--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abricate_report_screening_files.loc.sample	Thu Oct 31 15:43:15 2019 -0400
@@ -0,0 +1,7 @@
+# Expect three columns, tab separated, as follows:
+# - value (Galaxy records this in the Galaxy DB)
+# - name (Galaxy shows this in the UI)
+# - path (Path to the abricate report screening file (tsv format))
+#
+# e.g.
+# 76cc857a-7747-4d69-b2a3-a8fbddbf64c2<tab>Carbapenemase Genes<tab>/path/to/screening_file.tsv

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/screen_abricate_report.py	Thu Oct 31 15:43:15 2019 -0400
@@ -0,0 +1,58 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+
+import argparse
+import os
+import re
+import sys
+import csv
+from pprint import pprint
+
+def parse_screen_file(screen_file):
+    screen = []
+    with open(screen_file) as f:
+        reader = csv.DictReader(f, delimiter="\t", quotechar='"')
+        for row in reader:
+            screen.append(row)
+    return screen
+
+def get_fieldnames(input_file):
+    with open(input_file) as f:
+        reader = csv.DictReader(f, delimiter="\t", quotechar='"')
+        row = next(reader)
+    fieldnames = row.keys()
+    return fieldnames
+    
+def main(args):
+    screen = parse_screen_file(args.screening_file)
+    abricate_report_fieldnames = get_fieldnames(args.abricate_report)
+    gene_detection_status_fieldnames = ['gene_name', 'detected']
+    with open(args.abricate_report, 'r') as f1, open(args.screened_report, 'w') as f2, open(args.gene_detection_status, 'w') as f3:
+        abricate_report_reader = csv.DictReader(f1, delimiter="\t", quotechar='"')
+        screened_report_writer = csv.DictWriter(f2, delimiter="\t", quotechar='"', fieldnames=abricate_report_reader.fieldnames)
+        gene_detection_status_writer = csv.DictWriter(f3, delimiter="\t", quotechar='"', fieldnames=gene_detection_status_fieldnames)
+        screened_report_writer.writeheader()
+        gene_detection_status_writer.writeheader()
+
+        for gene in screen:
+            gene_detection_status = {
+                'gene_name': gene['gene_name'],
+                'detected': False
+            }
+            for abricate_report_row in abricate_report_reader:
+                if re.search(gene['regex'], abricate_report_row['GENE']):
+                    gene_detection_status['detected'] = True
+                    screened_report_writer.writerow(abricate_report_row)
+            gene_detection_status_writer.writerow(gene_detection_status)
+            f1.seek(0) # return file pointer to start of abricate report
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument("abricate_report", help="Input: Abricate report to screen (tsv)")
+    parser.add_argument("--screening_file", help="Input: List of genes to screen for (tsv)")
+    parser.add_argument("--screened_report", help="Output: Screened abricate report including only genes of interest (tsv)")
+    parser.add_argument("--gene_detection_status", help="Output: detection status for all genes listed in the screening file (tsv)")
+    args = parser.parse_args()
+    main(args)

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/screen_abricate_report.xml	Thu Oct 31 15:43:15 2019 -0400
@@ -0,0 +1,36 @@
+<tool id="screen_abricate_report" name="Screen Abricate Report" version="0.1.0">
+    <description>Screens an abricate report for genes of interest</description>
+    <requirements>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        '${__tool_directory__}/screen_abricate_report.py'
+             '${abricate_report}'
+             --screening_file '${screening_file.fields.path}'
+             --screened_report '${screened_report}'
+             --gene_detection_status '${gene_detection_status}'
+    ]]></command>
+    <inputs>
+        <param name="abricate_report" type="data" format="tabular" />
+        <param name="screening_file" type="select" format="tabular">
+	    <options from_data_table="abricate_report_screening_files">
+	        <validator type="no_options" message="No abricate report screening files are available" />
+            </options>
+	</param>
+    </inputs>
+    <outputs>
+        <data name="screened_report" type="data" format="tabular" label="Screened Abricate Report" />
+        <data name="gene_detection_status" type="data" format="tabular" label="Gene Detection Status" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="screening_file" value="test_entry"/>
+            <param name="abricate_report" value="SAMN13042171_abricate_report.tsv"/>
+	    <output name="screened_report" file="SAMN13042171_abricate_report_screened.tsv" ftype="tabular"/>
+	    <output name="gene_detection_status" file="SAMN13042171_gene_detection_status.tsv" ftype="tabular"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+    ]]></help>
+    <citations>
+    </citations>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SAMN13042171_abricate_report.tsv	Thu Oct 31 15:43:15 2019 -0400
@@ -0,0 +1,47 @@
+#FILE	SEQUENCE	START	END	STRAND	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION	PRODUCT	RESISTANCE
+SAMN13042171.fasta	contig00001	181303	181975	+	kdpE	1-673/678	===============	0/0	99.26	76.08	card	U00096.3:721056-721734	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
+SAMN13042171.fasta	contig00001	362878	363231	-	ramA	21-375/375	========/======	1/1	94.40	80.56	card	JQ727668:1-376	RamA (resistance antibiotic multiple) is a positive regulator of AcrAB-TolC and leads to high level multidrug resistance in Klebsiella pneumoniae Salmonella enterica and Enterobacter aerugenes increasing the expression of both the mar operon as well as AcrAB. RamA also decreases OmpF expression.	cephamycin/aminocoumarin/aminoglycoside/carbapenem/fluoroquinolone/cephalosporin/triclosan/tetracycline/acridine_dye/phenicol/monobactam/glycylcycline/antibacterial_free_fatty_acids/penem/diaminopyrimidine/penam/macrolide/rifamycin
+SAMN13042171.fasta	contig00001	568102	569295	+	Klebsiella_pneumoniae_acrA	1-1197/1197	========/======	2/3	99.75	95.07	card	AJ318073.1:794-1991	AcrA is a subunit of the AcrAB multidrug efflux system that in K. pneumoniae which is encoded by the acrRAB operon.	aminocoumarin/carbapenem/aminoglycoside/triclosan/tetracycline/acridine_dye/cephalosporin/fluoroquinolone/monobactam/glycylcycline/phenicol/diaminopyrimidine/antibacterial_free_fatty_acids/macrolide/penam/rifamycin
+SAMN13042171.fasta	contig00001	569318	572462	+	acrB	1-3148/3150	========/======	1/3	99.84	83.74	card	U00096.3:481254-484404	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	antibacterial_free_fatty_acids/diaminopyrimidine/rifamycin/penam/macrolide/aminoglycoside/carbapenem/aminocoumarin/phenicol/monobactam/glycylcycline/fluoroquinolone/cephalosporin/tetracycline/triclosan/acridine_dye
+SAMN13042171.fasta	contig00001	698224	699350	+	Escherichia_coli_ampH	1-1127/1158	===============	0/0	97.32	77.46	card	AP012030.1:395554-396712	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin/penam
+SAMN13042171.fasta	contig00002	345289	346827	-	Klebsiella_pneumoniae_KpnH	1-1539/1539	===============	0/0	100.00	84.41	card	ASTU01000063.1:61249-62788	KpnH consists of ~511 residues resembles EmrB of E. coli and is probably a translocase in the KpnGH-TolC efflux protein in K. pneumoniae. Disruption of the pump components KpnG-KpnH signficantly decrease resistance to azithromycin ceftazidime ciprofloxacin ertapenem erythromycin gentamicin imipenem ticarcillin norfloxacin polymyxin-B piperacillin spectinomycin tobramycin and streptomycin.	isoniazid/lincosamide/benzalkonium_chloride/diaminopyrimidine/penem/bicyclomycin/antibacterial_free_fatty_acids/macrolide/penam/nucleoside/nitroimidazole/peptide/rhodamine/acridine_dye/oxazolidinone/cephalosporin/fluoroquinolone/phenicol/fosfomycin/rifamycin/carbapenem/aminoglycoside/tetracycline/glycylcycline
+SAMN13042171.fasta	contig00002	346843	348015	-	Klebsiella_pneumoniae_KpnG	1-1173/1173	===============	0/0	100.00	94.54	card	ACWO01000051.1:22093-23266	KpnG consists of ~390 residues and resembles EmrA of E. coli. Disruption of the pump components KpnG-KpnH signficantly decrease resistance to azithromycin ceftazidime ciprofloxacin ertapenem erythromycin gentamicin imipenem ticarcillin norfloxacin polymyxin-B piperacillin spectinomycin tobramycin and streptomycin	penam/macrolide/nitroimidazole/nucleoside/benzalkonium_chloride/lincosamide/isoniazid/bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/penem/fluoroquinolone/cephalosporin/acridine_dye/oxazolidinone/fosfomycin/phenicol/rhodamine/peptide/rifamycin/tetracycline/glycylcycline/aminoglycoside/carbapenem
+SAMN13042171.fasta	contig00002	348162	348671	-	emrR	1-510/531	===============	0/0	96.05	83.33	card	U00096.3:2810770-2811301	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	rifamycin/nitroimidazole/nucleoside/macrolide/penam/bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/lincosamide/isoniazid/benzalkonium_chloride/fosfomycin/glycylcycline/phenicol/cephalosporin/fluoroquinolone/oxazolidinone/acridine_dye/tetracycline/rhodamine/peptide
+SAMN13042171.fasta	contig00002	389327	392479	-	oqxB	1-3153/3153	===============	0/0	100.00	95.53	card	EU370913.1:47851-51004	RND efflux pump conferring resistance to fluoroquinolone	tetracycline/triclosan/acridine_dye/fluoroquinolone/penam/nitrofuran/macrolide/phenicol/monobactam/glycylcycline/aminocoumarin/aminoglycoside/carbapenem/diaminopyrimidine/antibacterial_free_fatty_acids
+SAMN13042171.fasta	contig00002	392503	393678	-	oqxA	1-1176/1176	===============	0/0	100.00	93.71	card	EU370913.1:46652-47828	RND efflux pump conferring resistance to fluoroquinolone	phenicol/monobactam/glycylcycline/penam/fluoroquinolone/nitrofuran/macrolide/tetracycline/triclosan/acridine_dye/antibacterial_free_fatty_acids/aminoglycoside/carbapenem/diaminopyrimidine/aminocoumarin
+SAMN13042171.fasta	contig00003	27739	29154	-	mdtK	1-1416/1425	========/======	2/2	99.30	76.71	card	CP014358.1:2161326-2162751	A multidrug and toxic compound extrusions (MATE) transporter conferring resistance to norfloxacin doxorubicin and acriflavine.	glycylcycline/fluoroquinolone/tetracycline/acridine_dye
+SAMN13042171.fasta	contig00003	144300	145294	+	mdtA	178-1172/1248	.=======/======	2/2	79.65	78.51	card	U00096:2154016-2155264	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	antibacterial_free_fatty_acids/aminoglycoside/diaminopyrimidine/carbapenem/aminocoumarin/phenicol/glycylcycline/monobactam/penam/fluoroquinolone/macrolide/acridine_dye/triclosan/tetracycline
+SAMN13042171.fasta	contig00003	145364	148486	+	mdtB	1-3123/3123	========/======	2/4	99.94	80.90	card	U00096:2155263-2158386	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin/aminoglycoside/diaminopyrimidine/carbapenem/antibacterial_free_fatty_acids/acridine_dye/tetracycline/triclosan/penam/fluoroquinolone/macrolide/phenicol/glycylcycline/monobactam
+SAMN13042171.fasta	contig00003	148487	151564	+	mdtC	1-3078/3078	===============	0/0	100.00	82.00	card	U00096:2158386-2161464	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	diaminopyrimidine/carbapenem/aminoglycoside/antibacterial_free_fatty_acids/aminocoumarin/glycylcycline/monobactam/phenicol/acridine_dye/triclosan/tetracycline/macrolide/fluoroquinolone/penam
+SAMN13042171.fasta	contig00003	152979	153244	+	baeS	2-267/1404	===............	0/0	18.95	80.45	card	AP009048:2165013-2166417	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin/carbapenem/diaminopyrimidine/aminoglycoside/antibacterial_free_fatty_acids/tetracycline/triclosan/acridine_dye/macrolide/fluoroquinolone/penam/monobactam/glycylcycline/phenicol
+SAMN13042171.fasta	contig00003	154462	155174	+	baeR	1-713/723	===============	0/0	98.62	82.61	card	AP009048.1:2166413-2167136	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	phenicol/monobactam/glycylcycline/tetracycline/triclosan/acridine_dye/penam/fluoroquinolone/macrolide/aminoglycoside/carbapenem/diaminopyrimidine/antibacterial_free_fatty_acids/aminocoumarin
+SAMN13042171.fasta	contig00003	277916	279555	-	yojI	1-1640/1644	========/======	6/6	99.57	75.65	card	U00096.3:2306972-2308616	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules.  The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide/nitroimidazole/rifamycin/pleuromutilin/penam/fluoroquinolone/cephalosporin/macrolide/tetracycline/acridine_dye
+SAMN13042171.fasta	contig00004	25617	26032	+	FosA5	1-416/420	===============	0/0	99.05	93.51	card	KP143090.1:1200-1620	fosA5 is a fosfomycin resistance gene isolated from clinical strain of Escherichia coli E265. It is susceptible to amikacin tetracycline and imipenem and resistant to sulphonamide cephalosporins gentamicin ciprofloxacin chloramphenicol and streptomycin	fosfomycin
+SAMN13042171.fasta	contig00006	173	577	-	H-NS	1-405/414	===============	0/0	97.83	87.16	card	BA000007.3:1737691-1738105	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/benzalkonium_chloride/isoniazid/lincosamide/nitroimidazole/rifamycin/nucleoside/penam/macrolide/aminoglycoside/carbapenem/rhodamine/cephamycin/aminocoumarin/peptide/fosfomycin/phenicol/glycylcycline/monobactam/fluoroquinolone/cephalosporin/acridine_dye/oxazolidinone/triclosan/tetracycline
+SAMN13042171.fasta	contig00007	21771	22687	-	pmrF	16-932/969	===============	0/0	94.63	76.77	card	U00096:2367071-2368040	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
+SAMN13042171.fasta	contig00008	29896	31020	-	Klebsiella_pneumoniae_OmpK37	1-1125/1125	===============	0/0	100.00	92.71	card	AJ011502.1:301-1426	Klebsiella pneumoniae outer membrane porin protein. Is preferentially detected in porin-deficient strains. Functional characterization of this new porin revealed a narrower pore than those of porins OmpK35 and OmpK36 which did not allow penetration by certain ##-lactams. Also when a resistant strain expresses porin OmpK37 is less susceptible to cefotaxime and cefoxitin than when it is expressing either OmpK36 or OmpK35.	cephalosporin/penam/cephamycin/monobactam/carbapenem/penem
+SAMN13042171.fasta	contig00008	175297	175659	+	Klebsiella_pneumoniae_KpnE	1-363/363	===============	0/0	100.00	88.43	card	AP006725.1:2483890-2484253	KpnE subunit of KpnEF resembles EbrAB from E. coli. Mutation in KpnEF resulted in increased susceptibility to cefepime ceftriaxon colistin erythromycin rifampin tetracycline and streptomycin as well as enhanced sensitivity toward sodium dodecyl sulfate deoxycholate dyes benzalkonium chloride chlorhexidine and triclosan	diaminopyrimidine/bicyclomycin/antibacterial_free_fatty_acids/benzalkonium_chloride/isoniazid/lincosamide/nucleoside/nitroimidazole/rifamycin/penam/macrolide/aminoglycoside/peptide/rhodamine/phenicol/glycylcycline/fosfomycin/oxazolidinone/acridine_dye/tetracycline/fluoroquinolone/cephalosporin
+SAMN13042171.fasta	contig00008	175646	175975	+	Klebsiella_pneumoniae_KpnF	1-330/330	===============	0/0	100.00	92.42	card	AP006725.1:2484239-2484569	KpnF subunit of KpnEF resembles EbrAB from E. coli. Mutation in KpnEF resulted in increased susceptibility to cefepime ceftriaxon colistin erythromycin rifampin tetracycline and streptomycin as well as enhanced sensitivity toward sodium dodecyl sulfate deoxycholate dyes benzalkonium chloride chlorhexidine and triclosan.	fosfomycin/glycylcycline/phenicol/cephalosporin/fluoroquinolone/acridine_dye/oxazolidinone/tetracycline/aminoglycoside/rhodamine/peptide/rifamycin/nitroimidazole/nucleoside/macrolide/penam/bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/isoniazid/lincosamide/benzalkonium_chloride
+SAMN13042171.fasta	contig00008	217869	218728	-	OKP-B-18	1-860/861	===============	0/0	99.88	99.53	card	AM850920:41-902	OKP-B-18 is a beta-lactamase found in Klebsiella pneumoniae	cephalosporin/penam
+SAMN13042171.fasta	contig00009	93196	94580	+	tolC	1-1403/1488	========/======	2/18	93.08	78.40	card	FJ768952:1-1489	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	rifamycin/triclosan/tetracycline/glycylcycline/cephamycin/carbapenem/aminoglycoside/macrolide/penam/pleuromutilin/nitroimidazole/nucleoside/isoniazid/lincosamide/benzalkonium_chloride/antibacterial_free_fatty_acids/bicyclomycin/penem/diaminopyrimidine/cephalosporin/fluoroquinolone/oxazolidinone/acridine_dye/fosfomycin/monobactam/phenicol/rhodamine/peptide/aminocoumarin
+SAMN13042171.fasta	contig00009	108077	108898	-	bacA	1-822/822	===============	0/0	100.00	80.53	card	U00096.3:3203310-3204132	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
+SAMN13042171.fasta	contig00012	114632	116380	-	msbA	1-1749/1749	===============	0/0	100.00	80.96	card	U00096.3:966621-968370	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	peptide/rifamycin/pleuromutilin/nitroimidazole/tetracycline/acridine_dye/cephalosporin/macrolide/penam/fluoroquinolone
+SAMN13042171.fasta	contig00012	155728	155882	-	macB	1586-1740/1935	............==.	0/0	8.01	76.13	card	AY768532:1-1936	MacB is an ATP-binding cassette (ABC) transporter that exports macrolides with 14- or 15- membered lactones. It forms an antibiotic efflux complex with MacA and TolC. macB corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	macrolide/cephalosporin/fluoroquinolone/penam/acridine_dye/tetracycline/pleuromutilin/rifamycin/nitroimidazole/peptide
+SAMN13042171.fasta	contig00015	140084	143160	+	acrF	1-3080/3105	========/======	7/9	99.00	76.74	card	U00096:3415033-3418138	AcrF is a inner membrane transporter similar to AcrB.	aminoglycoside/carbapenem/diaminopyrimidine/antibacterial_free_fatty_acids/aminocoumarin/cephamycin/phenicol/monobactam/glycylcycline/tetracycline/triclosan/acridine_dye/fluoroquinolone/penam/cephalosporin/macrolide
+SAMN13042171.fasta	contig00016	114383	115015	-	CRP	1-633/633	===============	0/0	100.00	87.36	card	AP009048.1:4153664-4154297	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	tetracycline/triclosan/acridine_dye/fluoroquinolone/penam/macrolide/phenicol/monobactam/glycylcycline/aminocoumarin/aminoglycoside/carbapenem/diaminopyrimidine/antibacterial_free_fatty_acids
+SAMN13042171.fasta	contig00018	59247	60613	-	cpxA	1-1367/1374	===============	0/0	99.49	81.71	card	BA000007.3:4903689-4905063	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	acridine_dye/tetracycline/triclosan/macrolide/fluoroquinolone/penam/glycylcycline/monobactam/phenicol/aminocoumarin/diaminopyrimidine/carbapenem/aminoglycoside/antibacterial_free_fatty_acids
+SAMN13042171.fasta	contig00019	55611	58724	+	acrD	1-3114/3114	========/======	2/2	99.97	80.58	card	AP009048.1:2586251-2589365	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminocoumarin/aminoglycoside/carbapenem/diaminopyrimidine/antibacterial_free_fatty_acids/tetracycline/triclosan/acridine_dye/fluoroquinolone/penam/macrolide/phenicol/monobactam/glycylcycline
+SAMN13042171.fasta	contig00024	52994	54169	+	mdtH	1-1176/1209	===============	0/0	97.27	77.04	card	U00096:1124118-1125327	Multidrug resistance protein MdtH	nitroimidazole/rifamycin/nucleoside/penam/macrolide/antibacterial_free_fatty_acids/bicyclomycin/diaminopyrimidine/benzalkonium_chloride/isoniazid/lincosamide/fosfomycin/phenicol/glycylcycline/fluoroquinolone/cephalosporin/tetracycline/acridine_dye/oxazolidinone/rhodamine/peptide
+SAMN13042171.fasta	contig00024	60718	61881	+	mdtG	18-1181/1227	========/======	3/8	94.54	76.03	card	CP000800.1:1191728-1192955	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	macrolide/penam/rifamycin/nitroimidazole/nucleoside/isoniazid/lincosamide/benzalkonium_chloride/bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/cephalosporin/fluoroquinolone/acridine_dye/oxazolidinone/tetracycline/fosfomycin/glycylcycline/phenicol/rhodamine/peptide
+SAMN13042171.fasta	contig00025	3007	3375	-	marA	1-369/384	===============	0/0	96.09	81.57	card	AP009048.1:1621288-1621672	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	antibacterial_free_fatty_acids/penem/diaminopyrimidine/macrolide/penam/rifamycin/cephamycin/aminocoumarin/carbapenem/aminoglycoside/cephalosporin/fluoroquinolone/tetracycline/triclosan/acridine_dye/monobactam/glycylcycline/phenicol
+SAMN13042171.fasta	contig00028	4483	5688	+	Escherichia_coli_mdfA	1-1206/1233	========/======	2/2	97.73	78.21	card	JQ394987:1-1234	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	antibacterial_free_fatty_acids/bicyclomycin/diaminopyrimidine/isoniazid/lincosamide/benzalkonium_chloride/rifamycin/nitroimidazole/nucleoside/macrolide/penam/rhodamine/peptide/fosfomycin/glycylcycline/phenicol/cephalosporin/fluoroquinolone/tetracycline/acridine_dye/oxazolidinone
+SAMN13042171.fasta	contig00030	26098	26477	-	Nocardia_rifampin_resistant_beta-subunit_of_RNA_polymerase_(rpoB2)	2980-3359/3489	......../...===	2/2	10.86	76.11	card	AP006618.1:4835200-4838689	Due to gene duplication the genomes of Nocardia species include both rifampin-sensitive beta-subunit of RNA polymerase (rpoB) and rifampin-resistant beta-subunit of RNA polymerase (rpoB2) genes with ~88% similarity between the two gene products. Expression of the rpoB2 variant results in replacement of rifampin sensitivity with rifampin resistance.	rifamycin
+SAMN13042171.fasta	contig00030	26758	26924	-	Nocardia_rifampin_resistant_beta-subunit_of_RNA_polymerase_(rpoB2)	2605-2771/3489	...........=...	0/0	4.79	75.45	card	AP006618.1:4835200-4838689	Due to gene duplication the genomes of Nocardia species include both rifampin-sensitive beta-subunit of RNA polymerase (rpoB) and rifampin-resistant beta-subunit of RNA polymerase (rpoB2) genes with ~88% similarity between the two gene products. Expression of the rpoB2 variant results in replacement of rifampin sensitivity with rifampin resistance.	rifamycin
+SAMN13042171.fasta	contig00035	7853	8713	-	TEM-150	1-861/861	===============	0/0	100.00	99.88	card	AM183304:209-1070	TEM-150 is a beta-lactamase found in Enterobacter spp. E. coli and Klebsiella pneumoniae.	penem/monobactam/cephalosporin/penam
+SAMN13042171.fasta	contig00035	9413	10237	-	OXA-9	1-825/825	===============	0/0	100.00	100.00	card	M55547:1-826	OXA-9 is a beta-lactamase found in Klebsiella pneumoniae.	cephalosporin/penam
+SAMN13042171.fasta	contig00035	10297	11098	-	ANT(3'')-IIa	168-972/972	..======/======	1/3	82.51	99.25	card	X02340.1:223-1195	ANT(3'')-IIa is a aminoglycoside nucleotidyltransferase identified in Acinetobacter spp. via horizontal gene transfer mechanisms.	aminoglycoside
+SAMN13042171.fasta	contig00035	10991	11741	-	AAC(6')-Ib7	234-980/980	...=====/======	2/4	76.22	96.67	card	Y11946.1:1-981	AAC(6')-Ib7 is a plasmid-encoded aminoglycoside acetyltransferase in E. cloacae and C. freundii	aminoglycoside
+SAMN13042171.fasta	contig00035	14582	15457	+	CTX-M-15	1-876/876	===============	0/0	100.00	100.00	card	AY044436:1436-2312	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
+SAMN13042171.fasta	contig00035	20098	20754	+	QnrS1	1-657/657	===============	0/0	100.00	100.00	card	DQ485529.1:1-658	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
+SAMN13042171.fasta	contig00063	2129	2494	-	determinant_of_bleomycin_resistance	1-366/366	===============	0/0	100.00	100.00	card	KC503911.1:9884-10250	A novel bleomycin resistance protein encoded by a metallo-beta-lactamase-associated ble gene. Expression of BRP(MBL) confers resistance to bleomycin and bleomycin-like antibiotics in Enterobacteriaceae and Acinetobacter where it is co-expressed with an MBL and controlled by the same promoter region.	glycopeptide
+SAMN13042171.fasta	contig00063	2498	3310	-	NDM-1	1-813/813	===============	0/0	100.00	100.00	card	FN396876:2407-3220	NDM-1 is a metallo-beta-lactamase isolated from Klebsiella pneumoniae with nearly complete resistance to all beta-lactam antibiotics.	cephalosporin/penam/carbapenem/cephamycin

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SAMN13042171_abricate_report_screened.tsv	Thu Oct 31 15:43:15 2019 -0400
@@ -0,0 +1,2 @@
+#FILE	SEQUENCE	START	END	STRAND	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION	PRODUCT	RESISTANCE
+SAMN13042171.fasta	contig00063	2498	3310	-	NDM-1	1-813/813	===============	0/0	100.00	100.00	card	FN396876:2407-3220	NDM-1 is a metallo-beta-lactamase isolated from Klebsiella pneumoniae with nearly complete resistance to all beta-lactam antibiotics.	cephalosporin/penam/carbapenem/cephamycin

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SAMN13042171_gene_detection_status.tsv	Thu Oct 31 15:43:15 2019 -0400
@@ -0,0 +1,4 @@
+gene_name	detected
+KPC	False
+NDM	True
+OXA-48	False

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/abricate_report_screening_files.loc	Thu Oct 31 15:43:15 2019 -0400
@@ -0,0 +1,6 @@
+# Tab separated with three columns:
+# - value (Galaxy records this in the Galaxy DB)
+# - name (Galaxy shows this in the UI)
+# - path (folder name containing the Kraken DB)
+#
+test_entry	"Test Screening File"	${__HERE__}/screening_file.tsv
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/screening_file.tsv	Thu Oct 31 15:43:15 2019 -0400
@@ -0,0 +1,4 @@
+gene_name	regex
+KPC	KPC
+NDM	NDM
+OXA-48	OXA\-48

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Thu Oct 31 15:43:15 2019 -0400
@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<tables>
+    <!-- Locations of abricate report screening files in the required format -->
+    <table name="abricate_report_screening_files" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/abricate_report_screening_files.loc" />
+    </table>
+</tables>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Thu Oct 31 15:43:15 2019 -0400
@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<tables>
+    <!-- Locations of abricate report screening files in the required format -->
+    <table name="abricate_report_screening_files" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__HERE__}/test-data/abricate_report_screening_files.loc" />
+    </table>
+</tables>