Mercurial > repos > lecorguille > xcms_xcmsset
comparison destinations_input_type.py @ 12:15646e937936 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
| author | lecorguille |
|---|---|
| date | Fri, 07 Apr 2017 07:35:01 -0400 |
| parents | |
| children | c934dd5c49a9 |
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| 11:91311aa08cdc | 12:15646e937936 |
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| 1 from galaxy.jobs import JobDestination | |
| 2 import logging | |
| 3 import os | |
| 4 | |
| 5 ''' | |
| 6 This file must be placed in lib/galaxy/jobs/rules/ | |
| 7 ''' | |
| 8 | |
| 9 def input_type(job): | |
| 10 ''' | |
| 11 This function checks the input file format/extension and decide which destination in the job_conf.xml using | |
| 12 - If it's a zip file, we will launch the job in multi-thread mode (-pe thread 8) | |
| 13 - If it's an individual file (mzxml, mzml, mzdata or netcdf), the job will use for instance (-pe thread 1) | |
| 14 ''' | |
| 15 log = logging.getLogger(__name__) | |
| 16 inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] ) | |
| 17 inp_data.update( [ ( da.name, da.dataset ) for da in job.input_library_datasets ] ) | |
| 18 input_extension = inp_data[ "input" ].extension | |
| 19 log.debug("The input extension is %s" % input_extension) | |
| 20 if input_extension in ["mzxml","mzml","mzdata","netcdf"]: | |
| 21 return 'thread1-men_free10' | |
| 22 else: # zip file | |
| 23 return 'thread4-men_free10' |