Mercurial > repos > devteam > basecoverage
annotate operation_filter.py @ 5:37652c34b3bf draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
| author | devteam |
|---|---|
| date | Thu, 22 Jun 2017 18:37:49 -0400 |
| parents | c929b6540d07 |
| children | 4d584cf5ced5 |
| rev | line source |
|---|---|
| 0 | 1 # runs after the job (and after the default post-filter) |
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5
37652c34b3bf
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents:
3
diff
changeset
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2 from galaxy.jobs.handler import JOB_ERROR |
| 0 | 3 from galaxy.tools.parameters import DataToolParameter |
| 4 | |
| 5 # Older py compatibility | |
| 6 try: | |
| 7 set() | |
| 8 except: | |
| 9 from sets import Set as set | |
| 10 | |
| 11 | |
| 12 def validate_input( trans, error_map, param_values, page_param_map ): | |
| 13 dbkeys = set() | |
| 14 data_param_names = set() | |
| 15 data_params = 0 | |
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5
37652c34b3bf
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents:
3
diff
changeset
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16 for name, param in page_param_map.items(): |
| 0 | 17 if isinstance( param, DataToolParameter ): |
| 18 # for each dataset parameter | |
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c929b6540d07
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
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changeset
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19 if param_values.get(name, None) is not None: |
| 0 | 20 dbkeys.add( param_values[name].dbkey ) |
| 21 data_params += 1 | |
| 22 # check meta data | |
| 23 try: | |
| 24 param = param_values[name] | |
| 25 if isinstance( param.datatype, trans.app.datatypes_registry.get_datatype_by_extension( 'gff' ).__class__ ): | |
| 26 # TODO: currently cannot validate GFF inputs b/c they are not derived from interval. | |
| 27 pass | |
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c929b6540d07
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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28 else: # Validate interval datatype. |
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c929b6540d07
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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29 int( param.metadata.startCol ) |
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c929b6540d07
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
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changeset
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30 int( param.metadata.endCol ) |
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c929b6540d07
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
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diff
changeset
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31 int( param.metadata.chromCol ) |
| 0 | 32 if param.metadata.strandCol is not None: |
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c929b6540d07
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
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diff
changeset
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33 int( param.metadata.strandCol ) |
| 0 | 34 except: |
| 35 error_msg = "The attributes of this dataset are not properly set. " + \ | |
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c929b6540d07
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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changeset
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36 "Click the pencil icon in the history item to set the chrom, start, end and strand columns." |
| 0 | 37 error_map[name] = error_msg |
| 38 data_param_names.add( name ) | |
| 39 if len( dbkeys ) > 1: | |
| 40 for name in data_param_names: | |
| 41 error_map[name] = "All datasets must belong to same genomic build, " \ | |
| 42 "this dataset is linked to build '%s'" % param_values[name].dbkey | |
| 43 if data_params != len(data_param_names): | |
| 44 for name in data_param_names: | |
| 45 error_map[name] = "A dataset of the appropriate type is required" | |
| 46 | |
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c929b6540d07
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
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changeset
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47 |
| 0 | 48 # Commented out by INS, 5/30/2007. What is the PURPOSE of this? |
| 49 def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None): | |
| 50 """Verify the output data after each run""" | |
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c929b6540d07
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
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diff
changeset
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51 for data in out_data.values(): |
| 0 | 52 try: |
| 53 if stderr and len( stderr ) > 0: | |
| 54 raise Exception( stderr ) | |
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c929b6540d07
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
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changeset
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55 except Exception: |
| 0 | 56 data.blurb = JOB_ERROR |
| 57 data.state = JOB_ERROR | |
| 58 | |
| 59 | |
| 60 def exec_after_merge(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None): | |
| 61 exec_after_process( | |
| 62 app, inp_data, out_data, param_dict, tool=tool, stdout=stdout, stderr=stderr) | |
| 63 | |
| 64 # strip strand column if clusters were merged | |
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c929b6540d07
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
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65 for data in out_data.values(): |
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c929b6540d07
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
66 if param_dict['returntype'] is True: |
| 0 | 67 data.metadata.chromCol = 1 |
| 68 data.metadata.startCol = 2 | |
| 69 data.metadata.endCol = 3 | |
| 70 # merge always clobbers strand | |
| 71 data.metadata.strandCol = None | |
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c929b6540d07
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
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diff
changeset
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72 |
| 0 | 73 |
| 74 def exec_after_cluster(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None): | |
| 75 exec_after_process( | |
| 76 app, inp_data, out_data, param_dict, tool=tool, stdout=stdout, stderr=stderr) | |
| 77 | |
| 78 # strip strand column if clusters were merged | |
| 79 if param_dict["returntype"] == '1': | |
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c929b6540d07
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
80 for data in out_data.values(): |
| 0 | 81 data.metadata.strandCol = None |