[galaxy-dev] Shared a value for multiple set-at-runtime workflow parameters

[Peter Cock]

Hi all,

I have a multi-step workflow where I've marked some parameters to be
set at run time (in this case, a minimum read length, used in two
different workflow steps). I want to use the same parameter value in
multiple tools, rather than give the user one prompt for each tool. Is
this possible?

Related to this, it would be nice to specify a default in the workflow
(overriding any default in the tool wrapper), and give some caption
text to the workflow level parameter. I guess some of this
functionality would be related to any enhancement to make a workflow
act like a tool (e.g. to combine subworkflows into larger workflows).

Thanks,

Peter
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Re: [galaxy-dev] Shared a value for multiple set-at-runtime workflow parameters

[Peter Cock]

On Wed, Mar 2, 2011 at 3:42 PM, Peter Cock p.j.a.c...@googlemail.com wrote:

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


That was the good news. Now the bad news - two bug reports.

Firstly if you clear the workflow parameter (leaving it empty), then
the caption is used for the highlighted placeholders BUT only the
first word is used, e.g.

${Minimum read length (after any clipping)}

Initially the the placeholders show Minimum read length (after any
clipping), and if you enter a value like 30 then 30 is shown. If
you then edit the field to become empty, the placeholder now
shows just Minimum.

Furthermore, if I leave my workflow parameters empty, and
press execute, I get a traceback ending with:

AttributeError: 'WorkflowStep' object has no attribute 'module'

Since an empty value is valid for some tools for some parameters
(e.g. optional text fields) I would have expected any error later -
from the tools themselves if they don't like the empty value.

Peter
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