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.fan@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 <jen@bx.psu.edu>
To: Jun Fan <j.fan@qmul.ac.uk>
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] customize tool display in the workflow
Message-ID: <5213B6C7.5030800@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 <jen@bx.psu.edu>
> To: Jun Fan <j.fan@qmul.ac.uk>
> Cc: galaxy-user@lists.bx.psu.edu
> Subject: Re: [galaxy-user] customize tool display in the workflow
> Message-ID: <52125368.1060308@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
>>
>>
>>
>> ___________________________________________________________
>> 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
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>>     http://lists.bx.psu.edu/
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> --
> Jennifer Hillman-Jackson
> http://galaxyproject.org
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> Please keep all replies on the list by using "reply all" in your mail
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http://galaxyproject.org

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