New tool addition: amas tool

[jchchiu]

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)

Regarding issue #7442

• Implemented the amas alignment concatenation action needed for the Biohackathon workflow
• Added a simple test case with corresponding expected outputs

The AMAS commands are:
  concat      Concatenate input alignments
  convert     Convert to other file format
  replicate   Create replicate data sets for phylogenetic jackknife
  split       Split alignment according to a partitions file
  summary     Write alignment summary
  remove      Remove taxa from alignment
  translate   Translate DNA alignment into protein alignment

• Command flags can be seen here
• Note, The Tool Standard Output for concat will say "Wrote concatenated sequences to fasta file 'concatenated.out'"; however the file obtained will be renamed with the output format you have chosen (e.g. 'concatenated.fasta' for fasta, 'concatenated.nex' for nexus and nexus-int)

To do:

• Add more test coverage
• Will also try to implement replicate and split (need to workout how to do outputs); others are already covered by existing Galaxy tools (unless there is something you think looks interesting to implement)
• Clean up code and help text
• Fix --check-align

For now, is it possible to review the code to see if it's on the right track, and if there are any better ways to structure it?

[jchchiu]

See updated changes from George at jchchiu#1

[bernt-matthias]

fasta phylip and nexus can be distinguishe automatically, e.g. $input_file.ext gives the Galaxy datatype. Is the info on interleaved/not needed? Can it be determined automatically?

[jchchiu]

https://github.com/marekborowiec/AMAS/blob/2e93d31638625135aa48a68251c363ac23a47c4a/amas/AMAS.py#L692

It doesn't seem like they have a function that detects the format for interleaved automatically; instead it depends on the input you give it. Can galaxy automatically distinguish interleaved?

[bernt-matthias]

We should set the format instead if format="data"

[jchchiu]

Could you have a look at the amas_split.xml at L55; is this what you were thinking?

[jchchiu]

Hey @bernt-matthias, could you have a look at amas_concat.xml and see if this is on the right track? If so, I'll update the rest of the subcommands with your suggestions.
Cheers for all the thorough comments.

[jchchiu]

I've been testing the split subcommand again and it seems like AMAS doesn't work when you use a RAxML or NEXUS formatted partitions file as an input.

The regex operator only works for the unspecified partitions:
matches = re.finditer(r"^(\s+)?([^ =]+)[ =]+([\0-9, -]+)", self.in_file_lines, re.MULTILINE)

I've updated the subcommand accordingly with some more info.

[bernt-matthias]

Maybe check that they all the same. Also I would just print the result and use non-zero exit code for the error case. Something like this:

Suggested change

	# NOTE: Do we need to check all files?
	if all(interleaved_status):
	return 0 # Exit code 0 = interleaved
	else:
	return 1 # Exit code 1 = sequential
	interleaved_status = list(set(interleaved_status))
	if len(interleaved_status) > 1:
	raise Exception("mixed interleaved")
	print(interleaved_status[0])

Or make the script output args.format + "-int" or args.format. Then you can set a bash variable in the command block. IN_FORMAT = \$(python '$__tool_directory__/check_interleaved.py' ...)

[bernt-matthias]

Looks good. Nearly there.

[bernt-matthias]

Suggested change

<expand macro="input_format" />

Analogous in all commands.

[bernt-matthias]

Also remove in_format from tests.

[bernt-matthias]

Use \$IN_FORMAT