From 8ceb7d2f1f172d5ec6446eff19152507927c9029 Mon Sep 17 00:00:00 2001
From: EVAN <543357597@qq.com>
Date: Wed, 27 Nov 2024 22:00:50 +0800
Subject: [PATCH] support --ctgs parameter

---
 tools/snippy/snippy.xml | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/tools/snippy/snippy.xml b/tools/snippy/snippy.xml
index e69f8a81b6e..a66158d80c6 100644
--- a/tools/snippy/snippy.xml
+++ b/tools/snippy/snippy.xml
@@ -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"/>
@@ -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
@@ -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
@@ -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"/>
@@ -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"/>
+            </when>
+
         </conditional>
 
         <section name="adv" title="Advanced parameters" expanded="false">