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. Eric On Tue, Nov 25, 2008 at 12:00 PM, <galaxy-user-request@bx.psu.edu> wrote:

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Today's Topics:

1. Re: Workflow improvement requests (long) (James Casbon)

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Message: 1 Date: Tue, 25 Nov 2008 11:14:14 +0000 From: "James Casbon" <casbon@gmail.com> Subject: Re: [galaxy-user] Workflow improvement requests (long) To: "Assaf Gordon" <gordon@cshl.edu> Cc: galaxy-user@bx.psu.edu Message-ID: <15d850bd0811250314h4075f1edld1ea2dc6b1a76fef@mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1

Hi Everyone,

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.

thanks, James

...

Dear all,

Recently, users (of our local galaxy server) started using workflows, and are very pleased. However, as workflows get more complicated, it gets harder to track the input and output of the workflows.

I'd like to share an example, to illustrate the problems that we encounter.

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 input datasets (They appear simply as "Step 1: Input dataset", "Step 2: Input 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

2008/11/14 Assaf Gordon <gordon@cshl.edu>: their

...

history) goes into what dataset. (see attached 'crosstab_workflow_input_datasets.jpg').

The second problem is that whenever I change something in the workflow and 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' from step 2" to "Output dataset' output' from step 4" - but this is very obscure...).

The third problem is that once the workflow completes, the resulting dataset have cryptic names such as "Join two queries on Data 10 and Data 2". Since "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 bit hard to know what's going on. (see attached 'crosstab_history.png').

For the meantime, I've simply gave written instructions on what each dataset 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 a descriptive name, so even if the order of the input datasets changes, users will know which dataset goes into which input.

Regarding the output dataset names, the 'label' option in the tools' XML is 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 great tool, and workflows are really cool - we have several long workflows which do wonderful things.

Thanks for reading so far, Gordon.

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End of galaxy-user Digest, Vol 29, Issue 16 *******************************************

-- ________________________________________________________ Eric M Schauberger Physician Scientist Training Program (DO/PhD) Genetics Program Ewart Lab MSU College of Osteopathic Medicine (MSUCOM) Email: Schaube2@msu.edu Skype: Emschaub See my availability: http://www.timebridge.com/mytime/eschauberger __________________________________________________________