Re: [galaxy-dev] list collection output - format set from input
You are giving Galaxy mixed signals :). format_source will say to use
the data type specified by the corresponding input - but
<discover_datasets pattern="__name_and_ext__" directory="splits"
/>
Is saying (with the pattern __name_and_ext__) read files of the form
out1.fastq and assign the collection identifier to "out1" and the
extension/format to "fastq".
Two things should work - one of them will and the other might but should.
One thing you can do is not override the extension in your pattern:
<discover_datasets pattern="__name__" directory="splits" />
or if you don't want to include the .fq in the output identifier (and
you probably don't want to)
<discover_datasets pattern="(?P<name>.+)\.fq" />
If that doesn't work - it is a bug and please let me know and I will
attempt to fix it.
The hackier way to get this to work that I am more confident will work
- is to drop the format_source - use the same pattern:
<discover_datasets pattern="__name_and_ext__" directory="splits"
/>
But just use a shell command or something to rename all files of the
form *.fq to *.${fastq_input1.ext}.
Hope this helps.
-John
On Thu, Jun 25, 2015 at 9:56 AM, Alexander Vowinkel
<vowinkel.alexander(a)gmail.com> wrote:
no - not a typo. The tool can process both.
It's just my naming, because I use it for fastq.
I'll change the help tag.
2015-06-25 3:44 GMT-05:00 Peter Cock <p.j.a.cock(a)googlemail.com>:
>
> Hi Alexander,
>
> If this wasn't a collection, I would expect format_source to work
> (possibly also using metadata_source="fastq_input1"), so perhaps
> this is a bug - John?
>
> Peter
>
> P.S. Your help caption and output label both say FASTQ, but the
> input also allows FASTA input. Typo?
>
> On Thu, Jun 25, 2015 at 2:39 AM, Alexander Vowinkel
> <vowinkel.alexander(a)gmail.com> wrote:
> > Hi,
> >
> > I have an input, that can be fasta,fastqsanger,fastqillumina:
> >
> > <param name="fastq_input1" type="data"
> > format="fasta,fastqsanger,fastqillumina" label="Select the fastq
file"
> > help="Specify fastq file with reads"/>
> >
> >
> > I have multiple outputfiles - bundled in a list collection:
> >
> > <collection name="split_output" type="list"
label="@OUTPUT_NAME_PREFIX@
> > on
> > ${on_string} (Fastq Collection)"
format_source="fastq_input1">
> > <discover_datasets pattern="__name_and_ext__"
directory="splits" />
> > </collection>
> >
> >
> > The format_source parameter doesn't work - the files in the list
> > (extension
> > fq) are of format "fq"
> >
> > How can I make it possible that they are fasta,fastqsanger,fastqillumina
> > depending on fastq_input1?
> >
> > Thanks,
> > Alexander
> >
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