Hello, 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 ] #else: 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, Felix
Hi Felix, Thanks for reporting this error, it has been fixed in revision 7663:cc064ff4249b. Please let us know if you encounter additional issues. Thanks for using Galaxy, Dan On Sep 10, 2012, at 12:23 PM, Felix Homa wrote:
Hello,
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 ] #else: 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,
Felix
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participants (2)
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Daniel Blankenberg -
Felix Homa