comparison rgFastQC.py @ 7:ec73b7c83b2c draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit 8918618a5ef7bdca55a31cd919efa593044a376e

6:e8c90ad3cbf9

import tempfile
import glob
import gzip
import bz2
import zipfile

class FastQCRunner(object):

    def __init__(self,opts=None):
        '''

        infname = self.opts.inputfilename
        linf = infname.lower()
        trimext = False
        # decompression at upload currently does NOT remove this now bogus ending - fastqc will barf
        # patched may 29 2013 until this is fixed properly
        if ( linf.endswith('.gz') or linf.endswith('.gzip') ):
            f = gzip.open(self.opts.input)
            try:
                f.readline()
            except:
                trimext = True

            command_line.append('--contaminants %s' % opts.contaminants)
        if opts.limits != None:
	    command_line.append('--limits %s' % opts.limits)
        command_line.append('--quiet')
        command_line.append('--extract') # to access the output text file
        command_line.append(self.fastqinfilename)
        command_line.append('-f %s' % opts.informat)
        self.command_line = ' '.join(command_line)

    def copy_output_file_to_dataset(self):
        '''
        Retrieves the output html and text files from the output directory and copies them to the Galaxy output files

7:ec73b7c83b2c

import tempfile
import glob
import gzip
import bz2
import zipfile
import mimetypes

class FastQCRunner(object):

    def __init__(self,opts=None):
        '''

        infname = self.opts.inputfilename
        linf = infname.lower()
        trimext = False
        # decompression at upload currently does NOT remove this now bogus ending - fastqc will barf
        # patched may 29 2013 until this is fixed properly
        type = mimetypes.guess_type(self.opts.input)
        if linf.endswith('.gz') or linf.endswith('.gzip') or type[-1] == "gzip":
            f = gzip.open(self.opts.input)
            try:
                f.readline()
            except:
                trimext = True

            command_line.append('--contaminants %s' % opts.contaminants)
        if opts.limits != None:
	    command_line.append('--limits %s' % opts.limits)
        command_line.append('--quiet')
        command_line.append('--extract') # to access the output text file
	if type[-1] != "gzip":
            command_line.append('-f %s' % opts.informat)
	else:
	    self.fastqinfilename += ".gz"
        command_line.append(self.fastqinfilename)
        self.command_line = ' '.join(command_line)

    def copy_output_file_to_dataset(self):
        '''
        Retrieves the output html and text files from the output directory and copies them to the Galaxy output files