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. < workflow .png > < crosstab_workflow_input_datasets .jpg > < crosstab_history .png > < crosstab_workflow_dataset_explnanations .jpg>_______________________________________________ galaxy-user mailing list galaxy-user(a)bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user

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.

Great, thanks a lot. You're way ahead of me here ;) 2008/11/25 James Taylor <james.taylor(a)emory.edu&gt;: > James, > > The datatypes are a hierarchy, and tools will accept any type that is more > specific than their defined input type. If you set the input type to "data" > the tool will accept anything, if you set it to "text" it will accept any > text format. > > For outputs, there is a special format "input" which copies the type of the > input dataset (first input I believe, this needs to be enhanced to allow > specifying a particular input). There is also the "metadata_source" > attribute for copying the input metadata. This is how many of our tools that > work on tabular data preserve the type and metadata of "interval" format > files. > > -- jt > > On Nov 25, 2008, at 6:14 AM, James Casbon wrote: > >> 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. >