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comparison operation_filter.py @ 5:73ca13a7ec5f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit d7b1a60c0aecc46b7f625c3e32f882562b512fd9
author devteam
date Mon, 13 Jun 2022 16:21:39 +0000
parents 32e1c8dac438
children
comparison
equal deleted inserted replaced
4:35a89f8cc96e 5:73ca13a7ec5f
43 if data_params != len(data_param_names): 43 if data_params != len(data_param_names):
44 for name in data_param_names: 44 for name in data_param_names:
45 error_map[name] = "A dataset of the appropriate type is required" 45 error_map[name] = "A dataset of the appropriate type is required"
46 46
47 47
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"""
51 for data in out_data.values():
52 try:
53 if stderr and len( stderr ) > 0:
54 raise Exception( stderr )
55 except Exception:
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): 48 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 49 # strip strand column if clusters were merged
65 for data in out_data.values(): 50 for data in out_data.values():
66 if param_dict['returntype'] is True: 51 if param_dict['returntype'] is True:
67 data.metadata.chromCol = 1 52 data.metadata.chromCol = 1
68 data.metadata.startCol = 2 53 data.metadata.startCol = 2
70 # merge always clobbers strand 55 # merge always clobbers strand
71 data.metadata.strandCol = None 56 data.metadata.strandCol = None
72 57
73 58
74 def exec_after_cluster(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None): 59 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 60 # strip strand column if clusters were merged
79 if param_dict["returntype"] == '1': 61 if param_dict["returntype"] == '1':
80 for data in out_data.values(): 62 for data in out_data.values():
81 data.metadata.strandCol = None 63 data.metadata.strandCol = None