Specifying data types for workflow inputs
I am developing a custom workflow in galaxy. I have 4 input files that need to be fed into various steps of the workflow. I would like to be able to specify a data type for the inputs such that the pre-populated drop downs are filtered to datasets of the appropriate type as well as being able to do some simple validation before the workflow begins. Is there someway to do this? Thanks much, Ann
Ann, Unless I misunderstand what you're asking for, this should already be the case. For instance, if a workflow step takes in a file of 'tabular' type, only tabular files (and subtypes, including interval, etc.) should be presented as dropdowns in the list. Types such as plain text, binary files, etc., should be excluded. Are you seeing other behavior? Thanks for using Galaxy! -Dannon On Oct 12, 2011, at 02:17 PM, Ann Black <annblack@eng.uiowa.edu> wrote: I am developing a custom workflow in galaxy. I have 4 input files that need to be fed into various steps of the workflow. I would like to be able to specify a data type for the inputs such that the pre-populated drop downs are filtered to datasets of the appropriate type as well as being able to do some simple validation before the workflow begins. Is there someway to do this? Thanks much, Ann ___________________________________________________________ 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/
Thanks for the response. I am not seeing this behavior in my workflows. When I go to run the workflow, a gatk dbsnp file is the default selected for all my input dataset steps, even though some of them must be fastqillumina or bed/interval files, etc (depending on the step they are wired into). All files in my history are exposed in the drop down for each input dataset step, vs. narrowing it down by type. Ann On Oct 12, 2011, at 1:30 PM, Dannon Baker wrote:
Ann,
Unless I misunderstand what you're asking for, this should already be the case. For instance, if a workflow step takes in a file of 'tabular' type, only tabular files (and subtypes, including interval, etc.) should be presented as dropdowns in the list. Types such as plain text, binary files, etc., should be excluded. Are you seeing other behavior?
Thanks for using Galaxy!
-Dannon
On Oct 12, 2011, at 02:17 PM, Ann Black <annblack@eng.uiowa.edu> wrote:
I am developing a custom workflow in galaxy. I have 4 input files that need to be fed into various steps of the workflow. I would like to be able to specify a data type for the inputs such that the pre-populated drop downs are filtered to datasets of the appropriate type as well as being able to do some simple validation before the workflow begins. Is there someway to do this?
Thanks much,
Ann ___________________________________________________________ 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:
Hi - Dannon I am attaching a sample workflow so you can hopefully reproduce locally: I have a history that contains datasets of various different types. I would expect when I run this workflow, however, that only the datasets in my history of type fastqillumina to appear in the drop downs for input datasets (step 1 & step 2) ... instead I see all my files from my history regardless of type (including output files of jobs that are queued... not even completed/ran) and it defaults to the output files of a job in my history that is queued but not even running/completed yet and of a type that is not supported by the bwa alignment. Hopes this makes sense ... is this a bug? Ann On Oct 12, 2011, at 1:30 PM, Dannon Baker wrote:
Ann,
Unless I misunderstand what you're asking for, this should already be the case. For instance, if a workflow step takes in a file of 'tabular' type, only tabular files (and subtypes, including interval, etc.) should be presented as dropdowns in the list. Types such as plain text, binary files, etc., should be excluded. Are you seeing other behavior?
Thanks for using Galaxy!
-Dannon
On Oct 12, 2011, at 02:17 PM, Ann Black <annblack@eng.uiowa.edu> wrote:
I am developing a custom workflow in galaxy. I have 4 input files that need to be fed into various steps of the workflow. I would like to be able to specify a data type for the inputs such that the pre-populated drop downs are filtered to datasets of the appropriate type as well as being able to do some simple validation before the workflow begins. Is there someway to do this?
Thanks much,
Ann ___________________________________________________________ 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:
participants (2)
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Ann Black -
Dannon Baker