Re: [galaxy-dev] multiple output tool in workflow
Hey Jun,
Like Jen mentioned, you should use multiple output elements if at all
possible. The format for specifying outputs you are describing should only
be used if the tool does not know the number of outputs to be used prior to
execution of the tool. I believe it is a known limitation of this mechanism
multiple output mechanism that such tools cannot be used in workflows -
many scientific workflow platforms more sophisticated than Galaxy cannot
handle such tools - it is hard to reason about workflows without knowledge
of their structure ahead of time.
That said, there is an open and high priority Trello card outlining
dataset collections that will hopefully provide some more robust
alternatives to address use cases currently addressed with this multiple
output mechanism - https://trello.com/c/325AXIEr.
-John
On Fri, Nov 8, 2013 at 8:47 PM, Jennifer Jackson wrote:
> Hi Fan,
>
> The block should contain one line for each of the
> output files. I believe that you need to name these differently. "output1",
> "output2", etc. Or you can add in text and use variables, if you add in the
> " label" option.
>
> Others can correct or add to my comments.
>
> Good luck!
>
> Jen
> Galaxy team
>
>
> On 11/8/13 5:41 PM, Jun Fan wrote:
>
> Hi Jen
>
>
>
> Thanks for your reply. Yes, it is my own tool.
>
> The outputs element is
>
>
>
>
>
>
>
> In the command element, the three output files are defined as below
>
> $output /$__new_file_path__/primary_${output.id}_samWithPeptides_visible_sam
> /$__new_file_path__/primary_${output.id}_longestORFs_visible_fasta
>
>
>
> Is there anything wrong here?
>
>
>
> Best regards!
>
> Jun
>
>
>
> *From:* Jennifer Jackson [mailto:j...@bx.psu.edu ]
> *Sent:* 09 November 2013 01:05
> *To:* Galaxy Dev
> *Cc:* Jun Fan
> *Subject:* multiple output tool in workflow
>
>
>
> Hi Jun,
>
> There is probably a problem with the tool design itself, but that may be
> what you are asking how to solve. I wouldn't think this is a problem with
> workflows at first pass.
>
> Is this your own tool? Or a tool from the tool shed (the repo developer is
> usually the one to make changes, unless you want to try)?
> This is the primary tool development wiki, the " tag set" is
> where I would double check the tool first.
> http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
>
> I am moving this over to the galaxy-...@bx.psu.edu mailing list since it
> is a tool development question.
>
> Jen
> Galaxy team
>
> On 11/8/13 10:19 AM, Jun Fan wrote:
>
> Hi all,
>
>
>
> I am trying to creating a workflow from history. One of the tool
> used generates multiple outputs in the format of gff3, fasta and sam. Gff3
> will be visualized in IGV and the fasta file is doing further BLAST
> analysis. Now the problem is that the automatically generated workflow does
> not connect the having-multiple-output tool and the BLAST tool. I failed
> even I tried to connect these two tools in the workflow by hand. I am
> guessing this is due to only the main output type (gff3) is recognized in
> the workflow. How could I solve this problem?
>
>
>
> Best regards and have a nice weekend!
>
> Jun
>
>
>
>
> ___
>
> The Galaxy User list should be used for the discussion of
>
> Galaxy analysis and other features on the public server
>
> at usegalaxy.org. Please keep all replies on the list by
>
> using "reply all" in your mail client. For discussion of
>
> local Galaxy instances and the Galaxy source code, please
>
> use the Galaxy Development list:
>
>
>
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
>
>
> To manage your subscriptions to this and other Galaxy lists,
>
> please use the interface at:
>
>
>
> http://lists.bx.psu.edu/
>
>
>
> To search Galaxy mailing lists use the unified search at:
>
>
>
> http://galaxyproject.org/search/mailinglists/
>
>
>
> --
>
> Jennifer Hillman-Jackson
>
> http://galaxyproject.org
>
>
> --
> Jennifer Hillman-Jacksonhttp://galaxyproject.org
>
>
> ___
> 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:
> http://lists.bx.psu.edu/
>
> 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:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] multiple output tool in workflow
Hi Fan,
The block should contain one line for each of the
output files. I believe that you need to name these differently.
"output1", "output2", etc. Or you can add in text and use variables, if
you add in the " label" option.
Others can correct or add to my comments.
Good luck!
Jen
Galaxy team
On 11/8/13 5:41 PM, Jun Fan wrote:
Hi Jen
Thanks for your reply. Yes, it is my own tool.
The outputs element is
In the command element, the three output files are defined as below
$output
/$__new_file_path__/primary_${output.id}_samWithPeptides_visible_sam
/$__new_file_path__/primary_${output.id}_longestORFs_visible_fasta
Is there anything wrong here?
Best regards!
Jun
*From:*Jennifer Jackson [mailto:j...@bx.psu.edu]
*Sent:* 09 November 2013 01:05
*To:* Galaxy Dev
*Cc:* Jun Fan
*Subject:* multiple output tool in workflow
Hi Jun,
There is probably a problem with the tool design itself, but that may
be what you are asking how to solve. I wouldn't think this is a
problem with workflows at first pass.
Is this your own tool? Or a tool from the tool shed (the repo
developer is usually the one to make changes, unless you want to try)?
This is the primary tool development wiki, the " tag set" is
where I would double check the tool first.
http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
I am moving this over to the galaxy-...@bx.psu.edu
mailing list since it is a tool
development question.
Jen
Galaxy team
On 11/8/13 10:19 AM, Jun Fan wrote:
Hi all,
I am trying to creating a workflow from history. One of the
tool used generates multiple outputs in the format of gff3, fasta
and sam. Gff3 will be visualized in IGV and the fasta file is
doing further BLAST analysis. Now the problem is that the
automatically generated workflow does not connect the
having-multiple-output tool and the BLAST tool. I failed even I
tried to connect these two tools in the workflow by hand. I am
guessing this is due to only the main output type (gff3) is
recognized in the workflow. How could I solve this problem?
Best regards and have a nice weekend!
Jun
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
--
Jennifer Hillman-Jackson
http://galaxyproject.org
--
Jennifer Hillman-Jackson
http://galaxyproject.org
___
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:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] multiple output tool in workflow
Hi Jen
Thanks for your reply. Yes, it is my own tool.
The outputs element is
In the command element, the three output files are defined as below
$output /$__new_file_path__/primary_${output.id}_samWithPeptides_visible_sam
/$__new_file_path__/primary_${output.id}_longestORFs_visible_fasta
Is there anything wrong here?
Best regards!
Jun
From: Jennifer Jackson [mailto:j...@bx.psu.edu]
Sent: 09 November 2013 01:05
To: Galaxy Dev
Cc: Jun Fan
Subject: multiple output tool in workflow
Hi Jun,
There is probably a problem with the tool design itself, but that may be what
you are asking how to solve. I wouldn't think this is a problem with workflows
at first pass.
Is this your own tool? Or a tool from the tool shed (the repo developer is
usually the one to make changes, unless you want to try)?
This is the primary tool development wiki, the " tag set" is where I
would double check the tool first.
http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
I am moving this over to the
galaxy-...@bx.psu.edu mailing list since it is a
tool development question.
Jen
Galaxy team
On 11/8/13 10:19 AM, Jun Fan wrote:
Hi all,
I am trying to creating a workflow from history. One of the tool used
generates multiple outputs in the format of gff3, fasta and sam. Gff3 will be
visualized in IGV and the fasta file is doing further BLAST analysis. Now the
problem is that the automatically generated workflow does not connect the
having-multiple-output tool and the BLAST tool. I failed even I tried to
connect these two tools in the workflow by hand. I am guessing this is due to
only the main output type (gff3) is recognized in the workflow. How could I
solve this problem?
Best regards and have a nice weekend!
Jun
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
--
Jennifer Hillman-Jackson
http://galaxyproject.org
___
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:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
