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Question: Running datasets through tools in batch
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gravatar for lubbertus.mulder
19 months ago by
lubbertus.mulder • 0
lubbertus.mulder • 0 wrote:

Question from an illiterate,

Can I use sixpack in batch?, and if yes how.

Thank you.

Ben.
tools galaxy batch collection dataset • 415 views
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modified 19 months ago by Jennifer Hillman Jackson ♦ 25k • written 19 months ago by lubbertus.mulder • 0
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gravatar for Jennifer Hillman Jackson
19 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hi Ben,

Most tool forms include all three of Galaxy's options for input selection. For example, the tool EMBOSS: sixpack has an input on the tool form named Sequences (with expected the format/datatype of "fasta") and it includes these buttons:

  1. The first button is used to input a single dataset
  2. The second button is used to input multiple individual datasets
  3. The third button is to input a dataset collection (multiple individual datasets in one or more defined groups, termed "collections")

Hover over the buttons to view the pop-up labels and click on one to make the choice. Datasets or dataset collections with the expected input format set as the datatype can then be selected/multi-selected.

The second or third option is considered batch processing. A distinct job will be run for each individual input fasta dataset contained within the batch with a single "Execute" click.

This is a good question and may help others, too.

Best, Jen, Galaxy team
ADD COMMENT • link modified 19 months ago • written 19 months ago by Jennifer Hillman Jackson ♦ 25k
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