Hello Gunnar,
This issue should be resolved in change set 3316:4686a93802c0, which
is now available in the Galaxy distribution. Let me know if you still
encounter problems. Thanks!
On Feb 1, 2010, at 11:23 AM, Gunnar Raetsch wrote:
> Hi Greg,
>
> thanks for opening the bitbucket issue.
> The bug is still there in the current release and we are bothered by
> it...
> Is there an estimate when it will be fixed?
>
> Cheers, Gunnar
>
>
> On 08.12.2009, at 19:34, Greg Von Kuster wrote:
>
>> Hello Gunnar,
>>
>> I've opened the following ticket for this issue - you can "follow"
>> the ticket in bitbucket if you want. Thanks for reporting this.
>>
>> http://bitbucket.org/galaxy/galaxy-central/issue/257/boolean-parameters-in-…
>>
>>
>> On Dec 1, 2009, at 10:40 AM, James Taylor wrote:
>>
>>>
>>>
>>> Begin forwarded message:
>>>
>>>> From: Gunnar Rätsch <Gunnar.Raetsch(a)tuebingen.mpg.de>
>>>> Date: December 1, 2009 7:16:43 AM EST
>>>> To: James Taylor <james(a)bx.psu.edu>
>>>> Subject: bug: boolean parameters in conditions always false
>>>>
>>>> Hi James,
>>>>
>>>> I recently encountered a bug in galaxy where the boolean
>>>> parameter passed to the command is always false (i.e. the value
>>>> given in falsevalue), even if the box is checked (truevalue never
>>>> shows up).
>>>> This reproducibly happens whenever the parameter is inside of a
>>>> conditional.
>>>> I verified that it works when it is outside and also works when I
>>>> replace the boolean parameter with a select-field (with two
>>>> options: true and false).
>>>>
>>>> Is this enough information to reproduce and fix it?
>>>>
>>>> Thanks a lot in advance!
>>>>
>>>> Cheers, Gunnar
>>>>
>>>>
>>>
>>>
>>> _______________________________________________
>>> galaxy-bugs mailing list
>>> galaxy-bugs(a)lists.bx.psu.edu
>>> http://lists.bx.psu.edu/listinfo/galaxy-bugs
>>
>> Greg Von Kuster
>> Galaxy Development Team
>> greg(a)bx.psu.edu
>>
>>
>>
>
>
Greg Von Kuster
Galaxy Development Team
greg(a)bx.psu.edu
Hello,
A new version of FASTX-Toolkit is available for download at
http://hannonlab.cshl.edu/fastx_toolkit/download.html
This version should be much easier to integrate with galaxy.
New tools:
fastq_masker (suggested by Ben Bimber)
New features:
fastx_trimmer can trim N nucleotides from the end of the sequences (a new command line option, and a separate tool in Galaxy)
fastx_clipper accepts minimum adapter length to clip (requested by Erick Antezana, command line only)
Improved Galaxy integration:
Almost all tools have working functional tests (except the plotting tools and barcode splitter).
Plotting tools (nucleotide distribution and quality boxplot) detect input file type and show a detailed warning if given a FASTA/Q file as input (hopefully reducing bug reports).
Tools read the input FASTQ type (sanger or solexa) and use the correct quality ASCII offset (33 for sanger, 64 for solexa).
Comments are welcomed,
-gordon