def add_args(self):
return [
Argument(Keys.WORKDIR, KeyHelp.WORKDIR),
Argument("DB_SOURCE", 'BioDB or PersonalDB'),
Argument("DBASE", 'Filepath (BioDB) or an openbis-dataset-code (PersonalDB)'),
Argument("DATASET_DIR", 'dataset cache')
]
def add_args(self):
return [
Argument(Keys.EXECUTABLE, KeyHelp.EXECUTABLE, default='cp'),
Argument("FILE", "File to be copied"),
Argument(
Keys.WORKDIR,
"folder where FILE will go into, created if not specified.")
]
def add_args(self):
return [
Argument("TPPDIR", KeyHelp.EXECDIR, default=''),
Argument("IPROPHET_EXE", KeyHelp.EXECUTABLE, default='InterProphetParser'),
Argument(Keys.WORKDIR, KeyHelp.WORKDIR),
Argument(Keys.PEPXML, KeyHelp.PEPXML),
Argument('IPROPHET_ARGS', 'Arguments for InterProphetParser', default='MINPROB=0'),
]
def add_args(self):
return [
Argument('SEQUESTHOST', 'Sequest host (1 or 2)'),
Argument('SEQUESTRESULTPATH',
'Sequest result path (/home/sorcerer/output/????)'),
Argument(Keys.SPLIT, KeyHelp.SPLIT),
Argument(Keys.WORKDIR, KeyHelp.WORKDIR),
Argument(Keys.ALL_ARGS, KeyHelp.ALL_ARGS)
]
def add_args(self):
ret = [
Argument(Keys.WORKDIR, KeyHelp.WORKDIR),
Argument('MPROPHET_TSV', 'mprophet outputfiles to use for alignment'),
Argument('ISOTOPIC_GROUPING','featurealingn+requant: enable/disable isotopic grouping'),
Argument("ALIGNER_REALIGN_METHOD", "realign_method")
]
for k, v in self.opts.iteritems():
ret.append(Argument(k, v))
return ret
def add_args(self):
return [
Argument('DROPBOXSTAGE', 'location of dropbox stage folder'),
Argument("EXPERIMENT_CODE", 'experiment code created by dropbox'),
Argument(
"VIEWER_BASEPATH",
'base folder for tpp2viewer',
default=
'/nfs/195.176.109.15/nas/fs2102/biol_ibt_usr_s1/%s/html/petunia'
),
Argument("RUNTPP2VIEWER", 'do run tpp2viewer'),
]
def add_args(self):
ret = [
Argument(Keys.WORKDIR, KeyHelp.WORKDIR),
Argument('PARAMETER_FILE', 'optional parameter file', default=""),
Argument(
'DSSOUT',
"if key MZXML not set, get from DSSOUT file (after getdataset)"
),
Argument('TMPDIR',
"tmpdir to use for intermediate results",
default="/tmp"),
]
return ret
def add_args(self):
args = super(Comet, self).add_args()
args.append(Argument('COMET_DIR', 'executable location.', default=''))
args.append(Argument('COMET_EXE', 'executable name.', default='comet'))
args.append(
Argument('COMET_FRAGMENT_IONS',
'fragment ions (ms/ms resolution)',
default='ion_trap'))
args.append(
Argument('COMET_SPECTRUM_BATCH_SIZE',
'max. # of spectra to search at a time',
default=0))
return args
def add_args(self):
return [
Argument(Keys.EXECUTABLE, KeyHelp.EXECUTABLE, default="alfq.R"),
Argument('DBASE', 'fasta dbase'),
Argument('ASSOC_FILE', 'assoc table'),
Argument('PEPCSV', 'pepxml2csv'),
Argument('IPROB', 'iprob', default='0.9'),
Argument('COMPPASS_CONFIDENCE', 'confidence', default='0.95'),
Argument(Keys.WORKDIR, KeyHelp.WORKDIR),
]
def add_args(self):
return [
Argument(Keys.WORKDIR, KeyHelp.WORKDIR),
Argument(Keys.EXECUTABLE, KeyHelp.EXECUTABLE, default='Mayu.pl'),
Argument(Keys.PEPXML, KeyHelp.PEPXML),
Argument('DBASE', 'fasta database'),
Argument('MISSEDCLEAVAGE', 'missed cleavages'),
Argument('MAYU_MASS_RANGE','min-max peptide mass to consider'),
Argument("MAYU_REMAMB",'mayu remove ambiguous peptides')
]
def add_args(self):
return [
Argument(Keys.WORKDIR, KeyHelp.WORKDIR),
Argument(Keys.PEPXML, KeyHelp.PEPXML),
Argument('ENZYME', 'Enzyme used for digest'),
Argument('DBASE', 'FASTA dbase'),
Argument('MZXML', 'Path to the original MZXML inputfile'),
Argument('DECOY', 'Decoy pattern', default='DECOY_'),
Argument('TPPDIR', 'Path to the tpp', default='')
]
def add_args(self):
return [
Argument(Keys.WORKDIR, KeyHelp.WORKDIR),
Argument('DO_CHROMML_REQUANT', 'to skip set to false'),
Argument('ALIGNMENT_TSV', 'featurealigner outfile'),
Argument('CHROM_MZML', 'the chrom.mzml to requant'),
Argument('TRAFO_FILES', 'all tr files'),
Argument('ALIGNER_METHOD', 'infers the REQUANT_METHOD'),
Argument(
'ALIGNER_REALIGN_METHOD',
'featurealingn+requant: RT realign method. req for SingleShortestPath'
),
Argument(
'ISOTOPIC_GROUPING',
'featurealingn+requant: enable/disable isotopic grouping'),
Argument('ISOTOPIC_TRANSFER',
'requant only: do isotopic transfer'),
]
def add_args(self):
ret = [
Argument(Keys.WORKDIR, KeyHelp.WORKDIR),
Argument('DSSOUT', "if key MZXML not set, get from DSSOUT file (after getdataset)"),
Argument('TRAML_CSV', "Path to the traml2csv library"),
Argument('WINDOW_UNIT', 'extraction window unit thompson/ppm'),
Argument('USE_MS1_TRACES', ""),
Argument('USE_UIS_SCORES', ''),
Argument('DO_CHROMML_REQUANT', 'to skip set to false'),
]
for k, v in self.opts.iteritems():
ret.append(Argument(k, v))
return ret
def add_args(self):
return [
Argument(Keys.WORKDIR, KeyHelp.WORKDIR),
Argument("ALIGNMENT_TSV", ""),
Argument("REQUANT_TSV", ""),
Argument("ALIGNMENT_YAML", ""),
Argument('MATRIX_FORMAT', '', default="xlsx"),
Argument('DO_CHROMML_REQUANT', 'to skip set to false'),
]
def add_args(self):
return [
Argument(Keys.WORKDIR, KeyHelp.WORKDIR),
Argument(Keys.EXECUTABLE, KeyHelp.EXECUTABLE),
Argument(Keys.PEPXML, KeyHelp.PEPXML),
Argument('MAYUOUT', 'mayu out csv'),
Argument('FDR_TYPE', "type of FDR: iprophet/mayu m/pep/protFDR"),
Argument("FDR_CUTOFF", "cutoff for FDR"),
]
def add_args(self):
return [
Argument(Keys.WORKDIR, KeyHelp.WORKDIR),
Argument(Keys.EXECUTABLE, KeyHelp.EXECUTABLE),
Argument(Keys.PEPXML, KeyHelp.PEPXML),
Argument('PROTXML', 'Path to a file in protXML format'),
Argument('DBASE',
'Sequence database file with target/decoy entries'),
Argument(
'IPROB',
'Use same iprob cutoff as used in ProteinProphet (before).'),
Argument('SPECTRALCOUNT_TYPE',
'type of spectralcount {all, unique}')
]
def add_args(self):
ret = [
Argument(Keys.WORKDIR, KeyHelp.WORKDIR),
Argument('FEATURETSV', 'input openswathfeaturetsv'),
Argument('MPR_MAINVAR', "main mprophet var"),
Argument('MPR_VARS', "side mprophet vars"),
]
for k, v in self.opts_bool.iteritems():
ret.append(Argument(k, 'true to enable %s' % v))
for k, v in self.opts.iteritems():
ret.append(Argument(k, v))
return ret
def add_args(self):
return [
Argument(Keys.WORKDIR, KeyHelp.WORKDIR),
Argument(Keys.MZXML, KeyHelp.MZXML),
Argument(Keys.PROTXML, Keys.PROTXML),
Argument('PROTCSV',
'Path to CSV input file containing prot abundances'),
Argument('PEPCSV',
'Path to CSV input file containing peptide abundances'),
Argument('DELIM',
'Field delimiter used in CSV input (optional)',
default=','),
Argument(
'INDENT',
'Additional indentation for abundance entries in the protXML output (optional)',
default=' ')
]
def add_args(self):
return [
Argument(Keys.WORKDIR, KeyHelp.WORKDIR),
Argument(Keys.EXECUTABLE,
"%s %s" % (KeyHelp.EXECUTABLE, self.ALLOWED_PREFIXES)),
Argument(Keys.DATASET_CODE,
'dataset code to get for getdataset or getmsdata'),
Argument('EXPERIMENT',
'experiment code to get for for getexperiment'),
Argument('DATASET_DIR', 'cache directory'),
Argument(
'DSS_KEEP_NAME',
"for 'getmsdata' only: output keeps original file name if set to true "
"(otherwise it will be changed to samplecode~dscode.mzXML)",
default='false')
]
def add_args(self):
return [
Argument(Keys.MZXML, KeyHelp.MZXML),
Argument("WINDOWTYPE", "window type"),
Argument(Keys.WORKDIR, KeyHelp.WORKDIR)
]
def add_args(self):
return [
Argument(Keys.ALL_ARGS, KeyHelp.ALL_ARGS),
Argument(Keys.WORKDIR, KeyHelp.WORKDIR)
]
def add_args(self):
return [
Argument('ENGINES', 'Engines available for doing search'),
Argument(Keys.MERGED, KeyHelp.MERGED),
Argument(Keys.ALL_ARGS, KeyHelp.ALL_ARGS),
]
def setup(self, app_args):
# basic arguments for every node
basic_args = [
Argument(Keys.INPUT, KeyHelp.INPUT, default=''),
Argument(Keys.OUTPUT, KeyHelp.OUTPUT, default=''),
Argument(Keys.MODULE, KeyHelp.MODULE, default=''),
Argument(Keys.LOG_LEVEL, KeyHelp.LOG_LEVEL, default="DEBUG")
]
# Fixme: Prettify WORKDIR creation system
# WORKDIR: if WORKDIR is defined add related args
for i, arg in enumerate(app_args):
if arg.name == Keys.WORKDIR:
app_args.insert(
i + 1, Argument(Keys.BASEDIR, KeyHelp.BASEDIR,
default='.'))
app_args.insert(
i + 2, Argument(Keys.JOB_ID, KeyHelp.JOB_ID, default=''))
app_args.insert(
i + 3,
Argument(Keys.SUBJOBLIST, KeyHelp.SUBJOBLIST, default=''))
app_args.insert(
i + 4,
Argument(Keys.NAME,
KeyHelp.NAME,
default=self.__class__.__name__))
break
defaults, cliargs = parse_sysargs(basic_args + app_args)
# construct info from defaults < info < commandlineargs
ih = get_handler(cliargs.get(Keys.INPUT, None))
fileinfo = ih.read(cliargs.get(Keys.INPUT, None))
info = dicts.merge(cliargs, dicts.merge(fileinfo, defaults))
# setup logging
log = Logger.create(info[Keys.LOG_LEVEL])
# request by malars: show dataset prominent in logger
if Keys.DATASET_CODE in info:
if not isinstance(info[Keys.DATASET_CODE], list):
if Keys.MZXML in info and not isinstance(
info[Keys.MZXML], list):
log.info("Dataset is %s (%s)" %
(info[Keys.DATASET_CODE],
os.path.basename(info[Keys.MZXML])))
else:
log.info("Dataset is %s" % info[Keys.DATASET_CODE])
else:
log.debug("Datasets are %s" % info[Keys.DATASET_CODE])
# WORKDIR: create WORKDIR (only after mk log)
info = dirs.create_workdir(log, info)
# filter to requested args
if Keys.ALL_ARGS in info:
# if ALL_ARGS is set give whole info to app...
req_info = info
else:
req_info = {}
# ...otherwise copy only explicitly requested args to app
for key in [arg.name for arg in basic_args + app_args]:
if key in info:
req_info[key] = info[key]
log.debug("info for app: %s" % req_info)
return log, req_info, info
def add_args(self):
return [
Argument(Keys.MZXML, KeyHelp.MZXML),
Argument(Keys.WORKDIR, KeyHelp.WORKDIR),
Argument(Keys.PEPXML, KeyHelp.PEPXML),
]
def add_args(self):
return [
Argument(Keys.EXECUTABLE, KeyHelp.EXECUTABLE),
Argument(Keys.WORKDIR, KeyHelp.WORKDIR),
Argument(Keys.THREADS, KeyHelp.THREADS),
Argument(Keys.MZXML, KeyHelp.MZXML),
Argument('FRAGMASSERR', 'Fragment mass error', default=0.4),
Argument('FRAGMASSUNIT',
'Unit of the fragment mass error',
default='Da'),
Argument('PRECMASSERR', 'Precursor mass error', default=15),
Argument('PRECMASSUNIT',
'Unit of the precursor mass error',
default='ppm'),
Argument('MISSEDCLEAVAGE',
'Number of maximal allowed missed cleavages',
default=1),
Argument('ENZYME',
'Enzyme used to digest the proteins',
default='Trypsin'),
Argument('STATIC_MODS',
'List of static modifications',
default='Carbamidomethyl (C)'),
Argument('VARIABLE_MODS', 'List of variable modifications'),
Argument('DBASE',
'Sequence database file with target/decoy entries'),
]
def add_args(self):
return [
Argument(Keys.ALL_ARGS, KeyHelp.ALL_ARGS),
Argument(Keys.COLLATE, KeyHelp.COLLATE)
]
def add_args(self):
args = super(Myrimatch, self).add_args()
args.append(Argument('MYRIMATCH_DIR', 'executable location.', default=''))
args.append(Argument('MYRIMATCH_EXE',KeyHelp.EXECUTABLE, default='myrimatch'))
return args
def add_args(self):
return [
Argument('SEARCH',
'Key where containing files of downloaded experiment')
]
def add_args(self):
return [
Argument(Keys.WORKDIR, KeyHelp.WORKDIR),
Argument('PEPCSV', 'pepcsv for samples')
]
def add_args(self):
args = super(Xtandem, self).add_args()
args.append(
Argument('XTANDEM_SCORE', 'Scoring algorithm used in the search.'))
return args