Hi Jun,
Thanks for the clarification. Workflow step annotations would best suit
your needs, I think. When you're in the editor, click on any step and on
the right side you'll see a field "Annotation / Notes" which will be
displayed when the workflow is viewed. This can be used to clear up any
confusion about what the individual step does.
Good luck!
Dannon
On Wed, Aug 21, 2013 at 8:22 PM, Jun Fan <j....@qmul.ac.uk> wrote:
> Hi Jen,
>
> Maybe I have not explained my question cleared which caused the
> confusion: I did not mean the name of dataset. Actually I asked about the
> display of the tool in the graphic view from the default value (guess it is
> the name attribute in the tool element of the wrapper) to something else in
> the workflow editor. As my ultimate purpose is to share my workflow with
> someone else. If they see three steps with the same displayed name and do
> not have the related knowledge, they will get lost. To help myself to
> explain well, here is the illustration:
> >From
> ------------------------------- -------------------------------
> -------------------------------
> | mzidLib:PostProcessing| | mzidLib:PostProcessing|
> | mzidLib:PostProcessing|
> |-----------------------------| |-----------------------------|
> |-----------------------------|
> | input file | ---------->| input file
> |
> ---------->| input file |
> |-----------------------------| |
> |-----------------------------| |
> |-----------------------------|
> |output (mzid) |----- |output (mzid)
> |----- |output (mzid) |
> ------------------------------- |-----------------------------|
> |-----------------------------|
> To
> -------------------------------------
> -------------------------------------------
> ------------------------------------------------
> | mzidLib:PostProcessing FDR| | mzidLib:PostProcessing
> Threshold| | mzidLib:PostProcessing ProteoGroup|
> |----------------------------------|
> |------------------------------------------|
> |----------------------------------------------|
> | input file | ---------->| input file
> | ------------>| input file |
> |----------------------------------| |
> |------------------------------------------| |
> |----------------------------------------------|
> |output (mzid) |----- |output (mzid)
> |----- |output (mzid) |
> -----------------------------------
> |------------------------------------------|
> |----------------------------------------------|
>
> Best regards!
> Jun
>
> Date: Tue, 20 Aug 2013 11:34:47 -0700
> From: Jennifer Jackson <j...@bx.psu.edu>
> To: Jun Fan <j....@qmul.ac.uk>
> Cc: galaxy-user@lists.bx.psu.edu
> Subject: Re: [galaxy-user] customize tool display in the workflow
> Message-ID: <5213b6c7.5030...@bx.psu.edu>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
> Hi Jun,
>
> You are very close - just click on the "create" button within the "Edit
> Step
> Actions" box and it will expand, where you can then enter the new custom
> name. It will look something like this:
>
>
>
> The other post you are referring to is a method to name the output dataset
> based on the input datasets name. You can certainly try this out and see if
> it is useful.
>
> Hope this helps,
>
> Jen
> Galaxy team
>
> On 8/20/13 9:34 AM, Jun Fan wrote:
> > Hi Jennifer,
> >
> > Many thanks for your reply. Unfortunately I am not clever to
> > figure out how to using the existing workflow dataset renaming
> > functions. I only know how to rename a dataset within history. Could
> > you show me how to do this? I have attached a screen shot of my
> > workflow. You can see that I have only managed to add annotation/notes
> > to this step. Ideally I would like to have the step with the label of
> > "mzidLib:PostProcessing FDR" in the graphic view. From other thread,
> > someone mentioned to use ${method} in the label, I failed to apply this
> trick.
> >
> > Best regards!
> > Jun
> >
> > Message: 3
> > Date: Mon, 19 Aug 2013 10:18:32 -0700
> > From: Jennifer Jackson <j...@bx.psu.edu>
> > To: Jun Fan <j....@qmul.ac.uk>
> > Cc: galaxy-user@lists.bx.psu.edu
> > Subject: Re: [galaxy-user] customize tool display in the workflow
> > Message-ID: <52125368.1060...@bx.psu.edu>
> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
> >
> > Hi Jun,
> >
> > I asked Dannon (our workflow lead developer) and he suggested just
> > using the existing workflow datastet renaming functions. These are in
> > the right panel when you click on a dataset within the workflow editor
> > (as you probably know).
> >
> > Inherited naming is not something that is currently being worked on,
> > but you can always start a Trello card and see if it gathers votes or
> > the attention of a contributor from the larger development community:
> > http://wiki.galaxyproject.org/Support#Galaxy_Issue_Board
> >
> > Take care,
> >
> > Jen
> > Galaxy team
> >
> > On 8/18/13 5:11 PM, Jun Fan wrote:
> >> Dear Galaxy develop team:
> >>
> >> Normally I generate the workflow from history. It works fine
> >> except one annoying problem: the display of step/tool is just the
> >> tool name, which can cause confusion in a big workflow. For example,
> >> I have a mixture of samples from multiple species and do the BLAST
> >> against Human, Virus, Mouse etc which will call BLAST several times.
> >> To make results distinguishable, I will rename the dataset in the
> >> history. But this will be lost when creating workflow from history.
> >> The workflow will have duplicate steps named as BLAST while I really
> >> want to have steps displayed as BLAST against Human etc. Could you
> >> tell me whether I have done something wrong? If not, could you kindly
> >> add this functionality into the new release of Galaxy? If it is
> >> possible to customize the tool display in the workflow, how to write
> >> the wrapper as setting the label to allow this?
> >>
> >> Best regards!
> >>
> >> Jun
> >>
> >>
> >>
> >> ___________________________________________________________
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> > --
> > Jennifer Hillman-Jackson
> > http://galaxyproject.org
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> --
> Jennifer Hillman-Jackson
> http://galaxyproject.org
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___________________________________________________________
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:
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