Mercurial > repos > lecorguille > xcms_xcmsset
diff destinations_input_type.py @ 28:378ddb410225 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4dc5751176d47d41fa1dec33eb443e335a1a316f
author | workflow4metabolomics |
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date | Fri, 26 Jul 2019 10:26:24 -0400 |
parents | b62808a2a008 |
children |
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--- a/destinations_input_type.py Tue Apr 30 04:41:11 2019 -0400 +++ b/destinations_input_type.py Fri Jul 26 10:26:24 2019 -0400 @@ -1,25 +1,28 @@ -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) + 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 + 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"]: + if input_extension in ["mzxml", "mzml", "mzdata", "netcdf"]: return 'thread1-mem_free8' # zip file return 'thread8-mem_free16'