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Make bamtools_split output a dataset collection #227

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pvanheus commented Sep 18, 2015

Replace the multiple output datasets of bamtools_split with a dataset collection output.

Also update the tests and the documentation to reflect this change.

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Code all looks good, assuming tests pass.

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erasche commented Sep 18, 2015

Code all looks good, assuming tests pass.

@@ -5,7 +5,6 @@
</requirements>
<command>

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bgruening Sep 18, 2015

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You should increase the version number.

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bgruening Sep 18, 2015

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You should increase the version number.

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pvanheus Sep 18, 2015

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There was some discussion on the Hangout earlier about the different semantic modes of bamtools split. Turns out they are:

  1. Split into mapped and unmapped reads
  2. Split paired-end reads into two single end collections
  3. Split by reference (split into one dataset for each reference contig)
  4. Split by tag

Modes 1 and 2 split into exactly 2 datasets. Modes 3 and 4 split into an undefined number of dataset, with mode 3 potentially most useful for parallel processing. There does not (except for, arguably, mode 3) be a "split into chunks" options. The discussion revolved around the differences between "split into chunks" and other split modes and the possible need to create different tools to address the different semantics of these modes. I'd like to see some comments on this issue before a merge.

Secondly, this change introduces a undocumented feature (output to dataset collection) as default behaviour in a devteam tool. This might prove confusing to users: should this merge wait on documentation?

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pvanheus commented Sep 18, 2015

There was some discussion on the Hangout earlier about the different semantic modes of bamtools split. Turns out they are:

  1. Split into mapped and unmapped reads
  2. Split paired-end reads into two single end collections
  3. Split by reference (split into one dataset for each reference contig)
  4. Split by tag

Modes 1 and 2 split into exactly 2 datasets. Modes 3 and 4 split into an undefined number of dataset, with mode 3 potentially most useful for parallel processing. There does not (except for, arguably, mode 3) be a "split into chunks" options. The discussion revolved around the differences between "split into chunks" and other split modes and the possible need to create different tools to address the different semantics of these modes. I'd like to see some comments on this issue before a merge.

Secondly, this change introduces a undocumented feature (output to dataset collection) as default behaviour in a devteam tool. This might prove confusing to users: should this merge wait on documentation?

@pvanheus pvanheus referenced this pull request Sep 19, 2015

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IUC Tools & Collections Hackathon (Fall 2015) #239

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@pvanheus can you add a few sentence to the documentation and a boolean "output to dataset collection" (default: no) for the next version. So we have a smooth transition. In the version after the next we will change the default to yes.

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bgruening commented Oct 16, 2015

@pvanheus can you add a few sentence to the documentation and a boolean "output to dataset collection" (default: no) for the next version. So we have a smooth transition. In the version after the next we will change the default to yes.

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bgruening commented Oct 31, 2015

ping @pvanheus

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bgruening commented Dec 23, 2015

ping @pvanheus

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bgruening commented Sep 25, 2016

ping @pvanheus

@davebx davebx referenced this pull request Jul 26, 2017

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Move bamtools to legacy. #481

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Implemented in and/or superseded by galaxyproject/tools-iuc#1359

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davebx commented Jul 31, 2017

Implemented in and/or superseded by galaxyproject/tools-iuc#1359

@davebx davebx closed this Jul 31, 2017

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