob.glob(self.opts.outputdir + '/*html')
1 67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	112 with open(result_file[0], 'rb') as fsrc:
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	113 with open(self.opts.htmloutput, 'wb') as fdest:
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	114 shutil.copyfileobj(fsrc, fdest)
6 e8c90ad3cbf9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8 devteam parents: 4 diff changeset	115
1 67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	116 # retrieve text file
8 5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	117 text_file = glob.glob(self.opts.outputdir + '/*/fastqc_data.txt')
1 67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	118 with open(text_file[0], 'rb') as fsrc:
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	119 with open(self.opts.textoutput, 'wb') as fdest:
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	120 shutil.copyfileobj(fsrc, fdest)
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	121
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	122 def run_fastqc(self):
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	123 '''
8 5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	124 Executes FastQC. Make sure the mandatory import parameters input, inputfilename, outputdir and htmloutput have been specified in the options
1 67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	125 '''
6 e8c90ad3cbf9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8 devteam parents: 4 diff changeset	126
1 67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	127 # Create a log file
8 5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	128 dummy, tlog = tempfile.mkstemp(prefix='rgFastQC', suffix=".log", dir=self.opts.outputdir)
1 67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	129 sout = open(tlog, 'w')
6 e8c90ad3cbf9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8 devteam parents: 4 diff changeset	130
1 67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	131 self.prepare_command_line()
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	132 sout.write(self.command_line)
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	133 sout.write('\n')
8 5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	134 sout.write("Creating symlink\n") # between the input (.dat) file and the given input file name
1 67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	135 os.symlink(self.opts.input, self.fastqinfilename)
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	136 sout.write("check_call\n")
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	137 subprocess.check_call(self.command_line, shell=True)
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	138 sout.write("Copying working %s file to %s \n" % (self.fastqinfilename, self.opts.htmloutput))
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	139 self.copy_output_file_to_dataset()
67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	140 sout.write("Finished")
0 d5e4121e45ed Imported from capsule None devteam parents: diff changeset	141 sout.close()
d5e4121e45ed Imported from capsule None devteam parents: diff changeset	142
8 5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	143
0 d5e4121e45ed Imported from capsule None devteam parents: diff changeset	144 if __name__ == '__main__':
d5e4121e45ed Imported from capsule None devteam parents: diff changeset	145 op = optparse.OptionParser()
d5e4121e45ed Imported from capsule None devteam parents: diff changeset	146 op.add_option('-i', '--input', default=None)
1 67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	147 op.add_option('-j', '--inputfilename', default=None)
0 d5e4121e45ed Imported from capsule None devteam parents: diff changeset	148 op.add_option('-o', '--htmloutput', default=None)
1 67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	149 op.add_option('-t', '--textoutput', default=None)
0 d5e4121e45ed Imported from capsule None devteam parents: diff changeset	150 op.add_option('-d', '--outputdir', default="/tmp/shortread")
d5e4121e45ed Imported from capsule None devteam parents: diff changeset	151 op.add_option('-f', '--informat', default='fastq')
d5e4121e45ed Imported from capsule None devteam parents: diff changeset	152 op.add_option('-n', '--namejob', default='rgFastQC')
d5e4121e45ed Imported from capsule None devteam parents: diff changeset	153 op.add_option('-c', '--contaminants', default=None)
1 67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	154 op.add_option('-l', '--limits', default=None)
0 d5e4121e45ed Imported from capsule None devteam parents: diff changeset	155 op.add_option('-e', '--executable', default='fastqc')
d5e4121e45ed Imported from capsule None devteam parents: diff changeset	156 opts, args = op.parse_args()
6 e8c90ad3cbf9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8 devteam parents: 4 diff changeset	157
8 5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	158 assert opts.input is not None
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	159 assert opts.inputfilename is not None
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702 iuc parents: 7 diff changeset	160 assert opts.htmloutput is not None
6 e8c90ad3cbf9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8 devteam parents: 4 diff changeset	161 if not os.path.exists(opts.outputdir):
0 d5e4121e45ed Imported from capsule None devteam parents: diff changeset	162 os.makedirs(opts.outputdir)
6 e8c90ad3cbf9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8 devteam parents: 4 diff changeset	163
1 67355741fbc3 Uploaded from GH devteam parents: 0 diff changeset	164 fastqc_runner = FastQCRunner(opts)
3 36980a78cc83 Uploaded devteam parents: 1 diff changeset	165 fastqc_runner.run_fastqc()

Mercurial > repos > devteam > fastqc

annotate rgFastQC.py @ 8:5b995cef2fbb draft