Mercurial > repos > lecorguille > xcms_xcmsset
comparison 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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27:3bd53dcfa438 | 28:378ddb410225 |
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1 from galaxy.jobs import JobDestination | |
2 import logging | 1 import logging |
3 import os | 2 |
4 | 3 |
5 ''' | 4 ''' |
6 This file must be placed in lib/galaxy/jobs/rules/ | 5 This file must be placed in lib/galaxy/jobs/rules/ |
7 ''' | 6 ''' |
8 | 7 |
8 | |
9 def input_type(job): | 9 def input_type(job): |
10 ''' | 10 ''' |
11 This function checks the input file format/extension and decide which destination in the job_conf.xml using | 11 This function checks the input file format/extension and decide which |
12 - If it's a zip file, we will launch the job in multi-thread mode (-pe thread 8) | 12 destination in the job_conf.xml using |
13 - If it's an individual file (mzxml, mzml, mzdata or netcdf), the job will use for instance (-pe thread 1) | 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) | |
14 ''' | 17 ''' |
15 log = logging.getLogger(__name__) | 18 log = logging.getLogger(__name__) |
16 inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] ) | 19 indata = dict([(da.name, da.dataset) for da in job.input_datasets]) |
17 inp_data.update( [ ( da.name, da.dataset ) for da in job.input_library_datasets ] ) | 20 indata.update([(da.name, da.dataset) for da in job.input_library_datasets]) |
18 input_extension = inp_data[ "input" ].extension | 21 input_extension = indata["input"].extension |
19 if 'input' in inp_data: | 22 if 'input' in indata: |
20 input_extension = inp_data[ "input" ].extension | 23 input_extension = indata["input"].extension |
21 log.debug("The input extension is %s" % input_extension) | 24 log.debug("The input extension is %s" % input_extension) |
22 if input_extension in ["mzxml","mzml","mzdata","netcdf"]: | 25 if input_extension in ["mzxml", "mzml", "mzdata", "netcdf"]: |
23 return 'thread1-mem_free8' | 26 return 'thread1-mem_free8' |
24 # zip file | 27 # zip file |
25 return 'thread8-mem_free16' | 28 return 'thread8-mem_free16' |