Fix checklist for tool-data

galaxy-iuc / standards

Documentation for standards and best practices from the Galaxy IUC

http://galaxy-iuc-standards.readthedocs.io/en/latest/

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Fix checklist for tool-data #47

Closed mblue9 closed 7 years ago

mblue9 commented 7 years ago

Suggesting these changes as it was not clear to me from this doc that I also needed additional files for testing a tool with a data table with Planemo.

peterjc commented 7 years ago

This information is worth including, but I would word it differently. To start with, you should be providing tool-data/effectiveT3.loc.sample and tool_data_table_conf.xml.sample anyway, regardless of the tests. Perhaps that should be moved above the section on tests?

Next, I would clarify that test-data/data_table_name.loc is only needed if tool-data/data_table_name.loc.sample is not suitable for the tests.

Likewise I suspect tool_data_table_conf.xml.test is only needed if tool_data_table_conf.xml.sample is not suitable for the tests (in fact, I don't recall ever using it).

nsoranzo commented 7 years ago

@peterjc In general tool-data/data_table_name.loc.sample and tool_data_table_conf.xml.sample should contain only comments, no? @mblue9 I'd also add a link to an example repo, e.g. https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers

peterjc commented 7 years ago

@nsoranzo if the tool is bundled with a default set of databases or configurations, then it makes sense to include entries in the sample configuration - e.g. https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 ships with https://github.com/peterjc/pico_galaxy/blob/master/tool-data/effectiveT3.loc.sample

nsoranzo commented 7 years ago

I said "in general", I think this is quite a specific case, all data tables for genome indexes and/or administered with a data manager come with an empty sample file.

peterjc commented 7 years ago

You're probably right, I've only relatively rarely used *.loc files.

I still think we should discuss the data tables before the tests though, with the change as is the data tables section becomes part of the paragraph on tests.

mblue9 commented 7 years ago

Hi @peterjc and @nsoranzo

Thanks for the comments!

I'm made some changes and, am not sure if I've got it right on what I should include (please let me know!), but based on your comments I've

adjusted the text and positioning of the tool-data mentions and testing of tool-data (I thought this was a combined tool-data/testing section because of how it was spaced :) so I've also removed the extra blank lines)

added in a link to the bowtie wrapper, and Nicola, I've used your info from here http://dev.list.galaxyproject.org/planemo-test-with-lt-options-from-data-table-gt-td4670119.html

because that post was how I finally cracked how to get the data table testing to work! That was the trickiest part of the tool testing to get working and I think it would be great if that info was easier to find.

What do you think? I'm happy to edit more?

peterjc commented 7 years ago

You should put the double-back-tick RST markup around the path names and XML snippet, but I think that is a big improvement.

mblue9 commented 7 years ago

Thanks @peterjc!

I've added the RST markup and also some links, see what you think.

If you (or anyone) think I should edit more just let me know!

peterjc commented 7 years ago

Good work - what do you think @nsoranzo - ready to merge?

nsoranzo commented 7 years ago

Thanks a lot @mblue9!