Question: How to write tests for tools that access built-in data from the data tables
0
gravatar for Thon deBoer
5 months ago by
Thon deBoer20
Thon deBoer20 wrote:

I am writing a tool wrapper for a tool that allows as FASTA file input something from the data-table all_fasta.

How do I write tests for these kinds of tools?

The tests I wrote that use data provided as test-data in the test-data directory work fine, but I want to test it using the data from a data-table...

ADD COMMENTlink modified 5 months ago by jmchilton1.1k • written 5 months ago by Thon deBoer20
3
gravatar for jmchilton
5 months ago by
jmchilton1.1k
United States
jmchilton1.1k wrote:

There is some documentation on how to do this here http://planemo.readthedocs.io/en/latest/writing_how_do_i.html#test-index-loc-data, I hope that helps.

ADD COMMENTlink written 5 months ago by jmchilton1.1k
1
gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The tests are self-contained per tool. Please see this tool's tests for an example that makes use of a data table within the test: https://toolshed.g2.bx.psu.edu/view/devteam/sam_to_bam/f7a0d41036c7

Using the data table fasta_indexes is a better choice than all_fasta for a few technical reasons, mostly to ensure that both manually indexed data and data manager indexed data are accessed by the tool once deployed. Not all servers have both types of indexes, but some do, and this makes the tool more robust.

Other references: - https://galaxyproject.org/tools/ - https://docs.galaxyproject.org/ - http://planemo.readthedocs.io/

Thanks! Jen, Galaxy team

ADD COMMENTlink written 5 months ago by Jennifer Hillman Jackson25k
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