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&lt;name&gt;.+).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&lt;name&gt;.+)\.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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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&lt;name&gt;.*)\.txt" format="fastqsanger" directory="results" visible="true" /> <!-- format_source input1 a fastq file (probably fastqsanger) --> <discover_datasets pattern="(?P&lt;name&gt;.*)\.txt" format_source="input_1" directory="results" visible="true" /> <!-- metadata_source input1 a fastq file (probably fastqsanger) --> <discover_datasets pattern="(?P&lt;name&gt;.*)\.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&lt;name&gt;.+).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&lt;name&gt;.+)\.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/