I second the request on sometype of labeling system for the workflow--at
least a numbering system. I made a workflow with many inputs, then when I
tried it out I realized that the first input that I was joining with the
second input was intermixed and unidentifable. Then I realized that the
inputs are ordered in their creation order and not anytype of order how they
are placed. Since I was making many, many, inputs I simply made a bunch of
them at once and didn't keep track of their order or where I put them.
Thank again for the sweet tool.
On Tue, Nov 25, 2008 at 12:00 PM, <galaxy-user-request(a)bx.psu.edu> wrote:
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1. Re: Workflow improvement requests (long) (James Casbon)
Date: Tue, 25 Nov 2008 11:14:14 +0000
From: "James Casbon" <casbon(a)gmail.com>
Subject: Re: [galaxy-user] Workflow improvement requests (long)
To: "Assaf Gordon" <gordon(a)cshl.edu>
Content-Type: text/plain; charset=ISO-8859-1
Slightly off-topic, but I see you have awk in your workflows. Awk
could work on text, tabular, and other formats but I'd rather not
define a new tool for each input type.
Is there a way to define a tool which accepts more any type of input?
It should ideally preserve the format in the output as well.
2008/11/14 Assaf Gordon <gordon(a)cshl.edu>:
> Dear all,
> Recently, users (of our local galaxy server) started using workflows, and
> are very pleased. However, as workflows get more complicated, it gets
> to track the input and output of the workflows.
> I'd like to share an example, to illustrate the problems that we
> The workflow (pictured in the attached 'workflow.jpg') takes 4 input
> datasets, and produces 4 output datasets.
> The first problem is that there's no way to differentiate between the
> datasets (They appear simply as "Step 1: Input dataset", "Step 2:
> Dataset", etc). Since each dataset has a specific role, I've had to print
> the workflow and give the users instructions as to which dataset (in
> history) goes into what dataset. (see attached
> The second problem is that whenever I change something in the workflow
> save it - the order of the dataset change!
> So what was once dataset 1, can now be dataset 2,3 or 4.
> Users have no way of knowing this... (keen users might notice the the
> description of the first tool changed from "Output dataset 'output'
> step 2" to "Output dataset' output' from step 4" - but this
> The third problem is that once the workflow completes, the resulting
> have cryptic names such as "Join two queries on Data 10 and Data 2".
> "Data 10" is "Awk on Data 8" and data-8 is "Generic
Annotations on Data 7
> and Data 1" and data-7 is "Intersect data 1 and data 6" - it gets a
> to know what's going on. (see attached 'crosstab_history.png').
> For the meantime, I've simply gave written instructions on what each
> means (see attached 'crosstab_workflow_dataset_explnanations.jpg).
> If I may suggest a feature - it would be great if I could name a dataset
> inside the workflow. Instead of naming it "Input dataset" I could give it
> descriptive name, so even if the order of the input datasets changes,
> will know which dataset goes into which input.
> Regarding the output dataset names, the 'label' option in the tools'
> a good start, but still creates very long, hard-to-understand names.
> Another great feature would be the possibility to add an 'output label'
> for each step in the workflow.
> Regardless of the above, I'd like to say (once again) that Galaxy is a
> tool, and workflows are really cool - we have several long workflows
> do wonderful things.
> Thanks for reading so far,
> galaxy-user mailing list
galaxy-user mailing list
End of galaxy-user Digest, Vol 29, Issue 16
Eric M Schauberger
Physician Scientist Training Program (DO/PhD)
MSU College of Osteopathic Medicine (MSUCOM)
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