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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