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:
- Re: Workflow improvement requests (long) (James Casbon)
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
2008/11/14 Assaf Gordon gordon@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
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
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
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Eric Schauberger