[2] | 1 | from galaxy import app |
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| 2 | import galaxy.util,string |
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| 3 | |
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| 4 | librepos = '/usr/local/galaxy/data/rg' |
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| 5 | myrepos = '/home/rerla/galaxy' |
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| 6 | marchinirepos = '/usr/local/galaxy/data/rg/snptest' |
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| 7 | |
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| 8 | #Provides Upload tool with access to list of available builds |
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| 9 | |
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| 10 | |
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| 11 | def get_rgRegionOutFormats(): |
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| 12 | """return options for formats""" |
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| 13 | dat = [['ucsc track','wig',False],['Strict genome graphs (rs+floats)','gg',True],['tab delimited','xls',False]] |
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| 14 | dat = [(x[0],x[1],x[2]) for x in dat] |
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| 15 | return dat |
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| 16 | |
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| 17 | |
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| 18 | def get_phecols(phef):
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| 19 | """return column names """
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| 20 | head = open(phef,'r').next()
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| 21 | c = head.strip().split()
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| 22 | res = [(cname,cname,False) for cname in c]
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| 23 | x,y,z = res[2] # 0,1 = fid,iid
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| 24 | res[2] = (x,y,True) # set second selected
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| 25 | return res |
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| 26 | |
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| 27 | |
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| 28 | def getAllcols(fname="/usr/local/galaxy/data/camp2007/camp2007.xls",outformat='gg'): |
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| 29 | """return column names other than chr offset as a select list""" |
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| 30 | head = open(fname,'r').next() |
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| 31 | c = head.strip().split() |
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| 32 | res = [(cname,'%d' % n,True) for n,cname in enumerate(c)] |
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| 33 | |
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| 34 | return res |
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| 35 | |
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| 36 | |
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| 37 | def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr): |
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| 38 | """Sets the name of the data""" |
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| 39 | data_name = param_dict.get( 'tag', 'My region' ) |
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| 40 | outformat = param_dict.get( 'outformat', 'gg' ) |
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| 41 | outfile = param_dict.get( 'outfile1', 'lped' ) |
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| 42 | for name, data in out_data.items(): |
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| 43 | if name == 'tag': |
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| 44 | data = app.datatypes_registry.change_datatype(data, outformat) |
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| 45 | data.name = data_name |
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| 46 | out_data[name] = data |
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| 47 | |
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