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Task #10329 (closed)

Opened 11 years ago

Closed 9 years ago

Improve documentation for Bio-Formats command-line tools

Reported by: mlinkert Owned by: mlinkert
Priority: major Milestone: 5.1.0
Component: Documentation Version: 4.4.8
Keywords: n.a. Cc: hflynn, ajpatterson
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.


The existing command line documentation is at best minimal. It would be nice to list the full options for each command, and perhaps some examples of how to accomplish common tasks.

See also this comment: https://www.openmicroscopy.org/community/viewtopic.php?f=13&t=1261#p5167

Change History (12)

comment:1 Changed 11 years ago by mlinkert

  • Milestone changed from Unscheduled to Testing
  • Sprint set to Testing and Docs (1)
  • Version set to 4.4.8

comment:2 Changed 11 years ago by jamoore

  • Milestone changed from Testing and Docs to Testing2
  • Sprint Testing and Docs (1) deleted

comment:3 Changed 11 years ago by ajpatterson

  • Cc ajpatterson added

comment:4 Changed 10 years ago by hflynn

Is there any chance some progress on this could go into the 5.0.0 docs @mlinkert? Only I'm deleting reference to the FARSIGHT tutorial from the OME Model and Formats docs about the BF command line tools for OME-XML validation (https://www.openmicroscopy.org/site/support/ome-model/ome-tiff/tools.html#validating-ome-xml) because it is full of LOCI tools references and out-of-date urls, which means the existing doc will now the only guidance we give anywhere. I can copy the content of http://www.farsight-toolkit.org/wiki/FARSIGHT_Tutorials/Bio-Formats over to our docs with updated links if that will help for now, assuming it is still correct?

comment:5 Changed 10 years ago by ajpatterson

The history shows the page as written by "curtis". Could he login and update? Or can we get a login on the system?


comment:6 Changed 10 years ago by mlinkert

Definitely +1 to removing the Farsight tutorial references for 5.0.0. I will get as far as I can before leaving for Dundee, and hopefully have a PR for reviewing early next week.

comment:7 Changed 10 years ago by hflynn

Thanks very much.

comment:8 Changed 10 years ago by mlinkert

Progress on this for 5.0.0 is here: https://github.com/openmicroscopy/bioformats/pull/927

There are plenty of additional things that can be done for 5.0.1+, but that should be sufficient to justify removing the Farsight link.

comment:9 Changed 10 years ago by mlinkert

  • Milestone changed from Testing2 to 5.0.3

comment:10 Changed 10 years ago by hflynn

I did a bit of work on this for 5.0.2 (adding stuff I found buried in the FAQs etc) and chatted to Graeme Ball who pointed out that you print all the options for each command by running it with no arguments (I stuck that info on the intro page). So I think definitely focus on the task-based stuff, and unless you've had specific requests, maybe assume this is low down the priority list.

comment:11 Changed 10 years ago by mlinkert

  • Milestone changed from 5.0.3 to 5.1.0

comment:12 Changed 9 years ago by mlinkert

  • Resolution set to fixed
  • Status changed from new to closed
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