Align and compute RMSDs

[thepineapplepirate]

This is a new tool that aligns different protein structures and assesses the accuracy based on measuring alpha carbon RMSDs. While this can be used for any set of proteins, it is especially useful when assessing the accuracy of a computational model versus a ground truth experimental solution. This will be very handy, as Galaxy continues to expand its portfolio of protein structure prediction tools. It can be readily used to compare structures predicted with alphafold, or even a quantum computer's prediction.

[bgruening]

Suggested change

	#if $skip_sidechain:
	-s
	#end if
	$skip_sidechain

[bgruening]

.. WARNING (TestsExpectNumOutputs): Test 1: should specify 'expect_num_outputs' if outputs have filters

And the tests are failing, can you have a look?

[thepineapplepirate]

.. WARNING (TestsExpectNumOutputs): Test 1: should specify 'expect_num_outputs' if outputs have filters

And the tests are failing, can you have a look?

Looks like both are failing due to the tool not being in shed.yml

"Tool tools/model_accuracy_analysis/align_and_rmsd/align_and_rmsd.xml not in changed repositories list: .shed.yml file missing"

Do I need to make a separate PR for this? Thanks!

[bgruening]

Not sure where you are seeing this. I see this here:

[thepineapplepirate]

Ok, so this is for the tLeap PR.

I'm not sure why all these PRs are going to the same place since they're coming from different branches on my end. I will change the tests for tLeap on my end in the mean time and see if this fixes things with this particular issue. Thanks you sir :).