On Wed, Mar 2, 2011 at 3:21 PM, Peter Cock p.j.a.cock@googlemail.com wrote:
On Wed, Mar 2, 2011 at 2:51 PM, Dannon Baker dannonbaker@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_...).
-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!