format="input"

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format="input"

Mariette
Hi everyone,

I'm facing a little problem ...

I have the following input :
<param name="input" type="data" format="sff,fasta,fastq" label="454
reads" />
<param name="qual_file" type="data" format="qual" optional="true"
label="Quality reads file (if input is a fasta)" />

and the following output:
<data name="output" format="input" label="${tool.name} on ${on_string}:
cleaned reads"/>
<data name="out_qual" format="qual" label="${tool.name} on ${on_string}:
cleaned reads">
    <filter>qual_file != None</filter>
</data>

If I provide the tool a sff file, the output is sff, if I only provide a
fasta file and no qual file the output will be a fasta.
However if I provide a fasta+qual the output will be considered as qual
file even if it's a fasta file.

I don't get how it can mark my output file as a qual file knowing it's
not a valid input file format.

Any ideas ?
thx,

Jerome
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Re: format="input"

Peter Cock
On Wed, Jun 8, 2011 at 4:36 PM, Mariette <[hidden email]> wrote:
> Hi everyone,
>
> I'm facing a little problem ...
> Any ideas ?
> thx,

I don't know what kind of tool you are working on, but personally I'd
consider dropping support for FASTA+QUAL and try and work with either
SFF or FASTQ only. It makes so many things easier.

Peter
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Re: format="input"

Mariette

Hi and thanks to you both !

Jim : I tryed your solution and it works just fine !
Peter : thanks for the advice, I'll support only sff/fastq as inputs
you're right it makes think easier !

Jerome



Peter Cock a écrit :

> On Wed, Jun 8, 2011 at 4:36 PM, Mariette <[hidden email]> wrote:
>  
>> Hi everyone,
>>
>> I'm facing a little problem ...
>> Any ideas ?
>> thx,
>>    
>
> I don't know what kind of tool you are working on, but personally I'd
> consider dropping support for FASTA+QUAL and try and work with either
> SFF or FASTQ only. It makes so many things easier.
>
> Peter
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>   http://lists.bx.psu.edu/
>  

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