Mercurial > repos > devteam > emboss_5
comparison emboss_format_corrector.py @ 10:9b98d3d903c6 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
author | devteam |
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date | Fri, 12 Aug 2016 19:17:10 -0400 |
parents | |
children | 0e2484b6829b |
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9:18a63c800a4d | 10:9b98d3d903c6 |
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1 #EMBOSS format corrector | |
2 | |
3 import operator | |
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 ): | |
7 #why isn't items an ordered list? | |
8 items = out_data.items() | |
9 #lets sort it ourselves.... | |
10 items = sorted(items, key=operator.itemgetter(0)) | |
11 #items is now sorted... | |
12 | |
13 #normal filetype correction | |
14 data_count=1 | |
15 for name, data in items: | |
16 outputType = param_dict.get( 'out_format'+str(data_count), None ) | |
17 #print "data_count",data_count, "name", name, "outputType", outputType | |
18 if outputType !=None: | |
19 if outputType == 'ncbi': | |
20 outputType = "fasta" | |
21 elif outputType == 'excel': | |
22 outputType = "tabular" | |
23 elif outputType == 'text': | |
24 outputType = "txt" | |
25 data = app.datatypes_registry.change_datatype(data, outputType) | |
26 app.model.context.add( data ) | |
27 app.model.context.flush() | |
28 data_count+=1 | |
29 | |
30 #html filetype correction | |
31 data_count=1 | |
32 for name, data in items: | |
33 wants_plot = param_dict.get( 'html_out'+str(data_count), None ) | |
34 ext = "html" | |
35 if wants_plot == "yes": | |
36 data = app.datatypes_registry.change_datatype(data, ext) | |
37 app.model.context.add( data ) | |
38 app.model.context.flush() | |
39 data_count+=1 | |
40 | |
41 #png file correction | |
42 data_count=1 | |
43 for name, data in items: | |
44 wants_plot = param_dict.get( 'plot'+str(data_count), None ) | |
45 ext = "png" | |
46 if wants_plot == "yes": | |
47 data = app.datatypes_registry.change_datatype(data, ext) | |
48 app.model.context.add( data ) | |
49 app.model.context.flush() | |
50 data_count+=1 |