Re: [galaxy-user] customize tool display in the workflow
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
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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 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:
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org
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Jennifer Jackson -
Jun Fan