Mercurial > repos > lecorguille > xcms_xcmsset
comparison destinations_input_type.py @ 33:f5d51091cf84 draft default tip
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
| author | workflow4metabolomics |
|---|---|
| date | Mon, 11 Sep 2023 09:22:36 +0000 |
| parents | b02d1992a43a |
| children |
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| 32:b02d1992a43a | 33:f5d51091cf84 |
|---|---|
| 1 import logging | |
| 2 | |
| 3 | |
| 4 ''' | |
| 5 This file must be placed in lib/galaxy/jobs/rules/ | |
| 6 ''' | |
| 7 | |
| 8 | |
| 9 def input_type(job): | |
| 10 ''' | |
| 11 This function checks the input file format/extension and decide which | |
| 12 destination in the job_conf.xml using | |
| 13 - If it's a zip file, we will launch the job in multi-thread mode | |
| 14 (-pe thread 8) | |
| 15 - If it's an individual file (mzxml, mzml, mzdata or netcdf), | |
| 16 the job will use for instance (-pe thread 1) | |
| 17 ''' | |
| 18 log = logging.getLogger(__name__) | |
| 19 indata = dict([(da.name, da.dataset) for da in job.input_datasets]) | |
| 20 indata.update([(da.name, da.dataset) for da in job.input_library_datasets]) | |
| 21 input_extension = indata["input"].extension | |
| 22 if 'input' in indata: | |
| 23 input_extension = indata["input"].extension | |
| 24 log.debug("The input extension is %s" % input_extension) | |
| 25 if input_extension in ["mzxml", "mzml", "mzdata", "netcdf"]: | |
| 26 return 'thread1-mem_free8' | |
| 27 # zip file | |
| 28 return 'thread8-mem_free16' |