add test for snippy --ctgs

galaxyproject · Jan 15, 2025 · 1cd8c49 · 1cd8c49
1 parent 8ceb7d2
commit 1cd8c49
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Showing 4 changed files with 38 additions and 4 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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