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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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

___________________________________________________________ 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: https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

The first example should now work - maybe your variant of Galaxy was to old at the time? I added that at the request of Michael Crusoe during the last virtual contribution fest. https://github.com/galaxyproject/galaxy/commit/07dd69edd5472afef305fb170f186... Otherwise, using ext instead of format will work for much older versions of Galaxy as well as new ones. format_source and metadata_source do not work with discover_datasets - you could create an issue for that - these really should work. -John On Wed, Oct 28, 2015 at 12:32 PM, Jelle Scholtalbers <j.scholtalbers@gmail.com> wrote:

Hi all,

I have a related issue as I'm trying to set the format on discovered datasets. Only setting e.g 'ext="fastqsanger"' seems to work. But the following variations do not work to set a format, and similar to Alexander, the history items do not show any datatype with these options.

<data name="summary" format="tabular" label="Summary"> <!-- explicitly set format --> <discover_datasets pattern="(?P<name>.*)\.txt" format="fastqsanger" directory="results" visible="true" /> <!-- format_source input1 a fastq file (probably fastqsanger) --> <discover_datasets pattern="(?P<name>.*)\.txt" format_source="input_1" directory="results" visible="true" /> <!-- metadata_source input1 a fastq file (probably fastqsanger) --> <discover_datasets pattern="(?P<name>.*)\.txt" metadata_source="input_1" directory="results" visible="true" /> </data>

Is there someway to set the format by input source without writing a wrapper script to change the extension as suggested by John?

Tested this with 'planemo serve'

Cheers, Jelle

On Thu, Jun 25, 2015 at 9:36 PM, Alexander Vowinkel <vowinkel.alexander@gmail.com> wrote:

...

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

___________________________________________________________ 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: https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

___________________________________________________________ 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: https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/