Mercurial > repos > devteam > emboss_5
comparison emboss_format_corrector.py @ 17:ce385837c160 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 4812c313fd8762b11f7fd002436e3a93b4c67f00"
author | iuc |
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date | Fri, 20 Nov 2020 16:51:11 +0000 |
parents | d49956b87f7e |
children |
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16:dba489bfcd62 | 17:ce385837c160 |
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1 # EMBOSS format corrector | 1 # EMBOSS format corrector |
2 import operator | 2 import operator |
3 | 3 |
4 | 4 |
5 # Properly set file formats before job run | 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 items = sorted(items, key=operator.itemgetter(0)) | 9 items = sorted(items, key=operator.itemgetter(0)) |
10 | 10 |
11 # normal filetype correction | 11 # normal filetype correction |
12 data_count = 1 | 12 data_count = 1 |
13 for name, data in items: | 13 for name, data in items: |
14 outputType = param_dict.get( 'out_format' + str(data_count), None ) | 14 outputType = param_dict.get('out_format' + str(data_count), None) |
15 if outputType is not None: | 15 if outputType is not None: |
16 if outputType == 'ncbi': | 16 if outputType == 'ncbi': |
17 outputType = "fasta" | 17 outputType = "fasta" |
18 elif outputType == 'excel': | 18 elif outputType == 'excel': |
19 outputType = "tabular" | 19 outputType = "tabular" |
20 elif outputType == 'text': | 20 elif outputType == 'text': |
21 outputType = "txt" | 21 outputType = "txt" |
22 data = app.datatypes_registry.change_datatype(data, outputType) | 22 data = app.datatypes_registry.change_datatype(data, outputType) |
23 app.model.context.add( data ) | 23 app.model.context.add(data) |
24 app.model.context.flush() | 24 app.model.context.flush() |
25 data_count += 1 | 25 data_count += 1 |
26 | 26 |
27 # html filetype correction | 27 # html filetype correction |
28 data_count = 1 | 28 data_count = 1 |
29 for name, data in items: | 29 for name, data in items: |
30 wants_plot = param_dict.get( 'html_out' + str(data_count), None ) | 30 wants_plot = param_dict.get('html_out' + str(data_count), None) |
31 ext = "html" | 31 ext = "html" |
32 if wants_plot == "yes": | 32 if wants_plot == "yes": |
33 data = app.datatypes_registry.change_datatype(data, ext) | 33 data = app.datatypes_registry.change_datatype(data, ext) |
34 app.model.context.add( data ) | 34 app.model.context.add(data) |
35 app.model.context.flush() | 35 app.model.context.flush() |
36 data_count += 1 | 36 data_count += 1 |
37 | 37 |
38 # png file correction | 38 # png file correction |
39 data_count = 1 | 39 data_count = 1 |
40 for name, data in items: | 40 for name, data in items: |
41 wants_plot = param_dict.get( 'plot' + str(data_count), None ) | 41 wants_plot = param_dict.get('plot' + str(data_count), None) |
42 ext = "png" | 42 ext = "png" |
43 if wants_plot == "yes": | 43 if wants_plot == "yes": |
44 data = app.datatypes_registry.change_datatype(data, ext) | 44 data = app.datatypes_registry.change_datatype(data, ext) |
45 app.model.context.add( data ) | 45 app.model.context.add(data) |
46 app.model.context.flush() | 46 app.model.context.flush() |
47 data_count += 1 | 47 data_count += 1 |