Mercurial > repos > lecorguille > xcms_xcmsset
view destinations_input_type.py @ 29:793f87231d49 draft
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 6e4ddadf085c7ce24cc6325c396872c135071de4"
author | workflow4metabolomics |
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date | Tue, 07 Jan 2020 08:16:02 -0500 |
parents | 378ddb410225 |
children |
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import logging ''' 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__) indata = dict([(da.name, da.dataset) for da in job.input_datasets]) indata.update([(da.name, da.dataset) for da in job.input_library_datasets]) input_extension = indata["input"].extension if 'input' in indata: input_extension = indata["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'