def execute(cls, choices, galaxyFn=None, username=''):
'''Is called when execute-button is pushed by web-user.
Should print output as HTML to standard out, which will be directed to a results page in Galaxy history. If getOutputFormat is anything else than HTML, the output should be written to the file with path galaxyFn.gtr
If needed, StaticFile can be used to get a path where additional files can be put (e.g. generated image files).
choices is a list of selections made by web-user in each options box.
'''
extraParams = ['direction=' + cls.DIRECTION_DICT[choices.direction].parseFileArg,\
'allSubTypes=' + choices.allSubTypes,\
'subTypeDepth=' + choices.subTypeDepth]
if len(cls._extraParams) > 0:
for i in range(len(cls._extraParams)):
paramName = choices[i * 2 + 9]
param = paramName[:paramName.find('(')].strip()
val = choices[i * 2 + 10].strip()
if val != '':
extraParams.append(param + '=' + val)
extraParams += [v.strip() for v in choices.kwArgs.split(',')
] if choices.kwArgs.strip() != '' else []
arguments = [choices.genome, choices.track, choices.parserClass
] + extraParams
print 'Running with these arguments: ', arguments
StandTrackFiles.runParserClass(arguments, printUsageWhenError=False)
try:
if choices.file:
filePathList = cls._getFilePathList(choices, input=False)
filePath = cls._getFilePath(filePathList, choices)
print ''
print ''
print '10 first lines of file: ' + filePath
print ''
fileObj = open(filePath, 'r')
for i in range(10):
print fileObj.readline().strip() #.replace('\n','<br>')
fileObj.close()
except:
pass
def execute(cls, choices, galaxyFn=None, username=''):
genome, history = choices[:2]
track, catColumn, numHeaderLines = choices[3], choices[4], choices[5]
suffix, catSuffix = choices[6], choices[7]
private = True if choices[-1]=='Yes' else False
GalaxyInterface.integrateTrackFromHistory(genome, history.split(':'), track.split(':'), privateAccess=private, username=username)
#ensurePathExists(NONSTANDARD_DATA_PATH+'/'+'/'.join( [genome]+track.split(':')+['fName.txt'] ) )
StandTrackFiles.runParserClass([genome, track, 'PlainCopier', 'direction=std_to_coll', 'allSubTypes=False', 'subTypeDepth=1'], printUsageWhenError=False)
StandTrackFiles.runParserClass([genome, track, 'SplitFileToSubDirs', 'direction=coll_to_coll', 'allSubTypes=False', \
'subTypeDepth=1', 'subTypeCol='+catColumn, 'numHeaderLines='+numHeaderLines, \
'suffix=.%s' % suffix, 'catSuffix=.%s' % catSuffix], printUsageWhenError=False)
StandTrackFiles.runParserClass([genome, track, 'PlainCopier', 'direction=coll_to_std', 'allSubTypes=True', 'subTypeDepth=1'], printUsageWhenError=False)
GalaxyInterface.startPreProcessing(genome, track, username)
def _setExtraParams(prevChoices):
paramList = StandTrackFiles.getFormattedParamList(
prevChoices.parserClass,
argStr='%s (Mandatory parameter)',
kwArgStr='%s (default: %s)')
StandardizeTrackFilesTool._extraParams = paramList
def getOptionsBoxDescription(prevChoices):
if prevChoices.parserClass:
docString = StandTrackFiles.getParserClassDocString(
prevChoices.parserClass)
if docString:
return (docString, len(docString.split('\n')), True)
def getOptionsBoxParserClass(prevChoices):
"Returns a list of options to be displayed in the first options box"
if prevChoices.file or prevChoices.allSubTypes == 'True':
#return [v[0] for v in getmembers(StandTrackFiles, isclass) if 'GeneralTrackDataModifier' in [c.__name__ for c in getmro(getattr(StandTrackFiles, v[0]))]]
return StandTrackFiles.getParserClassList()
def getOptionsBoxPrevRun(prevChoices):
if prevChoices.file or prevChoices.allSubTypes == 'True':
stored = StandTrackFiles.getStandTrackFileToolCache(
prevChoices.genome, prevChoices.track.split(':'))
if stored:
return (stored, 1, True)
def standardizeTrackData(genome, tn):
import quick.extra.StandardizeTrackFiles as StandTrackFiles
arguments = [genome, ':'.join(tn), 'SplitFileToSubDirs'
] + ['direction=coll_to_std']
print 'Running standardizer with these arguments: ' + str(arguments)
StandTrackFiles.runParserClass(arguments, printUsageWhenError=False)