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annotate dexseq_helper.py @ 0:276833129f97 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
author iuc
date Thu, 24 Sep 2015 17:16:56 -0400
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children 28a2181df3b9
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276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
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276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
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2 from galaxy.tools.parameters import DataToolParameter
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
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4 def validate_input( trans, error_map, param_values, page_param_map ):
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
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5 """
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
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6 Validates the user input, before execution.
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
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7 """
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
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8 factors = param_values['rep_factorName']
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
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9 factor_name_list = []
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
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10 factor_duplication = False
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
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11 level_duplication = False
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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13 for factor in factors:
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
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14 # factor names should be unique
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
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15 fn = factor['factorName']
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
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16 if fn in factor_name_list:
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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17 factor_duplication = True
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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18 break
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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19 factor_name_list.append( fn )
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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21 level_name_list = list()
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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22 factor_index_list = list()
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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24 for level in factor['rep_factorLevel']:
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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25 # level names under one factor should be unique
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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26 fl = level['factorLevel']
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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27 if fl in level_name_list:
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
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28 level_duplication = True
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
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29 level_name_list.append( fl )
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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31 if level_duplication:
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
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32 error_map['rep_factorName'] = [ dict() for t in factors ]
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
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33 for i in range( len( factors ) ):
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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34 error_map['rep_factorName'][i]['rep_factorLevel'] = [ {'factorLevel': 'Factor levels for each factor need to be unique'} for t in factor['rep_factorLevel'] ]
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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35 break
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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37 if factor_duplication:
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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38 error_map['rep_factorName'] = [ dict() for t in factors ]
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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39 for i in range( len( factors ) ):
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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40 error_map['rep_factorName'][i]['factorName'] = 'Factor names need to be unique.'
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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