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  1. UGENE
  2. UGENE-6050

Modification of the "Filter by Classification" element

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Blocker
    • Resolution: Fixed
    • Affects Version/s: virogenesis
    • Fix Version/s: 1.31
    • Component/s: NGS, Workflow
    • Labels:
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      Description

      The "Taxons" parameter of the "Filter by Classification" element is currently mandatory. Thus, it is not possible to use the "Resolution for unspecific" parameter only, i.e. get only NGS reads with taxID=0.

      The following modifications of the element are required:

      1. Modify the element description in the Property Editor as follows:
        The filter takes files with NGS reads or scaffolds, classified by one of the tools: Kraken, CLARK, DIAMOND, WEVOTE. For each input file it outputs a file with unspecific sequences (i.e. sequences not classified by the tools, taxID = 0) and/or one or several files with sequences that belong to specific taxonomic group(s).
        
      2. Rename "Resolution for unspecific" to "Save unspecific sequences".
      3. Change the values to "True" and "False". Make "True" the default value.
      4. Change the parameter description to the following:
        Select "True" to put all unspecific input sequences (i. e. sequences with tax ID = 0) into a separate file. 
        Select "False" to skip unspecific sequences. At least one specific taxon should be selected in the "Save sequences with taxID" parameter in this case.
        
      5. Rename "Taxons" to "Save sequences with taxID".
      6. Change the parameter description to the following:
        Select a taxID to put all sequences that belong to this taxonomic group (i. e. the specified taxID and all children in the taxonomy tree) into a separate file.
        
      7. The parameter shouldn't be mandatory anymore. However, if "Save unspecific sequences" is set to "False" and no taxons are selected, show the following error:
        Set "Save unspecific sequences" to "True" or select a taxon in "Save sequences with taxID".
        

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            Assignee:
            atiunov Aleksey Tiunov [X] (Inactive)
            Reporter:
            oigl Olga Golosova
            Assigned Tester:
            Kirill Rasputin
            Watchers:
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              Dates

              Created:
              Updated:
              Resolved: