No change when using option "unsorted" as sort order with picard_sortsam

[jennaj]

The purpose of this option "unsorted" is unclear. From what I can tell, the dataset is unchanged. Could we clarify what the purpose of the option is in the tool form? Is it a needed option but not functional yet?

Also, samtools_sort does the same operations (without the "unsorted" option) and succeeds with both coordinate and read name options. Users will probably install both picard and samtools as complete packages. Do we need both of these tools? Or should one be retained to avoid user confusion?

Galaxy Tool Version 1.126.0

[bgruening]

Hi Jen, judging from the code it seems unsorted is used and should work: https://github.com/galaxyproject/tools-devteam/blob/master/tools/picard/picard_SortSam.xml

The question is what is picard doing with this option :)

[nsoranzo]

I think that this simply does not sort the input file and set the SO header of the output file to unsorted. Not very useful...

From the SAM specification: "SO: Sorting order of alignments. Valid values: unknown (default), unsorted, queryname and coordinate."

[jennaj]

Hum, perhaps there is a use case for changing the header .. but I can't think of one! :)

The alternative bam sort tool works great.

[bgruening]

@jennaj, @nsoranzo not sure if we should remove this option. But if this is to confusing for users you can review https://github.com/galaxyproject/tools-devteam/pull/165

[jennaj]

I will let you all decide, just an observation. Maybe clarification in the help about what this option actually does is the best call?

[bgruening]

Template for @jennaj

• [ ] in the main tool shed
• [ ] installed successfully and tested via the UI with sample data on:
• [ ] Test (https://test.galaxyproject.org) and Main (http://usegalaxy.org)
• [ ] Local (default getgalaxy.org, master branch)
• [ ] Cloudman (default cloudlaunch, latest master)