How to re-use a parameter in a workflow?
Galaxy Users, I have a workflow where I'd like the user to input a value once, say a number of nucleotides. That value would then be used as an input parameter to several different tasks, for example, to two instances of "Operate on Genomic Intervals > Get flanks" , where it would be used both for the "offset" and "length of flanking regions(s)" in one instance, and it's value and it's *negative* would be used for the second instance. Thus, the user inputs "20", and Get_flanks(20,20) and Get_flanks(-20,20) get run. For this workflow, it's important that those parameters all be of the same magnitude, or things will get messy later, so I don't want the user having to input them separately, or to have to remember which one gets negated... All suggestions welcome, Curtis
Hi Curtis, In the workflow editor, you can specify a parameter name within the text boxes for the tool inputs that you want to be set at runtime to the same value. This is done using notation like "${A user entered value}", as seen in these screen shots: Please let us know if we can provide further assistance. Thanks for using Galaxy, Dan On Jul 5, 2011, at 3:15 PM, Robert Curtis Hendrickson wrote:
Galaxy Users,
I have a workflow where I’d like the user to input a value once, say a number of nucleotides. That value would then be used as an input parameter to several different tasks, for example, to two instances of “Operate on Genomic Intervals > Get flanks” , where it would be used both for the “offset” and “length of flanking regions(s)” in one instance, and it’s value and it’s *negative* would be used for the second instance.
Thus, the user inputs “20”, and Get_flanks(20,20) and Get_flanks(-20,20) get run.
For this workflow, it’s important that those parameters all be of the same magnitude, or things will get messy later, so I don’t want the user having to input them separately, or to have to remember which one gets negated…
All suggestions welcome, Curtis
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Daniel, Great. That exactly and perfectly solves my problem! Thanks so much. Regards, Curtis From: Daniel Blankenberg [mailto:dan@bx.psu.edu] Sent: Friday, July 08, 2011 10:25 AM To: Robert Curtis Hendrickson Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] How to re-use a parameter in a workflow? Hi Curtis, In the workflow editor, you can specify a parameter name within the text boxes for the tool inputs that you want to be set at runtime to the same value. This is done using notation like "${A user entered value}", as seen in these screen shots: [cid:image001.png@01CC3D87.DE617530] [cid:image002.png@01CC3D87.DE617530] Please let us know if we can provide further assistance. Thanks for using Galaxy, Dan On Jul 5, 2011, at 3:15 PM, Robert Curtis Hendrickson wrote: Galaxy Users, I have a workflow where I'd like the user to input a value once, say a number of nucleotides. That value would then be used as an input parameter to several different tasks, for example, to two instances of "Operate on Genomic Intervals > Get flanks" , where it would be used both for the "offset" and "length of flanking regions(s)" in one instance, and it's value and it's *negative* would be used for the second instance. Thus, the user inputs "20", and Get_flanks(20,20) and Get_flanks(-20,20) get run. For this workflow, it's important that those parameters all be of the same magnitude, or things will get messy later, so I don't want the user having to input them separately, or to have to remember which one gets negated... All suggestions welcome, Curtis ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org<http://usegalaxy.org>. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
participants (2)
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Daniel Blankenberg -
Robert Curtis Hendrickson