galaxyproject / galaxyproject/galaxy

extend input dataset to allow choosing entries from data tables

Open
#9,840 4 comments 1 reaction 0 assignees View on GitHub
area/workflows friendliness/unfriendly kind/enhancement
Dominant language
Python
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Avg merge
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Merged PRs (30d)
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Description

One challenge when using complex workflows in galaxy is the need to correctly assign all the input files (e.g. gff, refflat, bed, etc) to their inputs.
e.g. Picard tools:
image

I'd love to move some of these inputs to data tables, (e.g. gff files), but that would require modification of all the tools to use those datatables one by one.

I propose an extension of the input dataset tool (or a new "input from datatable" tool) to allow specification of which datatable to use and optionally, which entry to default to in the workflow editor

I think it would be better to include this as a built-in galaxy feature than a dataset picker tool because I don't think we have access to the a list of all data tables installed in galaxy from the tool xml.

Contributor guide

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Research direction

The issue names no files, tests, or entry points. Start by examining the existing input dataset tool and data-table handling; the work is complete when users can select a data table and optionally choose a default entry in the workflow editor without modifying each tool individually.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
backend, data
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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