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snippy: support --ctgs parameter #6591

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snippy: support --ctgs parameter #6591

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11 changes: 10 additions & 1 deletion tools/snippy/snippy.xml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
<tool id="snippy" name="snippy" version="@WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@">
<description>
<description>
Snippy finds SNPs between a haploid reference genome and your NGS sequence reads.
</description>
<expand macro="bio_tools"/>
Expand All @@ -22,6 +22,8 @@
#set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_single.element_identifier)
#elif str( $fastq_input.fastq_input_selector ) == "paired_iv"
#set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_interleaved.element_identifier)
#elif str( $fastq_input.fastq_input_selector ) == "contigs"
#set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fasta_input.element_identifier)
#end if

snippy
Expand Down Expand Up @@ -50,6 +52,8 @@
--se '$fastq_input.fastq_input_single'
#elif str( $fastq_input.fastq_input_selector ) == "paired_iv"
--peil '$fastq_input.fastq_input_interleaved'
#elif str( $fastq_input.fastq_input_selector ) == "contigs"
--ctgs '$fastq_input.fasta_input'
#end if

#if "outcon" in str($outputs) and $adv.rename_cons
Expand All @@ -68,6 +72,7 @@
<option value="single">Single</option>
<option value="paired_collection">Paired Collection</option>
<option value="paired_iv">Paired Interleaved</option>
<option value="contigs">Assembled Contigs</option>
</param>
<when value="paired">
<param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="Select first set of reads" help="Specify dataset with forward reads"/>
Expand All @@ -82,6 +87,10 @@
<when value="paired_iv">
<param name="fastq_input_interleaved" type="data" format="fastqsanger,fastqsanger.gz" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
</when>
<when value="contigs">
<param name="fasta_input" type="data" format="fasta,fa,fna" label="Select fasta dataset" help="Specify dataset with assembled contigs"/>
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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.

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

</when>

</conditional>

<section name="adv" title="Advanced parameters" expanded="false">
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