def getExtraHistElements(cls, choices):
hEList = []
if choices.regionsGSuite:
hEList.append(HistElement('Repeat regions (bed) GSuite', 'gsuite'))
if choices.monomersGSuite:
hEList.append(HistElement('Repeat monomers (bed) GSuite', 'gsuite'))
return hEList
def getExtraHistElements(cls, choices):
if choices.genome and choices.catTrack:
from quick.webtools.GeneralGuiTool import HistElement
genome = choices.genome
outputType = choices.outputType
catTrack = choices.catTrack.split(':')
geSource = ExternalTrackManager.getGESourceFromGalaxyOrVirtualTN(
catTrack, genome)
return [HistElement(ge.val, outputType) for ge in geSource
] + [HistElement('GSuite from categorical', 'gsuite')]
def getExtraHistElements(cls, choices):
fileList = []
if choices.outFormat == 'gsuite':
from gold.gsuite.GSuiteConstants import GSUITE_SUFFIX, GSUITE_STORAGE_SUFFIX
from quick.webtools.GeneralGuiTool import HistElement
fileList.append( HistElement(cls.HISTORY_PROGRESS_TITLE, 'customhtml') )
fileList.append( HistElement(cls.HISTORY_HIDDEN_TRACK_STORAGE, GSUITE_STORAGE_SUFFIX, hidden=True))
return fileList
def getExtraHistElements(cls, choices):
from quick.webtools.GeneralGuiTool import HistElement
return [
HistElement(
getGSuiteHistoryOutputName('nopreprocessed',
datasetInfo=choices.history),
'gsuite'),
HistElement(
getGSuiteHistoryOutputName('preprocessed',
datasetInfo=choices.history),
'gsuite')
]
def getExtraHistElements(cls, choices):
from quick.webtools.GeneralGuiTool import HistElement
from gold.gsuite.GSuiteConstants import GSUITE_SUFFIX, GSUITE_STORAGE_SUFFIX
fileList = [HistElement(getGSuiteHistoryOutputName(
'nomanipulate', datasetInfo=choices.history), GSUITE_SUFFIX)]
fileList += [HistElement(getGSuiteHistoryOutputName(
'primary', cls.OUTPUT_DESCRIPTION, choices.history), GSUITE_SUFFIX)]
fileList += [HistElement(getGSuiteHistoryOutputName(
'storage', cls.OUTPUT_DESCRIPTION, choices.history),
GSUITE_STORAGE_SUFFIX, hidden=True)]
return fileList
def getExtraHistElements(cls, choices):
from quick.webtools.GeneralGuiTool import HistElement
histList = []
histList.append(
HistElement(
getGSuiteHistoryOutputName('primary',
datasetInfo=choices.gsuite),
GSuiteConstants.GSUITE_SUFFIX))
histList.append(
HistElement(getGSuiteHistoryOutputName('storage',
datasetInfo=choices.gsuite),
GSuiteConstants.GSUITE_SUFFIX,
hidden=True))
return histList
def getExtraHistElements(cls, choices):
desc = cls.OUTPUT_GSUITE_DESCRIPTION
return [HistElement(getGSuiteHistoryOutputName(
'nointersect', description=desc, datasetInfo=choices.gSuite),
GSuiteConstants.GSUITE_SUFFIX),
HistElement(getGSuiteHistoryOutputName(
'primary', description=desc, datasetInfo=choices.gSuite),
GSuiteConstants.GSUITE_SUFFIX),
HistElement(getGSuiteHistoryOutputName(
'nopreprocessed', description=desc, datasetInfo=choices.gSuite),
GSuiteConstants.GSUITE_SUFFIX),
HistElement(getGSuiteHistoryOutputName(
'preprocessed', description=desc, datasetInfo=choices.gSuite),
GSuiteConstants.GSUITE_SUFFIX),
HistElement(getGSuiteHistoryOutputName(
'storage', description=desc, datasetInfo=choices.gSuite),
GSuiteConstants.GSUITE_STORAGE_SUFFIX, hidden=True)]
def getExtraHistElements(cls, choices):
from quick.webtools.GeneralGuiTool import HistElement
from gold.gsuite.GSuiteConstants import GSUITE_STORAGE_SUFFIX, GSUITE_SUFFIX
desc = cls._getOutputHistoryDescription(choices)
fileList = [
HistElement(getGSuiteHistoryOutputName('primary', desc),
GSUITE_SUFFIX),
HistElement(getGSuiteHistoryOutputName('storage', desc),
GSUITE_STORAGE_SUFFIX,
hidden=True)
]
# if choices.archive:
#for archivedFile in cls._getArchiveReader(choices):
# fileList.append( HistElement(archivedFile.title, archivedFile.suffix, hidden=True) )
return fileList
def getExtraHistElements(cls, choices):
from quick.webtools.GeneralGuiTool import HistElement
fileList = [
HistElement(
getGSuiteHistoryOutputName('nodownload',
datasetInfo=choices.history),
GSUITE_SUFFIX)
]
fileList += [
HistElement(
getGSuiteHistoryOutputName('primary',
datasetInfo=choices.history),
GSUITE_SUFFIX)
]
if choices.preProcess == 'Yes':
fileList += [
HistElement(
getGSuiteHistoryOutputName('nopreprocessed',
datasetInfo=choices.history),
GSUITE_SUFFIX)
]
fileList += [
HistElement(
getGSuiteHistoryOutputName('preprocessed',
datasetInfo=choices.history),
GSUITE_SUFFIX)
]
fileList += [
HistElement(getGSuiteHistoryOutputName(
'storage', datasetInfo=choices.history),
GSUITE_STORAGE_SUFFIX,
hidden=True)
]
# if choices.history:
#from quick.multitrack.MultiTrackCommon import getGSuiteFromGalaxyTN
#gSuite = getGSuiteFromGalaxyTN(choices.history)
#
#for track in gSuite.allTracks():
# from gold.gsuite.GSuiteDownloader import getTitleAndSuffixWithCompressionSuffixesRemoved
# title, suffix = getTitleAndSuffixWithCompressionSuffixesRemoved(track)
# fileList.append( HistElement(title, suffix, hidden=True) )
return fileList
def getExtraHistElements(cls, choices):
if choices.gsuite:
gSuite = getGSuiteFromGalaxyTN(choices.gsuite)
newSuffix = cls._getNewSuffixIfAny(choices)
return [
HistElement(
*cls._getExportTrackTitleAndSuffix(track, newSuffix))
for track in cls._getSelectedTracks(choices, gSuite)
]
def getExtraHistElements(cls, choices):
from gold.gsuite.GSuiteConstants import GSUITE_SUFFIX, GSUITE_STORAGE_SUFFIX
fileList = []
if choices.outputType and choices.downloadAndPreprocess == 'Yes' and \
choices.source.find('HyperBrowser') == -1 and \
choices.transfer != 'Yes':
from quick.webtools.GeneralGuiTool import HistElement
desc = unidecode(choices.subCategory)
fileList += \
[HistElement(getGSuiteHistoryOutputName('remote', desc), GSUITE_SUFFIX),
HistElement(getGSuiteHistoryOutputName('nodownload', desc), GSUITE_SUFFIX),
HistElement(getGSuiteHistoryOutputName('primary', desc), GSUITE_SUFFIX),
HistElement(getGSuiteHistoryOutputName('nopreprocessed', desc), GSUITE_SUFFIX),
HistElement(getGSuiteHistoryOutputName('preprocessed', desc), GSUITE_SUFFIX),
HistElement(getGSuiteHistoryOutputName('storage', desc), GSUITE_STORAGE_SUFFIX,
hidden=True)]
return fileList
def getExtraHistElements(cls, choices):
return [HistElement('synthetic GSuite', 'gsuite')]
def _getExtraHistElements(cls, choices):
return [
HistElement('name ?=?=++0', 'txt'),
HistElement('name 1', 'html', label='WHAT'),
HistElement(choices[1], 'gtrack', hidden=True)
]
def getExtraHistElements(cls, choices):
return [HistElement('Kmers GSuite', 'gsuite')]
def getExtraHistElements(cls, choices):
from quick.webtools.GeneralGuiTool import HistElement
return [HistElement(cls.NEXT_TOOL_TITLE, 'customhtml')]