On 11/17/2015 01:32 PM, John Chilton wrote:
> Eric - yeah - it should be straight forward to add these to workflow
> editor - it is just sort of a matter of how to represent this I think.
> I don't have any clues.
I do!

Advanced settings -> "Enable tool ordering/dummy IO" -> has a checkbox

When checked an extra input + output would appear at the bottom of the tool 
(ideally both at the same vertical height for a nice compact ordering 
selector). Could then connect just like regular IO.
>
> The relevant commit is at:
>
> https://github.com/galaxyproject/galaxy/commit/e0a5e82bdae407535b9d7c98e3dcf851b63d01a0
>
> This includes example workflows built up using YAML that establish
> these kinds of connections. This connections are what enabled Dan
> Blankenberg's work on workflows for data managers that he presented at
> the GCC 2015 and that he will post to Github within in a week or two
> of GCC 2015 ;).
>
> More background on building up workflows from YAML can be found at
> https://github.com/galaxyproject/galaxy/pull/1096 and
> https://github.com/galaxyproject/bioblend/pull/143.
>
> -John
>
>
> On Tue, Nov 17, 2015 at 7:24 PM, Eric Rasche <e...@tamu.edu> wrote:
> >
> > On 11/17/2015 01:18 PM, John Chilton wrote:
> >> The workflow subsystem has the ability to define a connection like
> >> this (just wait for one tool to pass before calling the next without a
> >> input/output relationship) but it hasn't been exposed in the workflow
> >> editor yet.
> > That's incredibly exciting John. Can't wait for workflow availability of 
> > that feature. It was a huge problem for my tools when I was writing 
> > internal wrappers which did ordering dependent operations on external 
> > databases. Good to hear it's going to be possible.
> >> -John
> >>
> >>
> >> On Sun, Nov 1, 2015 at 8:12 PM, Dooley, Damion <damion.doo...@bccdc.ca> 
> >> wrote:
> >>> Has anyone done a tool part of which simply takes in a data collection 
> >>> and provides it (symlinked) in a corresponding output data collection?  
> >>> We have a quality control tool that enables us to stop workflow, 
> >>> preventing subsequent jobs to be run if a problem has been detected.  
> >>> Currently our tool only sym-links through an individual dataset.  It 
> >>> would be great if it could work on a whole data collection of any sort.
> >>>
> >>> I see there’s a <collections> tag now – is there an easy solution using 
> >>> this – and that doesn’t loose metadata?
> >>>
> >>> <collection name=“genericCollectionSymlink" label=“Workflow datasets”>
> >>>    <discover_datasets pattern=???????????? visible="true"  
> >>> ......................?????????
> >>> </collection>
> >>>
> >>> At moment we use parameters for format_source="workflow_files" 
> >>> metadata_source=“workflow_files” to pass through all the info on an input 
> >>> dataset...
> >>>
> >>> <inputs>
> >>>    …
> >>>    <param name="workflow_files" type="data" optional="True" 
> >>> multiple=“False" label="Workflow data" help="Select dataset(s) that 
> >>> subsequent workflow stages can consume if report status is not fail'." />
> >>> </inputs>
> >>> <outputs>
> >>>    <data name="workflow_files_pass" format_source="workflow_files" 
> >>> label="Workflow datasets"  metadata_source="workflow_files” >
> >>>       <filter>(workflow_files)</filter>
> >>>    </data>
> >>> </outputs>
> >>>
> >>>
> >>> Much obliged!
> >>>
> >>>
> >>> Damion
> >>>
> >>>
> >>> Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC 
> >>> Centre for Disease Control
> >>> 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada
> >>> ___________________________________________________________
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> >> ___________________________________________________________
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> >>
> >
> > --
> > Eric Rasche
> > Programmer II
> >
> > Center for Phage Technology
> > Rm 312A, BioBio
> > Texas A&M University
> > College Station, TX 77843
> > 404-692-2048
> > e...@tamu.edu
> >

-- 
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
404-692-2048
e...@tamu.edu

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