Mercurial > repos > devteam > emboss_5

comparison emboss_format_corrector.py @ 11:0e2484b6829b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
author iuc
date Mon, 30 Jan 2017 13:27:40 -0500
parents 9b98d3d903c6
children c2228166c035
comparison
equal deleted inserted replaced
10:9b98d3d903c6 11:0e2484b6829b
1 #EMBOSS format corrector 1 # EMBOSS format corrector
2
3 import operator 2 import operator
4 3
5 #Properly set file formats before job run 4
5 # Properly set file formats before job run
6 def exec_before_job( app, inp_data=None, out_data=None, tool=None, param_dict=None ): 6 def exec_before_job( app, inp_data=None, out_data=None, tool=None, param_dict=None ):
7 #why isn't items an ordered list? 7 # why isn't items an ordered list?
8 items = out_data.items() 8 items = out_data.items()
9 #lets sort it ourselves....
10 items = sorted(items, key=operator.itemgetter(0)) 9 items = sorted(items, key=operator.itemgetter(0))
11 #items is now sorted... 10
12 11 # normal filetype correction
13 #normal filetype correction 12 data_count = 1
14 data_count=1
15 for name, data in items: 13 for name, data in items:
16 outputType = param_dict.get( 'out_format'+str(data_count), None ) 14 outputType = param_dict.get( 'out_format' + str(data_count), None )
17 #print "data_count",data_count, "name", name, "outputType", outputType 15 if outputType is not None:
18 if outputType !=None:
19 if outputType == 'ncbi': 16 if outputType == 'ncbi':
20 outputType = "fasta" 17 outputType = "fasta"
21 elif outputType == 'excel': 18 elif outputType == 'excel':
22 outputType = "tabular" 19 outputType = "tabular"
23 elif outputType == 'text': 20 elif outputType == 'text':
24 outputType = "txt" 21 outputType = "txt"
25 data = app.datatypes_registry.change_datatype(data, outputType) 22 data = app.datatypes_registry.change_datatype(data, outputType)
26 app.model.context.add( data ) 23 app.model.context.add( data )
27 app.model.context.flush() 24 app.model.context.flush()
28 data_count+=1 25 data_count += 1
29 26
30 #html filetype correction 27 # html filetype correction
31 data_count=1 28 data_count = 1
32 for name, data in items: 29 for name, data in items:
33 wants_plot = param_dict.get( 'html_out'+str(data_count), None ) 30 wants_plot = param_dict.get( 'html_out' + str(data_count), None )
34 ext = "html" 31 ext = "html"
35 if wants_plot == "yes": 32 if wants_plot == "yes":
36 data = app.datatypes_registry.change_datatype(data, ext) 33 data = app.datatypes_registry.change_datatype(data, ext)
37 app.model.context.add( data ) 34 app.model.context.add( data )
38 app.model.context.flush() 35 app.model.context.flush()
39 data_count+=1 36 data_count += 1
40 37
41 #png file correction 38 # png file correction
42 data_count=1 39 data_count = 1
43 for name, data in items: 40 for name, data in items:
44 wants_plot = param_dict.get( 'plot'+str(data_count), None ) 41 wants_plot = param_dict.get( 'plot' + str(data_count), None )
45 ext = "png" 42 ext = "png"
46 if wants_plot == "yes": 43 if wants_plot == "yes":
47 data = app.datatypes_registry.change_datatype(data, ext) 44 data = app.datatypes_registry.change_datatype(data, ext)
48 app.model.context.add( data ) 45 app.model.context.add( data )
49 app.model.context.flush() 46 app.model.context.flush()
50 data_count+=1 47 data_count += 1