Mercurial > repos > lecorguille > xcms_xcmsset
annotate destinations_input_type.py @ 15:b62808a2a008 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
author | lecorguille |
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date | Tue, 18 Sep 2018 16:07:36 -0400 |
parents | 363cce459fff |
children | 378ddb410225 |
rev | line source |
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15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
changeset
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1 from galaxy.jobs import JobDestination |
15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
changeset
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2 import logging |
15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
changeset
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3 import os |
15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
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4 |
15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
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5 ''' |
15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
changeset
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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
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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
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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
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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
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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
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15 log = logging.getLogger(__name__) |
15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
changeset
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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
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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
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18 input_extension = inp_data[ "input" ].extension |
14
363cce459fff
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
lecorguille
parents:
13
diff
changeset
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19 if 'input' in inp_data: |
363cce459fff
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
lecorguille
parents:
13
diff
changeset
|
20 input_extension = inp_data[ "input" ].extension |
363cce459fff
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
lecorguille
parents:
13
diff
changeset
|
21 log.debug("The input extension is %s" % input_extension) |
363cce459fff
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
lecorguille
parents:
13
diff
changeset
|
22 if input_extension in ["mzxml","mzml","mzdata","netcdf"]: |
363cce459fff
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
lecorguille
parents:
13
diff
changeset
|
23 return 'thread1-mem_free8' |
363cce459fff
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
lecorguille
parents:
13
diff
changeset
|
24 # zip file |
15
b62808a2a008
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
14
diff
changeset
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25 return 'thread8-mem_free16' |