We noticed a problem with the tool Filter Fastq. It seemed to mishandle the
paired-end checkbox. Here is the XML which seems to not work:


  <param name="paired_end" label="This is paired end data" type="boolean"
truevalue="paired_end" falsevalue="single_end" checked="False"/>


Concretely, $paired_end.value return True or False as value and not
"paired_end" or "single_end", so in the python code execution,


#if $paired_end.value == 'single_end':

     qual_scores_split = [ qual_scores ]


     qual_scores_split = [ qual_scores[ 0:int( len( qual_scores ) / 2 ) ],
qual_scores[ int( len( qual_scores ) / 2 ): ]]


Always go in the else, always splitting reads even when they are single_end.


It induces wrong results in our read filtering.


I hope the explanation is clear enough


Best regards,




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