Mercurial > repos > lecorguille > xcms_xcmsset
view destinations_input_type.py @ 17:ea974024a6c6 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 8dfca81480bcbfb5b164ee736b2e2cad324ad8a1-dirty
author | lecorguille |
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date | Tue, 02 Oct 2018 09:17:50 -0400 |
parents | b62808a2a008 |
children | 378ddb410225 |
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from galaxy.jobs import JobDestination import logging import os ''' This file must be placed in lib/galaxy/jobs/rules/ ''' def input_type(job): ''' This function checks the input file format/extension and decide which destination in the job_conf.xml using - If it's a zip file, we will launch the job in multi-thread mode (-pe thread 8) - If it's an individual file (mzxml, mzml, mzdata or netcdf), the job will use for instance (-pe thread 1) ''' log = logging.getLogger(__name__) inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] ) inp_data.update( [ ( da.name, da.dataset ) for da in job.input_library_datasets ] ) input_extension = inp_data[ "input" ].extension if 'input' in inp_data: input_extension = inp_data[ "input" ].extension log.debug("The input extension is %s" % input_extension) if input_extension in ["mzxml","mzml","mzdata","netcdf"]: return 'thread1-mem_free8' # zip file return 'thread8-mem_free16'