/tools/rgenetics/rgQC_code.py

 1"""
 2# after running the qc, need to rename various output files
 3       <data format="html" name="html_file" />
 4       <data format="txt" name="log_file" parent="html_file" />
 5       <data format="tabular" name="marker_file" parent="html_file" />
 6       <data format="tabular" name="subject_file" parent="html_file" />
 7       <data format="tabular" name="freq_file" parent="html_file" />
 8   </outputs>
 9"""
10from galaxy import datatypes,model 
11import sys,time
12
13def timenow():
14    """return current time as a string
15    """
16    return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
17
18
19def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
20    """Change data file names
21
22    """
23    job_name = param_dict.get( 'out_prefix', 'rgQCdefault' )
24    html = ['html','%s.html' % job_name]
25    lookup={}
26    lookup['html_file'] = html
27    info = '%s QC report by rgQC at %s' % (job_name,timenow())
28    for aname in lookup.keys():
29       data = out_data[aname]
30       data_type,newname = lookup[aname]
31       data = app.datatypes_registry.change_datatype(data, data_type)
32       data.name = newname
33       data.info = info
34       out_data[aname] = data
35    app.model.context.flush()
36
37
38