Mercurial > repos > devteam > emboss_5
view emboss_format_corrector.py @ 15:dc492eb6a4fc draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 431486be049407b094d495ae4a68bf76d27fa522
author | iuc |
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date | Mon, 28 Jan 2019 14:50:36 -0500 |
parents | d49956b87f7e |
children | ce385837c160 |
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# EMBOSS format corrector import operator # Properly set file formats before job run def exec_before_job( app, inp_data=None, out_data=None, tool=None, param_dict=None ): # why isn't items an ordered list? items = out_data.items() items = sorted(items, key=operator.itemgetter(0)) # normal filetype correction data_count = 1 for name, data in items: outputType = param_dict.get( 'out_format' + str(data_count), None ) if outputType is not None: if outputType == 'ncbi': outputType = "fasta" elif outputType == 'excel': outputType = "tabular" elif outputType == 'text': outputType = "txt" data = app.datatypes_registry.change_datatype(data, outputType) app.model.context.add( data ) app.model.context.flush() data_count += 1 # html filetype correction data_count = 1 for name, data in items: wants_plot = param_dict.get( 'html_out' + str(data_count), None ) ext = "html" if wants_plot == "yes": data = app.datatypes_registry.change_datatype(data, ext) app.model.context.add( data ) app.model.context.flush() data_count += 1 # png file correction data_count = 1 for name, data in items: wants_plot = param_dict.get( 'plot' + str(data_count), None ) ext = "png" if wants_plot == "yes": data = app.datatypes_registry.change_datatype(data, ext) app.model.context.add( data ) app.model.context.flush() data_count += 1