def main():
filename = sys.argv[1]
output = filename
params = hg.fileToParams(filename)
file_path = params.get('file_path')
genome = params.get('dbkey')
track1Name = params.get('track1')
method = params.get('method')
if method == 'binfile':
binfile = params.get('binfile').split(',')
binspec = hg.getDataFilePath(file_path, binfile[1])
regspec = binfile[2]
elif method != 'auto':
regspec = method
binspec = params.get(method)
else:
regspec = params.get('region', '*')
binspec = params.get('binsize', '*')
intensityname = params.get('intensityname') if params.has_key('intensityname') else None
track1File = params.get('track1file')
if track1Name == 'galaxy' and track1File != None:
tfa = track1File.split(',')
tracks1 = ['galaxy', tfa[2], hg.getDataFilePath(file_path, tfa[1]), unquote(tfa[3])]
else:
tracks1 = track1Name.split(':')
if intensityname not in [None, '']:
intensityname = intensityname.split(':')
else:
intensityname = 'galaxy:hbfunction:'+filename+':Create intensity track'
numctrltracks = int(params.get('numctrltracks'))
ctrltracks = []
for num in range(numctrltracks):
trackName = params.get('track' + str(num+2))
trackFile = params.get('track' + str(num+2) + 'file')
if trackName == 'galaxy' and trackFile != None:
tfa = trackFile.split(',')
track = ['galaxy', tfa[2], hg.getDataFilePath(file_path, tfa[1]), unquote(tfa[3])]
else:
track = trackName.split(':')
ctrltracks.append(track)
sys.stdout = open(output, "w", 0)
#print 'GalaxyInterface.createIntensityTrack', (tracks1, ctrltracks, intensityname, region, binSize, genome)
GalaxyInterface.createIntensityTrack(tracks1, ctrltracks, intensityname, regspec, binspec, genome, output)
def trackNameForHistoryItem(field, params):
item = params[field]
file_path = params['file_path']
gal,id,type,name = item.split(',')
filename = getDataFilePath(file_path, id)
return [gal, type, filename, name]
def trackNameForHistoryItem(field, params):
item = params[field]
file_path = params['file_path']
gal,id,type,name = item.split(',')
filename = getDataFilePath(file_path, id)
return [gal, type, filename, name]