/tools/rgenetics/rgQC_code.py
https://bitbucket.org/h_morita_dbcls/galaxy-central · Python · 38 lines · 25 code · 6 blank · 7 comment · 1 complexity · ccf8932589590836eec11749696497cc MD5 · raw file
- """
- # after running the qc, need to rename various output files
- <data format="html" name="html_file" />
- <data format="txt" name="log_file" parent="html_file" />
- <data format="tabular" name="marker_file" parent="html_file" />
- <data format="tabular" name="subject_file" parent="html_file" />
- <data format="tabular" name="freq_file" parent="html_file" />
- </outputs>
- """
- from galaxy import datatypes,model
- import sys,time
-
- def timenow():
- """return current time as a string
- """
- return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
-
-
- def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
- """Change data file names
-
- """
- job_name = param_dict.get( 'out_prefix', 'rgQCdefault' )
- html = ['html','%s.html' % job_name]
- lookup={}
- lookup['html_file'] = html
- info = '%s QC report by rgQC at %s' % (job_name,timenow())
- for aname in lookup.keys():
- data = out_data[aname]
- data_type,newname = lookup[aname]
- data = app.datatypes_registry.change_datatype(data, data_type)
- data.name = newname
- data.info = info
- out_data[aname] = data
- app.model.context.flush()