/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

  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. """
  10. from galaxy import datatypes,model
  11. import sys,time
  12. def timenow():
  13. """return current time as a string
  14. """
  15. return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
  16. def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
  17. """Change data file names
  18. """
  19. job_name = param_dict.get( 'out_prefix', 'rgQCdefault' )
  20. html = ['html','%s.html' % job_name]
  21. lookup={}
  22. lookup['html_file'] = html
  23. info = '%s QC report by rgQC at %s' % (job_name,timenow())
  24. for aname in lookup.keys():
  25. data = out_data[aname]
  26. data_type,newname = lookup[aname]
  27. data = app.datatypes_registry.change_datatype(data, data_type)
  28. data.name = newname
  29. data.info = info
  30. out_data[aname] = data
  31. app.model.context.flush()