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 1/4] 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">

From 1cd8c49432101d32b97a116ea1fd5aa353182927 Mon Sep 17 00:00:00 2001
From: EVAN <543357597@qq.com>
Date: Thu, 16 Jan 2025 00:56:22 +0800
Subject: [PATCH 2/4] add test for snippy --ctgs

---
 tools/snippy/snippy.xml                       | 21 +++++++++++++++----
 tools/snippy/test-data/contigs.fasta          | 11 ++++++++++
 .../d_fna_ref_mincov_1_minqual_60.snps.gff    |  3 +++
 .../d_fna_ref_mincov_1_minqual_60.snps.txt    |  7 +++++++
 4 files changed, 38 insertions(+), 4 deletions(-)
 create mode 100644 tools/snippy/test-data/contigs.fasta
 create mode 100644 tools/snippy/test-data/d_fna_ref_mincov_1_minqual_60.snps.gff
 create mode 100644 tools/snippy/test-data/d_fna_ref_mincov_1_minqual_60.snps.txt

diff --git a/tools/snippy/snippy.xml b/tools/snippy/snippy.xml
index a66158d80c6..1792406e2a5 100644
--- a/tools/snippy/snippy.xml
+++ b/tools/snippy/snippy.xml
@@ -1,8 +1,7 @@
 <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"/>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -69,8 +68,8 @@
         <conditional name="fastq_input">
             <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>
@@ -88,7 +87,7 @@
                 <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"/>
+                <param name="fasta_input" type="data" format="fasta" label="Select fasta dataset" help="Specify dataset with assembled contigs"/>
             </when>
 
         </conditional>
@@ -228,6 +227,20 @@
             <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="8" />
             <output name="snpgff" ftype="gff3" file="b_2_fna_ref_mincov_2_minqual_60.snps.gff" lines_diff="2"/>
         </test>
+
+        <test>            <!-- test 5 - fasta ref one snp single -->
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="history"/>
+                <param name="ref_file" value="reference.fasta" ftype="fasta"/>
+            </conditional>
+            <param name="fastq_input_selector" value="contigs" />
+            <param name="fasta_input" value="contigs.fasta" ftype="fasta" />
+            <param name="mincov" value="2" />
+            <param name="minqual" value="60" />
+            <param name="outputs" value="outgff,outsum" />
+            <output name="snpsum" ftype="tabular" file="d_fna_ref_mincov_1_minqual_60.snps.txt" lines_diff="6" />
+            <output name="snpgff" ftype="gff3" file="d_fna_ref_mincov_1_minqual_60.snps.gff" lines_diff="2"/>
+        </test>
     </tests>
 
 
diff --git a/tools/snippy/test-data/contigs.fasta b/tools/snippy/test-data/contigs.fasta
new file mode 100644
index 00000000000..ecdab141ed5
--- /dev/null
+++ b/tools/snippy/test-data/contigs.fasta
@@ -0,0 +1,11 @@
+>reference
+TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAAGGTTATCCAC
+AATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTTCATTGCGCCAATGTGTTAAA
+TTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTTGTGAAAAATGATATTTCAACGGCTTTTGAA
+GACTAGAGATACAGAGTTTTATCGAGTTATACAAAACAGGAATATTGACGACGTATTTGGATACTTATTA
+ATTCACGATAAACGGGAACCAGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAG
+AAGCTTTTTCAGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA
+AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTTTCAGCCAGAA
+ACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGAATATCCTGCTGAATTTGAGA
+AAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGGTCGTAAAATTACTATTCCAGACACAACGAG
+AGAAAAATATATCTATTTAACGCAATAATTTTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA
diff --git a/tools/snippy/test-data/d_fna_ref_mincov_1_minqual_60.snps.gff b/tools/snippy/test-data/d_fna_ref_mincov_1_minqual_60.snps.gff
new file mode 100644
index 00000000000..efce0e49f5a
--- /dev/null
+++ b/tools/snippy/test-data/d_fna_ref_mincov_1_minqual_60.snps.gff
@@ -0,0 +1,3 @@
+##gff-version 3
+reference	snippy:4.6.0	variation	141	141	.	.	0	note=snp C=>T T:4 C:0
+reference	snippy:4.6.0	variation	211	211	.	.	0	note=snp A=>G G:5 A:0
diff --git a/tools/snippy/test-data/d_fna_ref_mincov_1_minqual_60.snps.txt b/tools/snippy/test-data/d_fna_ref_mincov_1_minqual_60.snps.txt
new file mode 100644
index 00000000000..2eb86565fef
--- /dev/null
+++ b/tools/snippy/test-data/d_fna_ref_mincov_1_minqual_60.snps.txt
@@ -0,0 +1,7 @@
+DateTime	2025-01-15T12:20:46
+ReadFiles	fake_reads.fq
+Reference	reference.fasta
+ReferenceSize	700
+Software	snippy 4.6.0
+Variant-SNP	2
+VariantTotal	2

From 0ef7539702c6911eca5754f6fc1c76ec306eac60 Mon Sep 17 00:00:00 2001
From: EVAN <543357597@qq.com>
Date: Sat, 18 Jan 2025 20:30:15 +0800
Subject: [PATCH 3/4] better snippy fastq_input_selector options

---
 tools/snippy/snippy.xml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tools/snippy/snippy.xml b/tools/snippy/snippy.xml
index 1792406e2a5..eeb3c151578 100644
--- a/tools/snippy/snippy.xml
+++ b/tools/snippy/snippy.xml
@@ -66,11 +66,11 @@
     <inputs>
         <expand macro="reference_selector" />
         <conditional name="fastq_input">
-            <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="paired_collection">Paired Collection</option>
-                <option value="single">Single</option>
-                <option value="paired_iv">Paired Interleaved</option>
+            <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>
             <when value="paired">

From 8ff92206440d10c6c3debfb40396d5fd773637ad Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Mon, 20 Jan 2025 09:41:20 +0100
Subject: [PATCH 4/4] Minor test improvement

---
 tools/snippy/snippy.xml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/tools/snippy/snippy.xml b/tools/snippy/snippy.xml
index eeb3c151578..de842e1d218 100644
--- a/tools/snippy/snippy.xml
+++ b/tools/snippy/snippy.xml
@@ -233,8 +233,10 @@
                 <param name="reference_source_selector" value="history"/>
                 <param name="ref_file" value="reference.fasta" ftype="fasta"/>
             </conditional>
-            <param name="fastq_input_selector" value="contigs" />
-            <param name="fasta_input" value="contigs.fasta" ftype="fasta" />
+            <conditional name="fastq_input">
+                <param name="fastq_input_selector" value="contigs" />
+                <param name="fasta_input" value="contigs.fasta" ftype="fasta" />
+            </conditional>
             <param name="mincov" value="2" />
             <param name="minqual" value="60" />
             <param name="outputs" value="outgff,outsum" />