[2] | 1 | #EMBOSS format corrector |
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| 2 | |
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| 3 | import operator |
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| 4 | #from galaxy import datatypes |
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| 5 | |
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| 6 | #Properly set file formats after job run |
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| 7 | def exec_after_process( app, inp_data, out_data, param_dict,tool, stdout, stderr): |
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| 8 | #Properly set file formats before job run |
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| 9 | #def exec_before_job(trans, inp_data, out_data, param_dict,tool): |
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| 10 | #why isn't items an ordered list? |
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| 11 | items = out_data.items() |
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| 12 | #lets sort it ourselves.... |
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| 13 | items = sorted(items, key=operator.itemgetter(0)) |
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| 14 | #items is now sorted... |
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| 15 | |
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| 16 | #normal filetype correction |
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| 17 | data_count=1 |
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| 18 | for name, data in items: |
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| 19 | outputType = param_dict.get( 'out_format'+str(data_count), None ) |
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| 20 | #print "data_count",data_count, "name", name, "outputType", outputType |
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| 21 | if outputType !=None: |
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| 22 | if outputType == 'ncbi': |
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| 23 | outputType = "fasta" |
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| 24 | elif outputType == 'excel': |
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| 25 | outputType = "tabular" |
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| 26 | elif outputType == 'text': |
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| 27 | outputType = "txt" |
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| 28 | data = app.datatypes_registry.change_datatype(data, outputType) |
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| 29 | app.model.context.add( data ) |
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| 30 | app.model.context.flush() |
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| 31 | data_count+=1 |
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| 32 | |
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| 33 | #html filetype correction |
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| 34 | data_count=1 |
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| 35 | for name, data in items: |
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| 36 | wants_plot = param_dict.get( 'html_out'+str(data_count), None ) |
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| 37 | ext = "html" |
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| 38 | if wants_plot == "yes": |
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| 39 | data = app.datatypes_registry.change_datatype(data, ext) |
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| 40 | app.model.context.add( data ) |
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| 41 | app.model.context.flush() |
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| 42 | data_count+=1 |
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| 43 | |
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| 44 | #png file correction |
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| 45 | data_count=1 |
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| 46 | for name, data in items: |
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| 47 | wants_plot = param_dict.get( 'plot'+str(data_count), None ) |
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| 48 | ext = "png" |
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| 49 | if wants_plot == "yes": |
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| 50 | data = app.datatypes_registry.change_datatype(data, ext) |
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| 51 | app.model.context.add( data ) |
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| 52 | app.model.context.flush() |
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| 53 | data_count+=1 |
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