[Feature Request] Explicit production of list:paired datasets about galaxy HOT 9 CLOSED

Thanks for the feature request and use case description - have been working on this today and yesterday. WIP @ https://github.com/galaxyproject/galaxy/compare/galaxyproject:dev...jmchilton:nested_collections?expand=1.

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If I can, I would love to contribute this tool. Might be useful for others (could result in lots of data usage XD )

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@MatthewRalston feel free to contribute this tool to the IUC repository: https://github.com/galaxyproject/tools-iuc
Also please have a look at: https://toolshed.g2.bx.psu.edu/view/matt-shirley/ncbi_sra_toolkit

Thanks for your work!
Bjoern

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Thanks everyone, I appreciate this. :) The ncbi_sra_toolkit looks great! I would be able to use it when I can convert a single input (e.g. an SRA "SRP" project accession) into a list RE: #469 (of SRA files), which could then be converted into fastq by this toolkit. Practically, it would just seem simpler to provide an SRP to download all available fastq files from an experiment.

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Waiting for #464 to be merged and I then I will open a PR with this jmchilton@cfa6f0d. That should allow fully dynamic creation of list:paired collections as would be required for an SRA download tool.

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+1 Would that commit also imply the dynamic creation of list collections with something like

<outputs>
   <collection name="list_output" type="list">
      <discover_datasets etc="etc"/>
   </collection>
</outputs>

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Hey @MatthewRalston. If you are interested in iterating over SRP accessions you could open an issue / PR in mdshw5/sra-tools-galaxy.

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Thank you, I have something that does 90% of what I need right now, and should be fine now that #538 was merged

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Please re-open if still an issue.

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