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annotate operation_filter.py @ 3:e0a23ab32d7f draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author devteam
date Wed, 11 Nov 2015 12:47:38 -0500
parents d958d5a0d1e8
children 38c8bb402872
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1 # runs after the job (and after the default post-filter)
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2 from galaxy.tools.parameters import DataToolParameter
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3
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4 from galaxy.jobs.handler import JOB_ERROR
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5
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6 # Older py compatibility
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7 try:
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8 set()
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9 except:
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10 from sets import Set as set
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11
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12
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13 def validate_input( trans, error_map, param_values, page_param_map ):
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14 dbkeys = set()
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15 data_param_names = set()
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16 data_params = 0
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17 for name, param in page_param_map.iteritems():
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18 if isinstance( param, DataToolParameter ):
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19 # for each dataset parameter
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20 if param_values.get(name, None) is not None:
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21 dbkeys.add( param_values[name].dbkey )
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22 data_params += 1
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23 # check meta data
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24 try:
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25 param = param_values[name]
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26 if isinstance( param.datatype, trans.app.datatypes_registry.get_datatype_by_extension( 'gff' ).__class__ ):
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27 # TODO: currently cannot validate GFF inputs b/c they are not derived from interval.
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28 pass
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29 else: # Validate interval datatype.
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30 int( param.metadata.startCol )
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31 int( param.metadata.endCol )
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32 int( param.metadata.chromCol )
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33 if param.metadata.strandCol is not None:
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34 int( param.metadata.strandCol )
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35 except:
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36 error_msg = "The attributes of this dataset are not properly set. " + \
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37 "Click the pencil icon in the history item to set the chrom, start, end and strand columns."
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38 error_map[name] = error_msg
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39 data_param_names.add( name )
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40 if len( dbkeys ) > 1:
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41 for name in data_param_names:
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42 error_map[name] = "All datasets must belong to same genomic build, " \
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43 "this dataset is linked to build '%s'" % param_values[name].dbkey
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44 if data_params != len(data_param_names):
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45 for name in data_param_names:
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46 error_map[name] = "A dataset of the appropriate type is required"
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47
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48
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49 # Commented out by INS, 5/30/2007. What is the PURPOSE of this?
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50 def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None):
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51 """Verify the output data after each run"""
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52 for data in out_data.values():
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53 try:
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54 if stderr and len( stderr ) > 0:
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55 raise Exception( stderr )
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56
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57 except Exception:
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58 data.blurb = JOB_ERROR
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59 data.state = JOB_ERROR
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60
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61
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62 def exec_after_merge(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None):
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63 exec_after_process(
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64 app, inp_data, out_data, param_dict, tool=tool, stdout=stdout, stderr=stderr)
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65
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66 # strip strand column if clusters were merged
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67 for data in out_data.values():
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68 if param_dict['returntype'] is True:
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69 data.metadata.chromCol = 1
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70 data.metadata.startCol = 2
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71 data.metadata.endCol = 3
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72 # merge always clobbers strand
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73 data.metadata.strandCol = None
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74
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75
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76 def exec_after_cluster(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None):
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77 exec_after_process(
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78 app, inp_data, out_data, param_dict, tool=tool, stdout=stdout, stderr=stderr)
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79
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80 # strip strand column if clusters were merged
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81 if param_dict["returntype"] == '1':
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82 for data in out_data.values():
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83 data.metadata.strandCol = None