fastqc: rgFastQC.py annotate

annotate rgFastQC.py @ 10:a00a6402d09a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1

author	iuc
date	Wed, 08 Feb 2017 12:43:43 -0500
parents	3a458e268066
children	db2dc6bc8f05

rev	line source
0 e28c965eeed4 Imported from capsule None devteam parents: diff changeset	1 """
1 8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	2 Rewrite of rgFastQC.py for Version 0.11.2 of FastQC.
8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	3
8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	4 Changes implemented from tmcgowan at
8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	5 https://testtoolshed.g2.bx.psu.edu/view/tmcgowan/fastqc
8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	6 and iuc at https://toolshed.g2.bx.psu.edu/view/iuc/fastqc
8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	7 with minor changes and bug fixes
0 e28c965eeed4 Imported from capsule None devteam parents: diff changeset	8
1 8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	9 SYNOPSIS
8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	10
8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	11 rgFastQC.py -i input_file -j input_file.name -o output_html_file [-d output_directory]
8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	12 [-f fastq\|bam\|sam] [-n job_name] [-c contaminant_file] [-e fastqc_executable]
0 e28c965eeed4 Imported from capsule None devteam parents: diff changeset	13
1 8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	14 EXAMPLE (generated by Galaxy)
0 e28c965eeed4 Imported from capsule None devteam parents: diff changeset	15
1 8fae48caaf06 Uploaded form 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
8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	17 -f fastq -n FastQC -c path/dataset_2.dat -e fastqc
0 e28c965eeed4 Imported from capsule None devteam parents: diff changeset	18 """
10 a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	19 import bz2
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	20 import glob
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	21 import gzip
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	22 import mimetypes
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	23 import optparse
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	24 import os
0 e28c965eeed4 Imported from capsule None devteam parents: diff changeset	25 import re
1 8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	26 import shutil
0 e28c965eeed4 Imported from capsule None devteam parents: diff changeset	27 import subprocess
e28c965eeed4 Imported from capsule None devteam parents: diff changeset	28 import tempfile
e28c965eeed4 Imported from capsule None devteam parents: diff changeset	29 import zipfile
10 a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	30
0 e28c965eeed4 Imported from capsule None devteam parents: diff changeset	31
1 8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	32 class FastQCRunner(object):
10 a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	33 def __init__(self, opts=None):
1 8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	34 '''
8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	35 Initializes an object to run FastQC in Galaxy. To start the process, use the function run_fastqc()
8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	36 '''
8 06819360a9e2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8 devteam parents: 7 diff changeset	37
1 8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	38 # Check whether the options are specified and saves them into the object
10 a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	39 assert opts is not None
1 8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	40 self.opts = opts
0 e28c965eeed4 Imported from capsule None devteam parents: diff changeset	41
1 8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	42 def prepare_command_line(self):
8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	43 '''
8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	44 Develops the Commandline to run FastQC in Galaxy
8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	45 '''
8 06819360a9e2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8 devteam parents: 7 diff changeset	46
1 8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	47 # Check whether a given file compression format is valid
8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	48 # This prevents uncompression of already uncompressed files
0 e28c965eeed4 Imported from capsule None devteam parents: diff changeset	49 infname = self.opts.inputfilename
e28c965eeed4 Imported from capsule None devteam parents: diff changeset	50 linf = infname.lower()
e28c965eeed4 Imported from capsule None devteam parents: diff changeset	51 trimext = False
e28c965eeed4 Imported from capsule None devteam parents: diff changeset	52 # decompression at upload currently does NOT remove this now bogus ending - fastqc will barf
e28c965eeed4 Imported from capsule None devteam parents: diff changeset	53 # patched may 29 2013 until this is fixed properly
9 3a458e268066 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit 8918618a5ef7bdca55a31cd919efa593044a376e devteam parents: 8 diff changeset	54 type = mimetypes.guess_type(self.opts.input)
3a458e268066 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit 8918618a5ef7bdca55a31cd919efa593044a376e devteam parents: 8 diff changeset	55 if linf.endswith('.gz') or linf.endswith('.gzip') or type[-1] == "gzip":
0 e28c965eeed4 Imported from capsule None devteam parents: diff changeset	56 f = gzip.open(self.opts.input)
e28c965eeed4 Imported from capsule None devteam parents: diff changeset	57 try:
1 8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	58 f.readline()
0 e28c965eeed4 Imported from capsule None devteam parents: diff changeset	59 except:
e28c965eeed4 Imported from capsule None devteam parents: diff changeset	60 trimext = True
e28c965eeed4 Imported from capsule None devteam parents: diff changeset	61 f.close()
e28c965eeed4 Imported from capsule None devteam parents: diff changeset	62 elif linf.endswith('bz2'):
10 a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	63 f = bz2.BZ2File(self.opts.input, 'r')
0 e28c965eeed4 Imported from capsule None devteam parents: diff changeset	64 try:
e28c965eeed4 Imported from capsule None devteam parents: diff changeset	65 f.readline()
e28c965eeed4 Imported from capsule None devteam parents: diff changeset	66 except:
e28c965eeed4 Imported from capsule None devteam parents: diff changeset	67 trimext = True
e28c965eeed4 Imported from capsule None devteam parents: diff changeset	68 f.close()
e28c965eeed4 Imported from capsule None devteam parents: diff changeset	69 elif linf.endswith('.zip'):
e28c965eeed4 Imported from capsule None devteam parents: diff changeset	70 if not zipfile.is_zipfile(self.opts.input):
e28c965eeed4 Imported from capsule None devteam parents: diff changeset	71 trimext = True
e28c965eeed4 Imported from capsule None devteam parents: diff changeset	72 if trimext:
10 a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	73 f = open(self.opts.input)
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	74 try:
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	75 f.readline()
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	76 except:
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	77 raise Exception("Input file corruption, could not identify the filetype")
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	78 infname = os.path.splitext(infname)[0]
8 06819360a9e2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8 devteam parents: 7 diff changeset	79
1 8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	80 # Replace unwanted or problematic charaters in the input file name
10 a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	81 self.fastqinfilename = re.sub(r'[^a-zA-Z0-9_\-\.]', '_', os.path.basename(infname))
4 8c650f7f76e9 Uploaded devteam parents: 3 diff changeset	82 # check that the symbolic link gets a proper ending, fastqc seems to ignore the given format otherwise
10 a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	83 if 'fastq' in self.opts.informat:
8 06819360a9e2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8 devteam parents: 7 diff changeset	84 # with fastq the .ext is ignored, but when a format is actually passed it must comply with fastqc's
4 8c650f7f76e9 Uploaded devteam parents: 3 diff changeset	85 # accepted formats..
10 a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	86 self.opts.informat = 'fastq'
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	87 elif not self.fastqinfilename.endswith(self.opts.informat):
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	88 self.fastqinfilename += '.%s' % self.opts.informat
4 8c650f7f76e9 Uploaded devteam parents: 3 diff changeset	89
1 8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	90 # Build the Commandline from the given parameters
10 a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	91 command_line = [opts.executable, '--outdir %s' % self.opts.outputdir]
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	92 if self.opts.contaminants is not None:
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	93 command_line.append('--contaminants %s' % self.opts.contaminants)
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	94 if self.opts.limits is not None:
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	95 command_line.append('--limits %s' % self.opts.limits)
1 8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	96 command_line.append('--quiet')
10 a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	97 command_line.append('--extract') # to access the output text file
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	98 if type[-1] != "gzip":
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	99 command_line.append('-f %s' % self.opts.informat)
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	100 else:
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	101 self.fastqinfilename += ".gz"
1 8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	102 command_line.append(self.fastqinfilename)
8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	103 self.command_line = ' '.join(command_line)
8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	104
8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	105 def copy_output_file_to_dataset(self):
8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	106 '''
8fae48caaf06 Uploaded form 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
8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	108 '''
8 06819360a9e2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8 devteam parents: 7 diff changeset	109
1 8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	110 # retrieve html file
10 a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	111 result_file = glob.glob(self.opts.outputdir + '/*html')
1 8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	112 with open(result_file[0], 'rb') as fsrc:
8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	113 with open(self.opts.htmloutput, 'wb') as fdest:
8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	114 shutil.copyfileobj(fsrc, fdest)
8 06819360a9e2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8 devteam parents: 7 diff changeset	115
1 8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	116 # retrieve text file
10 a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	117 text_file = glob.glob(self.opts.outputdir + '/*/fastqc_data.txt')
1 8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	118 with open(text_file[0], 'rb') as fsrc:
8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	119 with open(self.opts.textoutput, 'wb') as fdest:
8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	120 shutil.copyfileobj(fsrc, fdest)
8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	121
8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	122 def run_fastqc(self):
8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	123 '''
10 a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	124 Executes FastQC. Make sure the mandatory import parameters input, inputfilename, outputdir and htmloutput have been specified in the options
1 8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	125 '''
8 06819360a9e2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8 devteam parents: 7 diff changeset	126
1 8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	127 # Create a log file
10 a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	128 dummy, tlog = tempfile.mkstemp(prefix='rgFastQC', suffix=".log", dir=self.opts.outputdir)
1 8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	129 sout = open(tlog, 'w')
8 06819360a9e2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8 devteam parents: 7 diff changeset	130
1 8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	131 self.prepare_command_line()
8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	132 sout.write(self.command_line)
8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	133 sout.write('\n')
10 a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	134 sout.write("Creating symlink\n") # between the input (.dat) file and the given input file name
1 8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	135 os.symlink(self.opts.input, self.fastqinfilename)
8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	136 sout.write("check_call\n")
8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	137 subprocess.check_call(self.command_line, shell=True)
8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	138 sout.write("Copying working %s file to %s \n" % (self.fastqinfilename, self.opts.htmloutput))
8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	139 self.copy_output_file_to_dataset()
8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	140 sout.write("Finished")
0 e28c965eeed4 Imported from capsule None devteam parents: diff changeset	141 sout.close()
e28c965eeed4 Imported from capsule None devteam parents: diff changeset	142
10 a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	143
0 e28c965eeed4 Imported from capsule None devteam parents: diff changeset	144 if __name__ == '__main__':
e28c965eeed4 Imported from capsule None devteam parents: diff changeset	145 op = optparse.OptionParser()
e28c965eeed4 Imported from capsule None devteam parents: diff changeset	146 op.add_option('-i', '--input', default=None)
1 8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	147 op.add_option('-j', '--inputfilename', default=None)
0 e28c965eeed4 Imported from capsule None devteam parents: diff changeset	148 op.add_option('-o', '--htmloutput', default=None)
1 8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	149 op.add_option('-t', '--textoutput', default=None)
0 e28c965eeed4 Imported from capsule None devteam parents: diff changeset	150 op.add_option('-d', '--outputdir', default="/tmp/shortread")
e28c965eeed4 Imported from capsule None devteam parents: diff changeset	151 op.add_option('-f', '--informat', default='fastq')
e28c965eeed4 Imported from capsule None devteam parents: diff changeset	152 op.add_option('-n', '--namejob', default='rgFastQC')
e28c965eeed4 Imported from capsule None devteam parents: diff changeset	153 op.add_option('-c', '--contaminants', default=None)
1 8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	154 op.add_option('-l', '--limits', default=None)
0 e28c965eeed4 Imported from capsule None devteam parents: diff changeset	155 op.add_option('-e', '--executable', default='fastqc')
e28c965eeed4 Imported from capsule None devteam parents: diff changeset	156 opts, args = op.parse_args()
8 06819360a9e2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8 devteam parents: 7 diff changeset	157
10 a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	158 assert opts.input is not None
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	159 assert opts.inputfilename is not None
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 9 diff changeset	160 assert opts.htmloutput is not None
8 06819360a9e2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8 devteam parents: 7 diff changeset	161 if not os.path.exists(opts.outputdir):
0 e28c965eeed4 Imported from capsule None devteam parents: diff changeset	162 os.makedirs(opts.outputdir)
8 06819360a9e2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8 devteam parents: 7 diff changeset	163
1 8fae48caaf06 Uploaded form GH devteam parents: 0 diff changeset	164 fastqc_runner = FastQCRunner(opts)
3 0b201de108b9 Uploaded devteam parents: 1 diff changeset	165 fastqc_runner.run_fastqc()

Mercurial > repos > devteam > fastqc

annotate rgFastQC.py @ 10:a00a6402d09a draft