patch krakentools beta_diversity.xml

[mthang]

FOR CONTRIBUTOR:

• I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• License permits unrestricted use (educational + commercial)
• This PR adds a new tool or tool collection
• This PR updates an existing tool or tool collection
• This PR does something else (explain below)

The header section of the krakentools beta_diversity.xml output file embedded the galaxy directory and It affects the file parsing in the downstream. Therefore, I made the simple patch by updating this wrapper. My colleague in Australia is submitting a workflow containing this tool to the workflowhub soon. I just patched the wrapper by adding the element_identifier to each input file.

Here's the screenshot of the beta_diversity output

Many thanks,

[bernt-matthias]

We need a bump of the version.

Wondering:

• should the output be tabular
• so we want to have more output assertions?

[mthang]

I believe you refer to the wrapper version not the tool version. I will bump the beta_diversity wrapper version up.

Re:

• should the output be tabular
  The output format is defined as txt in the wrapper not tabular
• so we want to have more output assertions?
  any suggestion? can you clarify what other outputs should be included in the test unit.

[bernt-matthias]

I believe you refer to the wrapper version not the tool version.

Yes.

The output format is defined as txt in the wrapper not tabular

The question is if this is correct :) The output looks pretty tabular to me :)

so we want to have more output assertions?

We could have an assertion that a line having the new identifiers in the output is included.

[mthang]

I bumped the galaxy from galaxy1 to galaxy2 and added the assertion to the test unit.

Re:
The question is if this is correct :) The output looks pretty tabular to me :)

It looked like a tabular to me in the beginning as well. Then, I looked closely and realised it's not tabular. They are just the header lines. see the attached.

Thanks

[bernt-matthias]

Its tab separated so it's tabular :) (# commend lines should be ignored).

I removed one extra requirement and included it directly in bioconda bioconda/bioconda-recipes#52125 as it should be. Saves us one container / environment (at least in new installations).

[mthang]

@bernt-matthias do you want me to replace "txt" with "tabular" in beta_diversity.xml wrapper? I can do that as well.

[bernt-matthias]

Already did so in ad1217d :)

[bernt-matthias]

I guess ..

Suggested change

	#set identifier = re.sub('[^\s\w\-\\.]', '_', str($input.element_identifier))
	#set identifier = re.sub('[^\s\w\-\.]', '_', str($input.element_identifier))

or just

Suggested change

	#set identifier = re.sub('[^\s\w\-\\.]', '_', str($input.element_identifier))
	#set identifier = re.sub('[^\s\w-.]', '_', str($input.element_identifier))

[bernt-matthias]

Seems to be the former one. Wanted to make some experiments yesterday which version is correct (we have all of them in the repo).. but did not finish yet.