Mercurial > repos > lecorguille > xcms_xcmsset
diff destinations_input_type.py @ 12:15646e937936 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
author | lecorguille |
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date | Fri, 07 Apr 2017 07:35:01 -0400 |
parents | |
children | c934dd5c49a9 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/destinations_input_type.py Fri Apr 07 07:35:01 2017 -0400 @@ -0,0 +1,23 @@ +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 + log.debug("The input extension is %s" % input_extension) + if input_extension in ["mzxml","mzml","mzdata","netcdf"]: + return 'thread1-men_free10' + else: # zip file + return 'thread4-men_free10'