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 ${on_string} (Fastq Collection)" format_source="fastq_input1"> <discover_datasets pattern="sample_(?P<name>.+)\.fq" directory="output" /> </collection>
It puts the samples into the collection correctly, but doesn't set a data type. Weird enough: In the collection, the files even don't show any format (in the small history view on the right). Is that normal? Addon: How can I let the files in the collection have the same database build attached? The other file (log file) gets it. Best, Alexander 2015-06-25 9:12 GMT-05:00 John Chilton <jmchilton@gmail.com>:
You are giving Galaxy mixed signals :). format_source will say to use the data type specified by the corresponding input - but
<discover_datasets pattern="__name_and_ext__" directory="splits" />
Is saying (with the pattern __name_and_ext__) read files of the form out1.fastq and assign the collection identifier to "out1" and the extension/format to "fastq".
Two things should work - one of them will and the other might but should.
One thing you can do is not override the extension in your pattern:
<discover_datasets pattern="__name__" directory="splits" />
or if you don't want to include the .fq in the output identifier (and you probably don't want to)
<discover_datasets pattern="(?P<name>.+)\.fq" />
If that doesn't work - it is a bug and please let me know and I will attempt to fix it.
The hackier way to get this to work that I am more confident will work - is to drop the format_source - use the same pattern:
<discover_datasets pattern="__name_and_ext__" directory="splits" />
But just use a shell command or something to rename all files of the form *.fq to *.${fastq_input1.ext}.
Hope this helps.
-John
On Thu, Jun 25, 2015 at 9:56 AM, Alexander Vowinkel <vowinkel.alexander@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@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@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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