Re: [galaxy-dev] list collection output - format set from input
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/07dd69edd5472afef305fb170f18628a0cf3402d
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
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.
>
>
>
> format="fastqsanger" directory="results" visible="true" />
>
> format_source="input_1" directory="results" visible="true" />
>
> metadata_source="input_1" directory="results" visible="true" />
>
>
> 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
> wrote:
>>
>> Hi John,
>>
>> yes - I created this hacky solution and it works.
>>
>> I now tried what you said, but no success.
>> Code:
>>
>>>
>>>
>>> >> directory="output" />
>>>
>>
>>
>> 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 :
>>>
>>> You are giving Galaxy mixed signals :). format_source will say to use
>>> the data type specified by the corresponding input - but
>>>
>>>
>>>
>>> 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:
>>>
>>>
>>>
>>> or if you don't want to include the .fq in the output identifier (and
>>> you probably don't want to)
>>>
>>>
>>>
>>> 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:
>>>
>>>
>>>
>>> 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
>>> 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 :
>>> >>
>>> >> 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
>>> >> wrote:
>>> >> > Hi,
>>> >> >
>>> >> > I have an input, that can be fasta,fastqsanger,fastqillumina:
>>> >> >
>>> >> > >> >> > format="fasta,fastqsanger,fastqillumina" label="Select the fastq
>>> >> > file"
>>> >> > help="Specify fastq file with reads"/>
>>> >> >
>>> >> >
>>> >> > I have multiple outputfiles - bundled in a list collection:
>>> >> >
>>> >> > >> >> > label="@OUTPUT_NAME_PREFIX@
>>> >> > on
>>> >> > ${on_string} (Fastq Collection)" format_source="fastq_input1">
>>> >> > >> >> > />
>>> >> >
>>> >> >
>>> >> >
>>> >> > 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/sear
Re: [galaxy-dev] list collection output - format set from input
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.
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.alexan...@gmail.com> wrote:
> Hi John,
>
> yes - I created this hacky solution and it works.
>
> I now tried what you said, but no success.
> Code:
>
>
>>
>> > directory="output" />
>>
>
>
> 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 :
>
>> You are giving Galaxy mixed signals :). format_source will say to use
>> the data type specified by the corresponding input - but
>>
>>
>>
>> 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:
>>
>>
>>
>> or if you don't want to include the .fq in the output identifier (and
>> you probably don't want to)
>>
>>
>>
>> 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:
>>
>>
>>
>> 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
>> 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 :
>> >>
>> >> 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
>> >> wrote:
>> >> > Hi,
>> >> >
>> >> > I have an input, that can be fasta,fastqsanger,fastqillumina:
>> >> >
>> >> > > >> > format="fasta,fastqsanger,fastqillumina" label="Select the fastq
>> file"
>> >> > help="Specify fastq file with reads"/>
>> >> >
>> >> >
>> >> > I have multiple outputfiles - bundled in a list collection:
>> >> >
>> >> > > label="@OUTPUT_NAME_PREFIX@
>> >> > on
>> >> > ${on_string} (Fastq Collection)" format_source="fastq_input1">
>> >> > > />
>> >> >
>> >> >
>> >> >
>> >> > 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/
>
___
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/
Re: [galaxy-dev] list collection output - format set from input
Hi John,
yes - I created this hacky solution and it works.
I now tried what you said, but no success.
Code:
>
> directory="output" />
>
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 :
> You are giving Galaxy mixed signals :). format_source will say to use
> the data type specified by the corresponding input - but
>
>
>
> 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:
>
>
>
> or if you don't want to include the .fq in the output identifier (and
> you probably don't want to)
>
>
>
> 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:
>
>
>
> 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
> 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 :
> >>
> >> 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
> >> wrote:
> >> > Hi,
> >> >
> >> > I have an input, that can be fasta,fastqsanger,fastqillumina:
> >> >
> >> > >> > format="fasta,fastqsanger,fastqillumina" label="Select the fastq file"
> >> > help="Specify fastq file with reads"/>
> >> >
> >> >
> >> > I have multiple outputfiles - bundled in a list collection:
> >> >
> >> > label="@OUTPUT_NAME_PREFIX@
> >> > on
> >> > ${on_string} (Fastq Collection)" format_source="fastq_input1">
> >> > />
> >> >
> >> >
> >> >
> >> > The format_source parameter doesn't work - the files in the list
> >> > (extension
> >> > fq) are of format "fq"
> >> >
> >> > How can I make it possible that they are
> fasta,fastqsanger,fastqillumina
> >> > depending on fastq_input1?
> >> >
> >> > Thanks,
> >> > Alexander
> >> >
> >> > ___
> >> > Please keep all replies on the list by using "reply all"
> >> > in your mail client. To manage your subscriptions to this
> >> > and other Galaxy lists, please use the interface at:
> >> > https://lists.galaxyproject.org/
> >> >
> >> > To search Galaxy mailing lists use the unified search at:
> >> > http://galaxyproject.org/search/mailinglists/
> >
> >
>
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] list collection output - format set from input
You are giving Galaxy mixed signals :). format_source will say to use
the data type specified by the corresponding input - but
Is saying (with the pattern __name_and_ext__) read files of the form
out1.fastq and assign the collection identifier to "out1" and the
extension/format to "fastq".
Two things should work - one of them will and the other might but should.
One thing you can do is not override the extension in your pattern:
or if you don't want to include the .fq in the output identifier (and
you probably don't want to)
If that doesn't work - it is a bug and please let me know and I will
attempt to fix it.
The hackier way to get this to work that I am more confident will work
- is to drop the format_source - use the same pattern:
But just use a shell command or something to rename all files of the
form *.fq to *.${fastq_input1.ext}.
Hope this helps.
-John
On Thu, Jun 25, 2015 at 9:56 AM, Alexander Vowinkel
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 :
>>
>> 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
>> wrote:
>> > Hi,
>> >
>> > I have an input, that can be fasta,fastqsanger,fastqillumina:
>> >
>> > > > format="fasta,fastqsanger,fastqillumina" label="Select the fastq file"
>> > help="Specify fastq file with reads"/>
>> >
>> >
>> > I have multiple outputfiles - bundled in a list 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/
Re: [galaxy-dev] list collection output - format set from input
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 : > 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 > wrote: > > Hi, > > > > I have an input, that can be fasta,fastqsanger,fastqillumina: > > > > > format="fasta,fastqsanger,fastqillumina" label="Select the fastq file" > > help="Specify fastq file with reads"/> > > > > > > I have multiple outputfiles - bundled in a list 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/
Re: [galaxy-dev] list collection output - format set from input
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 wrote: > Hi, > > I have an input, that can be fasta,fastqsanger,fastqillumina: > > format="fasta,fastqsanger,fastqillumina" label="Select the fastq file" > help="Specify fastq file with reads"/> > > > I have multiple outputfiles - bundled in a list 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/
