Hi John,
yes - I created this hacky solution and it works.
I now tried what you said, but no success.
Code:
> <collection name="split_output" type="list" label="@OUTPUT_NAME_PREFIX@
> on ${on_string} (Fastq Collection)" format_source="fastq_input1">
> <discover_datasets pattern="sample_(?P<name>.+)\.fq"
> directory="output" />
> </collection>
It puts the samples into the collection correctly, but doesn't set a data
type.
Weird enough: In the collection, the files even don't show any format
(in the small history view on the right). Is that normal?
Addon: How can I let the files in the collection have the same database
build
attached? The other file (log file) gets it.
Best,
Alexander
2015-06-25 9:12 GMT-05:00 John Chilton <jmchil...@gmail.com>:
> You are giving Galaxy mixed signals :). format_source will say to use
> the data type specified by the corresponding input - but
>
> <discover_datasets pattern="__name_and_ext__" directory="splits" />
>
> Is saying (with the pattern __name_and_ext__) read files of the form
> out1.fastq and assign the collection identifier to "out1" and the
> extension/format to "fastq".
>
> Two things should work - one of them will and the other might but should.
>
> One thing you can do is not override the extension in your pattern:
>
> <discover_datasets pattern="__name__" directory="splits" />
>
> or if you don't want to include the .fq in the output identifier (and
> you probably don't want to)
>
> <discover_datasets pattern="(?P<name>.+)\.fq" />
>
> If that doesn't work - it is a bug and please let me know and I will
> attempt to fix it.
>
> The hackier way to get this to work that I am more confident will work
> - is to drop the format_source - use the same pattern:
>
> <discover_datasets pattern="__name_and_ext__" directory="splits" />
>
> But just use a shell command or something to rename all files of the
> form *.fq to *.${fastq_input1.ext}.
>
> Hope this helps.
>
> -John
>
>
> On Thu, Jun 25, 2015 at 9:56 AM, Alexander Vowinkel
> <vowinkel.alexan...@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.c...@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.alexan...@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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> >
>
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