comparison hardklor.py @ 6:73fc27617b2e draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit 44c3e37a12f60b01521d3e3f18b7f16664f954cc"

5:c5b3b7eafd46

import subprocess


CONFIG_FILE = 'hk.conf'
extension_lookup = {
    'mzml'  :   'mzML',
    'mzxml' :   'mzXML',
    'ms1'   :   'MS1',
    }

# input:
ms1_ext = sys.argv[1]
ms1_file = sys.argv[2]
output_file = sys.argv[3]

# create softlinks since hardklor needs "proper" extensions for input files
if ms1_ext in extension_lookup:
    ms1_ext = extension_lookup[ms1_ext]
    linkname = 'ms1_dsetlink.{0}'.format(ms1_ext)
    os.symlink(ms1_file, linkname)
    ms1_file = linkname 

# load template and dump to config file
with open(config_load) as fp:
    config_str = fp.read()
config_to_dump = config_str.format(

    correlation=options['correlation'],
    sensitivity=options['sensitivity'],
    maxfeat=options['maxfeat'],
    inputfile=ms1_file,
    outputfile=output_file,
    )
with open(CONFIG_FILE, 'w') as fp:
    fp.write(config_to_dump)

# Run hardklor
err = subprocess.call(['hardklor', CONFIG_FILE])

6:73fc27617b2e

import subprocess


CONFIG_FILE = 'hk.conf'
extension_lookup = {
    'mzml': 'mzML',
    'mzxml': 'mzXML',
    'ms1': 'MS1',
}

# input:
ms1_ext = sys.argv[1]
ms1_file = sys.argv[2]
output_file = sys.argv[3]

# create softlinks since hardklor needs "proper" extensions for input files
if ms1_ext in extension_lookup:
    ms1_ext = extension_lookup[ms1_ext]
    linkname = 'ms1_dsetlink.{0}'.format(ms1_ext)
    os.symlink(ms1_file, linkname)
    ms1_file = linkname

# load template and dump to config file
with open(config_load) as fp:
    config_str = fp.read()
config_to_dump = config_str.format(

    correlation=options['correlation'],
    sensitivity=options['sensitivity'],
    maxfeat=options['maxfeat'],
    inputfile=ms1_file,
    outputfile=output_file,
)
with open(CONFIG_FILE, 'w') as fp:
    fp.write(config_to_dump)

# Run hardklor
err = subprocess.call(['hardklor', CONFIG_FILE])