specifying default file by name in workflows
I don't know all the subtleties of the galaxy workflow syntax. My goal is to specify the default input file names for a number of tools in a workflow. Is this possible, or am I limited to only providing the file type or extension? If possible, can you provide an example? Thanks, -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan@msi.umn.edu boll0107@umn.edu
To clarify, I want to specify the default selected file name for an Input Dataset block in the workflow, but I'd like to keep the option open to select other input names with the same type. When I specify a file type for a tool's input, it is not enough. The input dataset can end up finding dozens of files that are txt for example. I want to know all possible tool_state annotations for Input Dataset (tool_id: null). Where would I find this? Cheers, -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan@msi.umn.edu boll0107@umn.edu ---------- Forwarded message ---------- From: Evan Bollig <boll0107@umn.edu> Date: Wed, Jun 18, 2014 at 11:19 AM Subject: specifying default file by name in workflows To: "<galaxy-dev@bx.psu.edu>" <galaxy-dev@bx.psu.edu> I don't know all the subtleties of the galaxy workflow syntax. My goal is to specify the default input file names for a number of tools in a workflow. Is this possible, or am I limited to only providing the file type or extension? If possible, can you provide an example? Thanks, -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan@msi.umn.edu boll0107@umn.edu
Hi Evan, Assuming you are talking about an input file from: <param type="data" .../> I don't think you can set a default - the possible files will depend on the current history, so could be zero, one or many files. Also, how would how specify a specific file? They would have Galaxy assigned *.dat filenames on disk, while the names could have been set to anything by the user. My guess is you may be better off defining a new datatype (a subclass of txt perhaps?). Regards, Peter On Wed, Jun 18, 2014 at 10:28 PM, Evan Bollig <boll0107@umn.edu> wrote:
To clarify, I want to specify the default selected file name for an Input Dataset block in the workflow, but I'd like to keep the option open to select other input names with the same type.
When I specify a file type for a tool's input, it is not enough. The input dataset can end up finding dozens of files that are txt for example. I want to know all possible tool_state annotations for Input Dataset (tool_id: null). Where would I find this?
Cheers,
-Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan@msi.umn.edu boll0107@umn.edu
---------- Forwarded message ---------- From: Evan Bollig <boll0107@umn.edu> Date: Wed, Jun 18, 2014 at 11:19 AM Subject: specifying default file by name in workflows To: "<galaxy-dev@bx.psu.edu>" <galaxy-dev@bx.psu.edu>
I don't know all the subtleties of the galaxy workflow syntax. My goal is to specify the default input file names for a number of tools in a workflow. Is this possible, or am I limited to only providing the file type or extension?
If possible, can you provide an example?
Thanks,
-Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan@msi.umn.edu boll0107@umn.edu ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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participants (2)
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Evan Bollig -
Peter Cock