Mercurial > repos > lecorguille > xcms_xcmsset
annotate destinations_input_type.py @ 13:c934dd5c49a9 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1
author | lecorguille |
---|---|
date | Wed, 29 Nov 2017 09:45:19 -0500 |
parents | 15646e937936 |
children | 363cce459fff |
rev | line source |
---|---|
12
15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
changeset
|
1 from galaxy.jobs import JobDestination |
15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
changeset
|
2 import logging |
15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
changeset
|
3 import os |
15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
changeset
|
4 |
15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
changeset
|
5 ''' |
15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
changeset
|
6 This file must be placed in lib/galaxy/jobs/rules/ |
15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
changeset
|
7 ''' |
15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
changeset
|
8 |
15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
changeset
|
9 def input_type(job): |
15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
changeset
|
10 ''' |
15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
changeset
|
11 This function checks the input file format/extension and decide which destination in the job_conf.xml using |
15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
changeset
|
12 - If it's a zip file, we will launch the job in multi-thread mode (-pe thread 8) |
15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
changeset
|
13 - If it's an individual file (mzxml, mzml, mzdata or netcdf), the job will use for instance (-pe thread 1) |
15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
changeset
|
14 ''' |
15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
changeset
|
15 log = logging.getLogger(__name__) |
15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
changeset
|
16 inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] ) |
15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
changeset
|
17 inp_data.update( [ ( da.name, da.dataset ) for da in job.input_library_datasets ] ) |
15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
changeset
|
18 input_extension = inp_data[ "input" ].extension |
15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
changeset
|
19 log.debug("The input extension is %s" % input_extension) |
15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
changeset
|
20 if input_extension in ["mzxml","mzml","mzdata","netcdf"]: |
13
c934dd5c49a9
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1
lecorguille
parents:
12
diff
changeset
|
21 return 'thread1-mem_free10' |
12
15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
changeset
|
22 else: # zip file |
15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
changeset
|
23 return 'thread4-men_free10' |