Question: How to write tests for tools that access built-in data from the data tables
0
gravatar for Thon deBoer
5 days ago by
Thon deBoer10
Thon deBoer10 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 4 days ago by jmchilton1.1k • written 5 days ago by Thon deBoer10
3
gravatar for jmchilton
4 days 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 4 days ago by jmchilton1.1k
1
gravatar for Jennifer Hillman Jackson
5 days 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 days ago by Jennifer Hillman Jackson25k
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