# HG changeset patch
# User nml
# Date 1693497349 0
# Node ID 141afacabcfa3a9e3630b191d5a0b73c521716f9
# Parent  4d83eccf5f81b4a468946906c2f03a35a46285f1
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e752f6e09372d3513de79d85baa619c5f5065303

diff -r 4d83eccf5f81 -r 141afacabcfa staramr_search.xml
--- a/staramr_search.xml	Mon Nov 07 17:33:35 2022 +0000
+++ b/staramr_search.xml	Thu Aug 31 15:55:49 2023 +0000
@@ -1,7 +1,7 @@
 <tool id="staramr_search" name="staramr" version="@VERSION@+galaxy0" profile="16.04">
     <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes.</description>
     <macros>
-        <token name="@VERSION@">0.9.1</token>
+        <token name="@VERSION@">0.10.0</token>
     </macros>
     <requirements>
         <requirement type="package" version="@VERSION@">staramr</requirement>
@@ -53,6 +53,11 @@
             --no-exclude-genes
         #end if
 
+
+        #if str($advanced.complex_mutations.complex_mutations_condition) == 'custom'
+	    --complex-mutations-file '${advanced.complex_mutations.complex_mutations_file}'
+	#end if
+
         #if str($advanced.plasmidfinder_type) != 'include_all'
             --plasmidfinder-database-type '${advanced.plasmidfinder_type}'
         #end if
@@ -292,6 +297,16 @@
                     <param type="data" name="exclude_genes_file" format="txt,tabular" label="Exclude genes file" help="Pass a file containing a list of genes to exclude from the ResFinder/PointFinder results" />
                 </when>
                 <when value="none" />
+       	    </conditional>
+            <conditional name="complex_mutations">
+                <param name="complex_mutations_condition" type="select" label="Provide a custom list of complex mutations">
+                    <option value="default" selected="true">Use default list of complex mutations</option>
+		    <option value="custom">Provide a custom list of complex mutations</option>
+                </param>
+                <when value="default" />
+                <when value="custom">
+                    <param type="data" name="complex_mutations_file" format="txt,tabular" label="Complex mutations file" help="Pass a file containing a list of complex mutations to group (if present) in the PointFinder results" />
+                </when>
             </conditional>
             <param name="plasmidfinder_type" type="select" label="Specify PlasmidFinder Database type">
                 <option value="include_all" selected="true">Include all available database types</option>
@@ -316,7 +331,7 @@
         </collection>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="9">
             <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
             <param name="use_pointfinder" value="salmonella" />
 
@@ -324,13 +339,13 @@
             <output name="detailed_summary" file="test1-detailed-summary.tsv" ftype="tabular" />
             <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" />
             <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" />
-            <output name="pointfinder" file="test1-pointfinder.tsv" ftype="tabular" />
+	    <output name="pointfinder" file="test1-pointfinder.tsv" ftype="tabular" />
             <output_collection name="blast_hits" type="list">
                 <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
                 <element name="pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
             </output_collection>
         </test>
-        <test>
+        <test expect_num_outputs="9">
             <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
             <param name="use_pointfinder" value="escherichia_coli" />
 
@@ -340,7 +355,7 @@
             <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" />
             <output name="pointfinder" file="test1-pointfinder-ecoli.tsv" ftype="tabular" />
         </test>
-        <test>
+        <test expect_num_outputs="8">
             <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
 
             <output name="summary" file="test2-summary.tsv" ftype="tabular" />
@@ -349,44 +364,44 @@
                 <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test2-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
             </output_collection>
         </test>
-        <test>
+        <test expect_num_outputs="8">
             <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
             <section name="advanced">
                 <param name="mlst_scheme" value="listeria_2" />
             </section>
             <output name="mlst" file="mlst.tsv" ftype="tabular" />
         </test>
-        <test>
+        <test expect_num_outputs="8">
             <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
             <param name="pid_threshold" value="99.8" />
 
             <output name="summary" file="test3-summary.tsv" ftype="tabular" />
         </test>
-        <test>
+        <test expect_num_outputs="8">
             <param name="genomes" value="16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa" ftype="fasta" />
             <param name="pid_threshold" value="99.8" />
 
             <output name="summary" file="test4-summary.tsv" ftype="tabular" />
         </test>
-        <test>
+	<test expect_num_outputs="8">
             <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" />
 
             <output name="summary" file="test5-summary.tsv" ftype="tabular" />
         </test>
-        <test>
+        <test expect_num_outputs="8">
             <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" />
             <param name="exclude_genes_condition" value="none" />
 
             <output name="summary" file="test6-summary.tsv" ftype="tabular" />
         </test>
-        <test>
+        <test expect_num_outputs="8">
             <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" />
             <param name="exclude_genes_condition" value="custom" />
             <param name="exclude_genes_file" value="genes_to_exclude.tsv" />
 
             <output name="summary" file="test5-summary.tsv" ftype="tabular" />
         </test>
-        <test>
+        <test expect_num_outputs="8">
             <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" />
             <param name="genome_size_lower_bound" value="1" />
             <param name="genome_size_upper_bound" value="10" />
diff -r 4d83eccf5f81 -r 141afacabcfa test-data/test1-detailed-summary-ecoli.tsv
--- a/test-data/test1-detailed-summary-ecoli.tsv	Mon Nov 07 17:33:35 2022 +0000
+++ b/test-data/test1-detailed-summary-ecoli.tsv	Thu Aug 31 15:55:49 2023 +0000
@@ -1,4 +1,4 @@
-Isolate ID	Data	Data Type	Predicted Phenotype	%Identity	%Overlap	HSP Length/Total Length	Contig	Start	End	Accession
-16S-rc_gyrA-rc_beta-lactam.fsa	ST- (-)	MLST								
-16S-rc_gyrA-rc_beta-lactam.fsa	None	Plasmid								
-16S-rc_gyrA-rc_beta-lactam.fsa	blaIMP-42	Resistance	ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem	99.73	100.0	741/741	16S_rrsD	4381	5121	AB753456
+Isolate ID	Data	Data Type	Predicted Phenotype	CGE Predicted Phenotype	%Identity	%Overlap	HSP Length/Total Length	Contig	Start	End	Accession
+16S-rc_gyrA-rc_beta-lactam.fsa	ST- (-)	MLST									
+16S-rc_gyrA-rc_beta-lactam.fsa	None	Plasmid									
+16S-rc_gyrA-rc_beta-lactam.fsa	blaIMP-42	Resistance	ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem	Amoxicillin, Amoxicillin+Clavulanic acid, Ampicillin, Ampicillin+Clavulanic acid, Cefepime, Cefixime, Cefotaxime, Cefoxitin, Ceftazidime, Ertapenem, Imipenem, Meropenem, Piperacillin, Piperacillin+Tazobactam	99.73	100.0	741/741	16S_rrsD	4381	5121	AB753456
diff -r 4d83eccf5f81 -r 141afacabcfa test-data/test1-detailed-summary.tsv
--- a/test-data/test1-detailed-summary.tsv	Mon Nov 07 17:33:35 2022 +0000
+++ b/test-data/test1-detailed-summary.tsv	Thu Aug 31 15:55:49 2023 +0000
@@ -1,6 +1,6 @@
-Isolate ID	Data	Data Type	Predicted Phenotype	%Identity	%Overlap	HSP Length/Total Length	Contig	Start	End	Accession
-16S-rc_gyrA-rc_beta-lactam.fsa	ST- (-)	MLST								
-16S-rc_gyrA-rc_beta-lactam.fsa	None	Plasmid								
-16S-rc_gyrA-rc_beta-lactam.fsa	16S_rrsD (C1065T)	Resistance	spectinomycin	99.94	100.0	1544/1544	16S_rrsD	1604	61	
-16S-rc_gyrA-rc_beta-lactam.fsa	blaIMP-42	Resistance	ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem	99.73	100.0	741/741	16S_rrsD	4381	5121	AB753456
-16S-rc_gyrA-rc_beta-lactam.fsa	gyrA (A67P)	Resistance	ciprofloxacin I/R, nalidixic acid	99.96	100.0	2637/2637	16S_rrsD	4317	1681	
+Isolate ID	Data	Data Type	Predicted Phenotype	CGE Predicted Phenotype	%Identity	%Overlap	HSP Length/Total Length	Contig	Start	End	Accession
+16S-rc_gyrA-rc_beta-lactam.fsa	ST- (-)	MLST									
+16S-rc_gyrA-rc_beta-lactam.fsa	None	Plasmid									
+16S-rc_gyrA-rc_beta-lactam.fsa	16S_rrsD (C1065T)	Resistance	spectinomycin	Spectinomycin	99.94	100.0	1544/1544	16S_rrsD	1604	61	
+16S-rc_gyrA-rc_beta-lactam.fsa	blaIMP-42	Resistance	ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem	Amoxicillin, Amoxicillin+Clavulanic acid, Ampicillin, Ampicillin+Clavulanic acid, Cefepime, Cefixime, Cefotaxime, Cefoxitin, Ceftazidime, Ertapenem, Imipenem, Meropenem, Piperacillin, Piperacillin+Tazobactam	99.73	100.0	741/741	16S_rrsD	4381	5121	AB753456
+16S-rc_gyrA-rc_beta-lactam.fsa	gyrA (A67P)	Resistance	ciprofloxacin I/R, nalidixic acid	Nalidixic acid,Ciprofloxacin	99.96	100.0	2637/2637	16S_rrsD	4317	1681	
diff -r 4d83eccf5f81 -r 141afacabcfa test-data/test1-pointfinder-ecoli.tsv
--- a/test-data/test1-pointfinder-ecoli.tsv	Mon Nov 07 17:33:35 2022 +0000
+++ b/test-data/test1-pointfinder-ecoli.tsv	Thu Aug 31 15:55:49 2023 +0000
@@ -1,1 +1,1 @@
-Isolate ID	Gene	Predicted Phenotype	Type	Position	Mutation	%Identity	%Overlap	HSP Length/Total Length	Contig	Start	End	Pointfinder Position
+Isolate ID	Gene	Predicted Phenotype	CGE Predicted Phenotype	Type	Position	Mutation	%Identity	%Overlap	HSP Length/Total Length	Contig	Start	End	Pointfinder Position	CGE Notes	CGE Required Mutation	CGE Mechanism	CGE PMID
diff -r 4d83eccf5f81 -r 141afacabcfa test-data/test1-pointfinder.tsv
--- a/test-data/test1-pointfinder.tsv	Mon Nov 07 17:33:35 2022 +0000
+++ b/test-data/test1-pointfinder.tsv	Thu Aug 31 15:55:49 2023 +0000
@@ -1,3 +1,3 @@
-Isolate ID	Gene	Predicted Phenotype	Type	Position	Mutation	%Identity	%Overlap	HSP Length/Total Length	Contig	Start	End	Pointfinder Position
-16S-rc_gyrA-rc_beta-lactam.fsa	16S_rrsD (C1065T)	spectinomycin	nucleotide	1065	C -> T	99.94	100.00	1544/1544	16S_rrsD	1604	61	C1065T
-16S-rc_gyrA-rc_beta-lactam.fsa	gyrA (A67P)	ciprofloxacin I/R, nalidixic acid	codon	67	GCC -> CCC (A -> P)	99.96	100.00	2637/2637	16S_rrsD	4317	1681	A67P
+Isolate ID	Gene	Predicted Phenotype	CGE Predicted Phenotype	Type	Position	Mutation	%Identity	%Overlap	HSP Length/Total Length	Contig	Start	End	Pointfinder Position	CGE Notes	CGE Required Mutation	CGE Mechanism	CGE PMID
+16S-rc_gyrA-rc_beta-lactam.fsa	16S_rrsD (C1065T)	spectinomycin	Spectinomycin	nucleotide	1065	C -> T	99.94	100.00	1544/1544	16S_rrsD	1604	61	C1065T			Target modification	12402084
+16S-rc_gyrA-rc_beta-lactam.fsa	gyrA (A67P)	ciprofloxacin I/R, nalidixic acid	Nalidixic acid,Ciprofloxacin	codon	67	GCC -> CCC (A -> P)	99.96	100.00	2637/2637	16S_rrsD	4317	1681	A67P		gyrA_G81C.S.H.D	Target modification	7492118
diff -r 4d83eccf5f81 -r 141afacabcfa test-data/test1-resfinder.tsv
--- a/test-data/test1-resfinder.tsv	Mon Nov 07 17:33:35 2022 +0000
+++ b/test-data/test1-resfinder.tsv	Thu Aug 31 15:55:49 2023 +0000
@@ -1,2 +1,2 @@
-Isolate ID	Gene	Predicted Phenotype	%Identity	%Overlap	HSP Length/Total Length	Contig	Start	End	Accession	Sequence
-16S-rc_gyrA-rc_beta-lactam.fsa	blaIMP-42	ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem	99.73	100.00	741/741	16S_rrsD	4381	5121	AB753456	ATGAGCAAGTTATCTGCATTCTTTATATTTTTGTTTTGCAGCATTGATACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACAGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA
+Isolate ID	Gene	Predicted Phenotype	CGE Predicted Phenotype	%Identity	%Overlap	HSP Length/Total Length	Contig	Start	End	Accession	Sequence	CGE Notes
+16S-rc_gyrA-rc_beta-lactam.fsa	blaIMP-42	ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem	Amoxicillin, Amoxicillin+Clavulanic acid, Ampicillin, Ampicillin+Clavulanic acid, Cefepime, Cefixime, Cefotaxime, Cefoxitin, Ceftazidime, Ertapenem, Imipenem, Meropenem, Piperacillin, Piperacillin+Tazobactam	99.73	100.00	741/741	16S_rrsD	4381	5121	AB753456	ATGAGCAAGTTATCTGCATTCTTTATATTTTTGTTTTGCAGCATTGATACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACAGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA	Subclass B1
diff -r 4d83eccf5f81 -r 141afacabcfa test-data/test1-summary-ecoli.tsv
--- a/test-data/test1-summary-ecoli.tsv	Mon Nov 07 17:33:35 2022 +0000
+++ b/test-data/test1-summary-ecoli.tsv	Thu Aug 31 15:55:49 2023 +0000
@@ -1,2 +1,2 @@
-Isolate ID	Quality Module	Genotype	Predicted Phenotype	Plasmid	Scheme	Sequence Type	Genome Length	N50 value	Number of Contigs Greater Than Or Equal To 300 bp	Quality Module Feedback
-16S-rc_gyrA-rc_beta-lactam.fsa	Failed	blaIMP-42	ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem	None	-	-	5220	5220	1	Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000]
+Isolate ID	Quality Module	Genotype	Predicted Phenotype	CGE Predicted Phenotype	Plasmid	Scheme	Sequence Type	Genome Length	N50 value	Number of Contigs Greater Than Or Equal To 300 bp	Quality Module Feedback
+16S-rc_gyrA-rc_beta-lactam.fsa	Failed	blaIMP-42	ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem	Amoxicillin, Amoxicillin+Clavulanic acid, Ampicillin, Ampicillin+Clavulanic acid, Cefepime, Cefixime, Cefotaxime, Cefoxitin, Ceftazidime, Ertapenem, Imipenem, Meropenem, Piperacillin, Piperacillin+Tazobactam	None	-	-	5220	5220	1	Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000]
diff -r 4d83eccf5f81 -r 141afacabcfa test-data/test1-summary.tsv
--- a/test-data/test1-summary.tsv	Mon Nov 07 17:33:35 2022 +0000
+++ b/test-data/test1-summary.tsv	Thu Aug 31 15:55:49 2023 +0000
@@ -1,2 +1,2 @@
-Isolate ID	Quality Module	Genotype	Predicted Phenotype	Plasmid	Scheme	Sequence Type	Genome Length	N50 value	Number of Contigs Greater Than Or Equal To 300 bp	Quality Module Feedback
-16S-rc_gyrA-rc_beta-lactam.fsa	Failed	16S_rrsD (C1065T), blaIMP-42, gyrA (A67P)	spectinomycin, ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem, ciprofloxacin I/R, nalidixic acid	None	-	-	5220	5220	1	Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000]
+Isolate ID	Quality Module	Genotype	Predicted Phenotype	CGE Predicted Phenotype	Plasmid	Scheme	Sequence Type	Genome Length	N50 value	Number of Contigs Greater Than Or Equal To 300 bp	Quality Module Feedback
+16S-rc_gyrA-rc_beta-lactam.fsa	Failed	16S_rrsD (C1065T), blaIMP-42, gyrA (A67P)	spectinomycin, ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem, ciprofloxacin I/R, nalidixic acid	Spectinomycin, Amoxicillin, Amoxicillin+Clavulanic acid, Ampicillin, Ampicillin+Clavulanic acid, Cefepime, Cefixime, Cefotaxime, Cefoxitin, Ceftazidime, Ertapenem, Imipenem, Meropenem, Piperacillin, Piperacillin+Tazobactam, Nalidixic acid, Ciprofloxacin	None	-	-	5220	5220	1	Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000]
diff -r 4d83eccf5f81 -r 141afacabcfa test-data/test2-resfinder.tsv
--- a/test-data/test2-resfinder.tsv	Mon Nov 07 17:33:35 2022 +0000
+++ b/test-data/test2-resfinder.tsv	Thu Aug 31 15:55:49 2023 +0000
@@ -1,2 +1,2 @@
-Isolate ID	Gene	Predicted Phenotype	%Identity	%Overlap	HSP Length/Total Length	Contig	Start	End	Accession	Sequence
-16S-rc_gyrA-rc_beta-lactam.fsa	blaIMP-42	ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem	99.73	100.00	741/741	16S_rrsD	4381	5121	AB753456	ATGAGCAAGTTATCTGCATTCTTTATATTTTTGTTTTGCAGCATTGATACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACAGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA
+Isolate ID	Gene	Predicted Phenotype	CGE Predicted Phenotype	%Identity	%Overlap	HSP Length/Total Length	Contig	Start	End	Accession	Sequence	CGE Notes
+16S-rc_gyrA-rc_beta-lactam.fsa	blaIMP-42	ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem	Amoxicillin, Amoxicillin+Clavulanic acid, Ampicillin, Ampicillin+Clavulanic acid, Cefepime, Cefixime, Cefotaxime, Cefoxitin, Ceftazidime, Ertapenem, Imipenem, Meropenem, Piperacillin, Piperacillin+Tazobactam	99.73	100.00	741/741	16S_rrsD	4381	5121	AB753456	ATGAGCAAGTTATCTGCATTCTTTATATTTTTGTTTTGCAGCATTGATACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACAGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA	Subclass B1
diff -r 4d83eccf5f81 -r 141afacabcfa test-data/test2-summary.tsv
--- a/test-data/test2-summary.tsv	Mon Nov 07 17:33:35 2022 +0000
+++ b/test-data/test2-summary.tsv	Thu Aug 31 15:55:49 2023 +0000
@@ -1,2 +1,2 @@
-Isolate ID	Quality Module	Genotype	Predicted Phenotype	Plasmid	Scheme	Sequence Type	Genome Length	N50 value	Number of Contigs Greater Than Or Equal To 300 bp	Quality Module Feedback
-16S-rc_gyrA-rc_beta-lactam.fsa	Failed	blaIMP-42	ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem	None	-	-	5220	5220	1	Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000]
+Isolate ID	Quality Module	Genotype	Predicted Phenotype	CGE Predicted Phenotype	Plasmid	Scheme	Sequence Type	Genome Length	N50 value	Number of Contigs Greater Than Or Equal To 300 bp	Quality Module Feedback
+16S-rc_gyrA-rc_beta-lactam.fsa	Failed	blaIMP-42	ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem	Amoxicillin, Amoxicillin+Clavulanic acid, Ampicillin, Ampicillin+Clavulanic acid, Cefepime, Cefixime, Cefotaxime, Cefoxitin, Ceftazidime, Ertapenem, Imipenem, Meropenem, Piperacillin, Piperacillin+Tazobactam	None	-	-	5220	5220	1	Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000]
diff -r 4d83eccf5f81 -r 141afacabcfa test-data/test3-summary.tsv
--- a/test-data/test3-summary.tsv	Mon Nov 07 17:33:35 2022 +0000
+++ b/test-data/test3-summary.tsv	Thu Aug 31 15:55:49 2023 +0000
@@ -1,2 +1,2 @@
-Isolate ID	Quality Module	Genotype	Predicted Phenotype	Plasmid	Scheme	Sequence Type	Genome Length	N50 value	Number of Contigs Greater Than Or Equal To 300 bp	Quality Module Feedback
-16S-rc_gyrA-rc_beta-lactam.fsa	Failed	None	Sensitive	None	-	-	5220	5220	1	Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000]
+Isolate ID	Quality Module	Genotype	Predicted Phenotype	CGE Predicted Phenotype	Plasmid	Scheme	Sequence Type	Genome Length	N50 value	Number of Contigs Greater Than Or Equal To 300 bp	Quality Module Feedback
+16S-rc_gyrA-rc_beta-lactam.fsa	Failed	None	Susceptible	-	None	-	-	5220	5220	1	Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000]
diff -r 4d83eccf5f81 -r 141afacabcfa test-data/test4-summary.tsv
--- a/test-data/test4-summary.tsv	Mon Nov 07 17:33:35 2022 +0000
+++ b/test-data/test4-summary.tsv	Thu Aug 31 15:55:49 2023 +0000
@@ -1,2 +1,2 @@
-Isolate ID	Quality Module	Genotype	Predicted Phenotype	Plasmid	Scheme	Sequence Type	Genome Length	N50 value	Number of Contigs Greater Than Or Equal To 300 bp	Quality Module Feedback
-16S_rc_gyrA_rc_beta-lactam_spaces__extra:characters_.fsa	Failed	None	Sensitive	None	-	-	5220	5220	1	Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000]
+Isolate ID	Quality Module	Genotype	Predicted Phenotype	CGE Predicted Phenotype	Plasmid	Scheme	Sequence Type	Genome Length	N50 value	Number of Contigs Greater Than Or Equal To 300 bp	Quality Module Feedback
+16S_rc_gyrA_rc_beta-lactam_spaces__extra:characters_.fsa	Failed	None	Susceptible	-	None	-	-	5220	5220	1	Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000]
diff -r 4d83eccf5f81 -r 141afacabcfa test-data/test5-summary.tsv
--- a/test-data/test5-summary.tsv	Mon Nov 07 17:33:35 2022 +0000
+++ b/test-data/test5-summary.tsv	Thu Aug 31 15:55:49 2023 +0000
@@ -1,2 +1,2 @@
-Isolate ID	Quality Module	Genotype	Predicted Phenotype	Plasmid	Scheme	Sequence Type	Genome Length	N50 value	Number of Contigs Greater Than Or Equal To 300 bp	Quality Module Feedback
-test-aminoglycoside.fsa	Failed	None	Sensitive	None	-	-	438	438	1	Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000]
+Isolate ID	Quality Module	Genotype	Predicted Phenotype	CGE Predicted Phenotype	Plasmid	Scheme	Sequence Type	Genome Length	N50 value	Number of Contigs Greater Than Or Equal To 300 bp	Quality Module Feedback
+test-aminoglycoside.fsa	Failed	None	Susceptible	-	None	-	-	438	438	1	Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000]
diff -r 4d83eccf5f81 -r 141afacabcfa test-data/test6-summary.tsv
--- a/test-data/test6-summary.tsv	Mon Nov 07 17:33:35 2022 +0000
+++ b/test-data/test6-summary.tsv	Thu Aug 31 15:55:49 2023 +0000
@@ -1,2 +1,2 @@
-Isolate ID	Quality Module	Genotype	Predicted Phenotype	Plasmid	Scheme	Sequence Type	Genome Length	N50 value	Number of Contigs Greater Than Or Equal To 300 bp	Quality Module Feedback
-test-aminoglycoside.fsa	Failed	aac(6')-Iaa	unknown[aac(6')-Iaa_1_NC_003197]	None	-	-	438	438	1	Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000]
+Isolate ID	Quality Module	Genotype	Predicted Phenotype	CGE Predicted Phenotype	Plasmid	Scheme	Sequence Type	Genome Length	N50 value	Number of Contigs Greater Than Or Equal To 300 bp	Quality Module Feedback
+test-aminoglycoside.fsa	Failed	aac(6')-Iaa	unknown[aac(6')-Iaa_1_NC_003197]	Amikacin, Tobramycin	None	-	-	438	438	1	Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000]
diff -r 4d83eccf5f81 -r 141afacabcfa test-data/test8-summary.tsv
--- a/test-data/test8-summary.tsv	Mon Nov 07 17:33:35 2022 +0000
+++ b/test-data/test8-summary.tsv	Thu Aug 31 15:55:49 2023 +0000
@@ -1,2 +1,2 @@
-Isolate ID	Quality Module	Genotype	Predicted Phenotype	Plasmid	Scheme	Sequence Type	Genome Length	N50 value	Number of Contigs Greater Than Or Equal To 300 bp	Quality Module Feedback
-test-aminoglycoside.fsa	Failed	None	Sensitive	None	-	-	438	438	1	Genome length is not within the acceptable length range [1,10] ; N50 value is not greater than the specified minimum value [10000]
+Isolate ID	Quality Module	Genotype	Predicted Phenotype	CGE Predicted Phenotype	Plasmid	Scheme	Sequence Type	Genome Length	N50 value	Number of Contigs Greater Than Or Equal To 300 bp	Quality Module Feedback
+test-aminoglycoside.fsa	Failed	None	Susceptible	-	None	-	-	438	438	1	Genome length is not within the acceptable length range [1,10] ; N50 value is not greater than the specified minimum value [10000]