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.
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:
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
On Tue, Nov 17, 2015 at 7:24 PM, Eric Rasche <esr(a)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.
>> On Sun, Nov 1, 2015 at 8:12 PM, Dooley, Damion <Damion.Dooley(a)bccdc.ca>
>>> 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
>>> <discover_datasets pattern=???????????? visible="true"
>>> At moment we use parameters for format_source="workflow_files"
metadata_source=“workflow_files” to pass through all the info on an input dataset...
>>> <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'." />
>>> <data name="workflow_files_pass"
format_source="workflow_files" label="Workflow datasets"
>>> Much obliged!
>>> 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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> Eric Rasche
> Programmer II
> Center for Phage Technology
> Rm 312A, BioBio
> Texas A&M University
> College Station, TX 77843
Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843