On Wed, Mar 2, 2011 at 3:21 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On Wed, Mar 2, 2011 at 2:51 PM, Dannon Baker <dannonba...@me.com> wrote:
>> Peter-
>>
>> Just a quick response to your first question-  you might want to give
>> the workflow parameters feature a shot to see if it does what you're
>> looking to do.  Within the workflow editor, instead of setting a value to
>> 'specify at runtime', use a variable tag in the format ${yourvariablename}.
>> This variable can be reused in as many steps as you want in the
>> workflow, and can also be used in the Rename Dataset action if you
>> wanted to tag datasets by the parameter used.  See the example from
>> the January news brief for screenshots
>> (https://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011_01_31).
>>
>> -Dannon
>
> Great - that seems to solve the core task I wanted to do :)
>
> I would say this isn't very intuitive or obvious... but once you know
> how it can be done it is pretty easy. Maybe some tooltip text would
> help?
>
> I'm also wondering about adding "Workflow Parameters" to the
> workflow menu (next to Edit Attributes, Layout, Save, Close),
> or simply adding them to the Workflow Attributes editor? That
> would  also give somewhere to add a text caption to the new
> workflow parameter (the second part of my query).

I've found that Galaxy seems quite happy to use variable
names with spaces in them, e.g.

${Minimum read length (after any clipping)}

or:

${Mismatches (0, 1 or 2)}

That addresses my need to give some explanatory text.

Peter

P.S. I do like the color highlighting and live substitution of
the workflow parameters into each tool step that uses them.
Very slick!

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