annotate emboss_format_corrector.py @ 0:de3a45e9ccce draft

"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
author brinkmanlab
date Tue, 25 Jan 2022 03:26:28 +0000
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de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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1 # EMBOSS format corrector
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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2 import operator
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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5 # Properly set file formats before job run
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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6 def exec_before_job(app, inp_data=None, out_data=None, tool=None, param_dict=None):
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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7 # why isn't items an ordered list?
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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8 items = out_data.items()
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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9 items = sorted(items, key=operator.itemgetter(0))
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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11 # normal filetype correction
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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12 data_count = 1
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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13 for name, data in items:
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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14 outputType = param_dict.get('out_format' + str(data_count), None)
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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15 if outputType is not None:
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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16 if outputType == 'ncbi':
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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17 outputType = "fasta"
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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18 elif outputType == 'excel':
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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19 outputType = "tabular"
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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20 elif outputType == 'text':
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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21 outputType = "txt"
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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22 data = app.datatypes_registry.change_datatype(data, outputType)
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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23 app.model.context.add(data)
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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24 app.model.context.flush()
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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25 data_count += 1
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27 # html filetype correction
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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28 data_count = 1
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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29 for name, data in items:
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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30 wants_plot = param_dict.get('html_out' + str(data_count), None)
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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31 ext = "html"
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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32 if wants_plot == "yes":
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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33 data = app.datatypes_registry.change_datatype(data, ext)
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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34 app.model.context.add(data)
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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35 app.model.context.flush()
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36 data_count += 1
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38 # png file correction
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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39 data_count = 1
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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40 for name, data in items:
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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41 wants_plot = param_dict.get('plot' + str(data_count), None)
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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42 ext = "png"
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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43 if wants_plot == "yes":
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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44 data = app.datatypes_registry.change_datatype(data, ext)
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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45 app.model.context.add(data)
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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46 app.model.context.flush()
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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47 data_count += 1