Mercurial > repos > devteam > basecoverage

comparison operation_filter.py @ 0:3755ee8a74d7

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Imported from capsule None
author devteam
date Tue, 01 Apr 2014 09:13:19 -0400
parents
children c929b6540d07
comparison
equal deleted inserted replaced
-1:000000000000 0:3755ee8a74d7
1 # runs after the job (and after the default post-filter)
2 import os
3 from galaxy import eggs
4 from galaxy import jobs
5 from galaxy.tools.parameters import DataToolParameter
6
7 from galaxy.jobs.handler import JOB_ERROR
8
9 # Older py compatibility
10 try:
11 set()
12 except:
13 from sets import Set as set
14
15 #def exec_before_process(app, inp_data, out_data, param_dict, tool=None):
16 # """Sets the name of the data"""
17 # dbkeys = sets.Set( [data.dbkey for data in inp_data.values() ] )
18 # if len(dbkeys) != 1:
19 # raise Exception, '<p><font color="yellow">Both Queries must be from the same genome build</font></p>'
20
21 def validate_input( trans, error_map, param_values, page_param_map ):
22 dbkeys = set()
23 data_param_names = set()
24 data_params = 0
25 for name, param in page_param_map.iteritems():
26 if isinstance( param, DataToolParameter ):
27 # for each dataset parameter
28 if param_values.get(name, None) != None:
29 dbkeys.add( param_values[name].dbkey )
30 data_params += 1
31 # check meta data
32 try:
33 param = param_values[name]
34 if isinstance( param.datatype, trans.app.datatypes_registry.get_datatype_by_extension( 'gff' ).__class__ ):
35 # TODO: currently cannot validate GFF inputs b/c they are not derived from interval.
36 pass
37 else: # Validate interval datatype.
38 startCol = int( param.metadata.startCol )
39 endCol = int( param.metadata.endCol )
40 chromCol = int( param.metadata.chromCol )
41 if param.metadata.strandCol is not None:
42 strandCol = int ( param.metadata.strandCol )
43 else:
44 strandCol = 0
45 except:
46 error_msg = "The attributes of this dataset are not properly set. " + \
47 "Click the pencil icon in the history item to set the chrom, start, end and strand columns."
48 error_map[name] = error_msg
49 data_param_names.add( name )
50 if len( dbkeys ) > 1:
51 for name in data_param_names:
52 error_map[name] = "All datasets must belong to same genomic build, " \
53 "this dataset is linked to build '%s'" % param_values[name].dbkey
54 if data_params != len(data_param_names):
55 for name in data_param_names:
56 error_map[name] = "A dataset of the appropriate type is required"
57
58 # Commented out by INS, 5/30/2007. What is the PURPOSE of this?
59 def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None):
60 """Verify the output data after each run"""
61 items = out_data.items()
62
63 for name, data in items:
64 try:
65 if stderr and len( stderr ) > 0:
66 raise Exception( stderr )
67
68 except Exception, exc:
69 data.blurb = JOB_ERROR
70 data.state = JOB_ERROR
71
72 ## def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None):
73 ## pass
74
75
76 def exec_after_merge(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None):
77 exec_after_process(
78 app, inp_data, out_data, param_dict, tool=tool, stdout=stdout, stderr=stderr)
79
80 # strip strand column if clusters were merged
81 items = out_data.items()
82 for name, data in items:
83 if param_dict['returntype'] == True:
84 data.metadata.chromCol = 1
85 data.metadata.startCol = 2
86 data.metadata.endCol = 3
87 # merge always clobbers strand
88 data.metadata.strandCol = None
89
90
91 def exec_after_cluster(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None):
92 exec_after_process(
93 app, inp_data, out_data, param_dict, tool=tool, stdout=stdout, stderr=stderr)
94
95 # strip strand column if clusters were merged
96 if param_dict["returntype"] == '1':
97 items = out_data.items()
98 for name, data in items:
99 data.metadata.strandCol = None