comparison sirius_csifingerid.py @ 7:e29e64ff50bb draft

"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit a2dd58962ce65259d79c7647efef1f0b18dce48c"

6:96b077221201

parser.add_argument('--cores_top_level', default=1)
parser.add_argument('--chunks', default=1)
parser.add_argument('--min_MSMS_peaks', default=1)
parser.add_argument('--rank_filter', default=0)
parser.add_argument('--confidence_filter', default=0)
parser.add_argument('--backwards_compatible',
                    default=False, action='store_true')
parser.add_argument('--schema', default='msp')
parser.add_argument('-a', '--adducts', action='append', nargs=1,
                    required=False, default=[], help='Adducts used')

args = parser.parse_args()

######################################################################
# outputs might have different headers. Need to get a list of all the headers
# before we start merging the files outfiles = [os.path.join(wd, f) for f in
# glob.glob(os.path.join(wd, "*_metfrag_result.csv"))]
def concat_output(filename, result_pth,
                  rank_filter, confidence_filter, backwards_compatible):
    outfiles = glob.glob(os.path.join(wd, '*', '*{}'.format(filename)))

    # sort files nicely
    outfiles.sort(key=lambda s: int(re.match(r'^.*/('
                                             r'\d+).*{}'.format(filename),

7:e29e64ff50bb

parser.add_argument('--cores_top_level', default=1)
parser.add_argument('--chunks', default=1)
parser.add_argument('--min_MSMS_peaks', default=1)
parser.add_argument('--rank_filter', default=0)
parser.add_argument('--confidence_filter', default=0)
parser.add_argument('--schema', default='msp')
parser.add_argument('-a', '--adducts', action='append', nargs=1,
                    required=False, default=[], help='Adducts used')

args = parser.parse_args()

######################################################################
# outputs might have different headers. Need to get a list of all the headers
# before we start merging the files outfiles = [os.path.join(wd, f) for f in
# glob.glob(os.path.join(wd, "*_metfrag_result.csv"))]
def concat_output(filename, result_pth,
                  rank_filter, confidence_filter):
    outfiles = glob.glob(os.path.join(wd, '*', '*{}'.format(filename)))

    # sort files nicely
    outfiles.sort(key=lambda s: int(re.match(r'^.*/('
                                             r'\d+).*{}'.format(filename),