snippy: support --ctgs parameter

[jianzuoyi]

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• 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
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[bernt-matthias]

Can you add a test case?

[bernt-matthias]

In Galaxy we always call this fasta:

Suggested change

	<param name="fasta_input" type="data" format="fasta,fa,fna" label="Select fasta dataset" help="Specify dataset with assembled contigs"/>
	<param name="fasta_input" type="data" format="fasta" label="Select fasta dataset" help="Specify dataset with assembled contigs"/>

Do you know if (gzip) compressed input is supported? If so you could add fasta.gz to the list.

[jianzuoyi]

Thank you for your help. I will add a test case, and check if fasta.gz is supported by snippy.

[jianzuoyi]

Hi @bernt-matthias ，I added a test. By the way, Snippy does not support assembled contigs in fasta.gz format.

[bernt-matthias]

Just one more thing. I think the test failure is just temporary.

[bernt-matthias]

I would suggest to modify the wording here, maybe like this:

Suggested change

	<param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
	<option value="paired">Paired</option>
	<option value="single">Single</option>
	<option value="paired_collection">Paired Collection</option>
	<option value="single">Single</option>
	<option value="paired_iv">Paired Interleaved</option>
	<option value="contigs">Assembled Contigs</option>
	</param>
	<param name="fastq_input_selector" type="select" label="Input type" help="Select paired/single end raw read data or assembled contigs">
	<option value="paired">Paired end reads</option>
	<option value="single">Single end reads</option>
	<option value="paired_collection">Paired end reads in a collection</option>
	<option value="paired_iv">Interleaved paired end reads</option>
	<option value="contigs">Assembled Contigs</option>
	</param>

[jianzuoyi]

Hi @bernt-matthias. Thank you for your suggestions and review. I have made the corresponding modifications.