Mercurial > repos > lecorguille > xcms_xcmsset
annotate 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 |
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rev | line source |
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15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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changeset
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1 import logging |
28
378ddb410225
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4dc5751176d47d41fa1dec33eb443e335a1a316f
workflow4metabolomics
parents:
15
diff
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2 |
12
15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
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3 |
15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
changeset
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4 ''' |
15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
changeset
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5 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
|
6 ''' |
15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
changeset
|
7 |
28
378ddb410225
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4dc5751176d47d41fa1dec33eb443e335a1a316f
workflow4metabolomics
parents:
15
diff
changeset
|
8 |
12
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 ''' |
28
378ddb410225
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4dc5751176d47d41fa1dec33eb443e335a1a316f
workflow4metabolomics
parents:
15
diff
changeset
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11 This function checks the input file format/extension and decide which |
378ddb410225
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4dc5751176d47d41fa1dec33eb443e335a1a316f
workflow4metabolomics
parents:
15
diff
changeset
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12 destination in the job_conf.xml using |
378ddb410225
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4dc5751176d47d41fa1dec33eb443e335a1a316f
workflow4metabolomics
parents:
15
diff
changeset
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13 - If it's a zip file, we will launch the job in multi-thread mode |
378ddb410225
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4dc5751176d47d41fa1dec33eb443e335a1a316f
workflow4metabolomics
parents:
15
diff
changeset
|
14 (-pe thread 8) |
378ddb410225
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4dc5751176d47d41fa1dec33eb443e335a1a316f
workflow4metabolomics
parents:
15
diff
changeset
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15 - If it's an individual file (mzxml, mzml, mzdata or netcdf), |
378ddb410225
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4dc5751176d47d41fa1dec33eb443e335a1a316f
workflow4metabolomics
parents:
15
diff
changeset
|
16 the job will use for instance (-pe thread 1) |
12
15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
changeset
|
17 ''' |
15646e937936
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
diff
changeset
|
18 log = logging.getLogger(__name__) |
28
378ddb410225
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4dc5751176d47d41fa1dec33eb443e335a1a316f
workflow4metabolomics
parents:
15
diff
changeset
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19 indata = dict([(da.name, da.dataset) for da in job.input_datasets]) |
378ddb410225
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4dc5751176d47d41fa1dec33eb443e335a1a316f
workflow4metabolomics
parents:
15
diff
changeset
|
20 indata.update([(da.name, da.dataset) for da in job.input_library_datasets]) |
378ddb410225
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4dc5751176d47d41fa1dec33eb443e335a1a316f
workflow4metabolomics
parents:
15
diff
changeset
|
21 input_extension = indata["input"].extension |
378ddb410225
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4dc5751176d47d41fa1dec33eb443e335a1a316f
workflow4metabolomics
parents:
15
diff
changeset
|
22 if 'input' in indata: |
378ddb410225
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4dc5751176d47d41fa1dec33eb443e335a1a316f
workflow4metabolomics
parents:
15
diff
changeset
|
23 input_extension = indata["input"].extension |
14
363cce459fff
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
lecorguille
parents:
13
diff
changeset
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24 log.debug("The input extension is %s" % input_extension) |
28
378ddb410225
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4dc5751176d47d41fa1dec33eb443e335a1a316f
workflow4metabolomics
parents:
15
diff
changeset
|
25 if input_extension in ["mzxml", "mzml", "mzdata", "netcdf"]: |
14
363cce459fff
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
lecorguille
parents:
13
diff
changeset
|
26 return 'thread1-mem_free8' |
363cce459fff
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
lecorguille
parents:
13
diff
changeset
|
27 # zip file |
15
b62808a2a008
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
14
diff
changeset
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28 return 'thread8-mem_free16' |