Embedding a help text in a Workflow?
Hello all, I've recently started sharing some sample workflows on the Galaxy Tool Shed, http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow When writing a Galaxy tool we have a lot of flexibility within the <help> tag to describe the tool, its output, and relevant references using some nice markup language for things like bold fonts and tables. I would very much like something similar for embedding README or help text into a workflow - which again should be shown to the user, both on the 'View workflow action' but also under the "Run workflow" / "Execute" button when actually running a workflow. Am I overlooking something or is the only workflow level description the plain text 'Annotation / Notes' field? Thanks, Peter P.S. I'm not talking about the repository level README text which I can use for a workflow repository - that is only really seen by the Galaxy administrator (not by the users within the Galaxy web-interface) and is not specific to each workflow.
Hey Peter, You're correct, currently the only top level description field for a workflow is that Annotation/Notes field. While it wouldn't have rich text, is it reasonable to programmatically generate something like what you're suggesting from the combination of the primary Annotation/Notes fields and each step Annotation (when available)? -Dannon On Mon, May 6, 2013 at 2:36 PM, Peter Cock <p.j.a.cock@googlemail.com>wrote:
Hello all,
I've recently started sharing some sample workflows on the Galaxy Tool Shed, http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow
When writing a Galaxy tool we have a lot of flexibility within the <help> tag to describe the tool, its output, and relevant references using some nice markup language for things like bold fonts and tables.
I would very much like something similar for embedding README or help text into a workflow - which again should be shown to the user, both on the 'View workflow action' but also under the "Run workflow" / "Execute" button when actually running a workflow.
Am I overlooking something or is the only workflow level description the plain text 'Annotation / Notes' field?
Thanks,
Peter
P.S. I'm not talking about the repository level README text which I can use for a workflow repository - that is only really seen by the Galaxy administrator (not by the users within the Galaxy web-interface) and is not specific to each workflow. ___________________________________________________________ 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/
On Fri, May 10, 2013 at 3:10 PM, Dannon Baker <dannon.baker@gmail.com> wrote:
Hey Peter,
You're correct, currently the only top level description field for a workflow is that Annotation/Notes field. While it wouldn't have rich text, is it reasonable to programmatically generate something like what you're suggesting from the combination of the primary Annotation/Notes fields and each step Annotation (when available)?
-Dannon
We have that already on the 'two column' workflow view, so I don't think it would add much. Do you think we could add a new 'rich text' field for a workflow free text help / readme file? Peter
On Fri, May 10, 2013 at 5:07 PM, Jeremy Goecks <jeremy.goecks@emory.edu> wrote:
Do you think we could add a new 'rich text' field for a workflow free text help / readme file?
Annotations will support HTML, and it's always been the long-term plan that they will include HTML. What's missing is a nice editor for creating HTML annotations.
Why HTML and not the same markup as the tool help? Either way, there are likely plugin editors that might be integrated... but for now I would be content to edit the *.ga file by hand if need be. Peter
On Fri, May 10, 2013 at 12:28 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Why HTML and not the same markup as the tool help? Either way, there are likely plugin editors that might be integrated... but for now I would be content to edit the *.ga file by hand if need be.
I don't believe there is any good javascript editor for reStructuredText which is used in the tool help. For non-html readable markup these days I'd prefer markdown since there seems to be so much consensus around it. Or a fairly minimal subset of HTML. -- James Taylor, Assistant Professor, Biology/CS, Emory University
Filed on Trello, https://trello.com/c/HaQnZGvW/1060-embedding-help-text-in-workflows-ideally-... Peter On Fri, May 10, 2013 at 3:10 PM, Dannon Baker <dannon.baker@gmail.com> wrote:
Hey Peter,
You're correct, currently the only top level description field for a workflow is that Annotation/Notes field. While it wouldn't have rich text, is it reasonable to programmatically generate something like what you're suggesting from the combination of the primary Annotation/Notes fields and each step Annotation (when available)?
-Dannon
On Mon, May 6, 2013 at 2:36 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hello all,
I've recently started sharing some sample workflows on the Galaxy Tool Shed, http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow
When writing a Galaxy tool we have a lot of flexibility within the <help> tag to describe the tool, its output, and relevant references using some nice markup language for things like bold fonts and tables.
I would very much like something similar for embedding README or help text into a workflow - which again should be shown to the user, both on the 'View workflow action' but also under the "Run workflow" / "Execute" button when actually running a workflow.
Am I overlooking something or is the only workflow level description the plain text 'Annotation / Notes' field?
Thanks,
Peter
P.S. I'm not talking about the repository level README text which I can use for a workflow repository - that is only really seen by the Galaxy administrator (not by the users within the Galaxy web-interface) and is not specific to each workflow. ___________________________________________________________ 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/
On Mon, Aug 19, 2013 at 3:34 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Filed on Trello, https://trello.com/c/HaQnZGvW/1060-embedding-help-text-in-workflows-ideally-...
Peter
On Fri, May 10, 2013 at 5:07 PM, Jeremy Goecks <jeremy.goecks@emory.edu> wrote:
Do you think we could add a new 'rich text' field for a workflow free text help / readme file?
Annotations will support HTML, and it's always been the long-term plan that they will include HTML. What's missing is a nice editor for creating HTML annotations.
I've taken advantage of this to add a sentence to my workflow annotation with a URL to the Tool Shed where the user can read the full README file. This is a reasonable compromise for now - the annotation needs to be short as it is shown at the top of the page when running a workflow. See: http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow/72f03c2... I presume this HTML field gets sanitised (to avoid security exploits), so the user text can't do anything too complicated. Right now actually editing this field is quite painful (and assumes you know raw HTML in order to do any formatting at all), but it works :) Peter
On Wed, Aug 21, 2013 at 5:40 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Mon, Aug 19, 2013 at 3:34 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Filed on Trello, https://trello.com/c/HaQnZGvW/1060-embedding-help-text-in-workflows-ideally-...
Peter
On Fri, May 10, 2013 at 5:07 PM, Jeremy Goecks <jeremy.goecks@emory.edu> wrote:
Do you think we could add a new 'rich text' field for a workflow free text help / readme file?
Annotations will support HTML, and it's always been the long-term plan that they will include HTML. What's missing is a nice editor for creating HTML annotations.
I've taken advantage of this to add a sentence to my workflow annotation with a URL to the Tool Shed where the user can read the full README file. This is a reasonable compromise for now - the annotation needs to be short as it is shown at the top of the page when running a workflow. See:
http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow/72f03c2...
I presume this HTML field gets sanitised (to avoid security exploits), so the user text can't do anything too complicated.
Right now actually editing this field is quite painful (and assumes you know raw HTML in order to do any formatting at all), but it works :)
Bug report for Greg/Dave, filed here: https://trello.com/c/2crUDlsr/1073-workflow-annotation-not-rendered-as-html-... The workflow annotation is isn't rendered as HTML on the Tool Shed :( e.g. http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow or http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow Peter
participants (4)
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Dannon Baker -
James Taylor -
Jeremy Goecks -
Peter Cock