root/galaxy-central/tools/rgenetics/rgTDT_code.py

リビジョン 2, 1.5 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1# before running the qc, need to rename various output files
2import time,string
3
4def timenow():
5    """return current time as a string
6    """
7    return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
8
9def get_out_formats():
10    """return options for formats"""
11    dat = [['ucsc genome graphs','gg',True],['ucsc track','wig',False],['tab delimited','xls',False]]
12    dat = [(x[0],x[1],x[2]) for x in dat]
13    return dat
14
15
16def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
17    """Sets the name of the data
18   <command interpreter="python2.4">
19        rgTDT.py -i $i.extra_files_path/$i.metadata.base_name -o $title -f $outformat -r $out_file1 -l $logf
20    </command>
21   
22    """
23    dbk = param_dict.get('dbkey','hg18')
24    job_name = param_dict.get( 'title1', 'rgTDTtest1' )
25    killme=string.punctuation+string.whitespace
26    trantab = string.maketrans(killme,'_'*len(killme))
27    job_name = job_name.encode().translate(trantab)
28    outxls = ['tabular','%s_TDT.xls' % job_name]
29    logtxt = ['txt','%s_TDT_log.txt' % job_name]
30    ggout = ['gg','%s_TDT_topTable.gff' % job_name]
31    lookup={}
32    lookup['out_file1'] = outxls
33    lookup['logf'] = logtxt
34    lookup['gffout'] = ggout
35    info = 'rgTDT run at %s' % timenow()
36    for name in lookup.keys():
37        data = out_data[name]
38        data_type,newname = lookup[name]
39        data.name = newname
40        data.info = info
41        data.dbkey = dbk
42        out_data[name] = data
43    app.model.context.flush()
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