# HG changeset patch
# User iuc
# Date 1587595446 14400
# Node ID b734db30557848cc086c5ded2d8120dbbb7656b3
# Parent  4efdca267d516170ae51995392e624b15f6c7c3f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit fc114fbebd3b866c33d2ad95b028cb719651689a"

diff -r 4efdca267d51 -r b734db305578 abricate.xml
--- a/abricate.xml	Tue Oct 29 19:24:59 2019 -0400
+++ b/abricate.xml	Wed Apr 22 18:44:06 2020 -0400
@@ -20,12 +20,15 @@
         #set $sample_name = re.sub('[^\w\-_\.]', '_', $file_input.element_identifier)
 
         ln -sf '${file_input}' ${sample_name} &&
-        
+
         abricate ${sample_name}
         $adv.no_header
         #if $adv.min_dna_id
             --minid=$adv.min_dna_id
         #end if
+        #if $adv.min_cov
+            --mincov=$adv.min_cov
+        #end if
         --db=$adv.db
         > '$report'
     ]]></command>
@@ -41,9 +44,12 @@
                 <option value="resfinder" selected="true">Resfinder</option>
                 <option value="plasmidfinder">PlasmidFinder</option>
                 <option value="vfdb">VFDB</option>
+                <option value="megares">megares</option>
+                <option value="ecoli_vf">Ecoli_VF</option>
             </param>
             <param name="no_header" argument="--noheader" type="boolean" truevalue="--noheader" falsevalue="" label="Suppress header" help="Suppress output file's column headings" />
-            <param name="min_dna_id" argument="--minid" type="float" value="75" min="0" max="100" optional="true" label="Minimum DNA identity" />
+            <param name="min_dna_id" argument="--minid" type="float" value="80" min="0" max="100" optional="true" label="Minimum DNA %identity" />
+            <param name="min_cov" argument="--mincov" type="float" value="80" min="0" max="100" optional="true" label="Minimum DNA %coverage" />
         </section>
     </inputs>
 
@@ -78,14 +84,28 @@
             <output name="report" ftype="tabular" file="output_db-card.txt" compare="contains"/>
         </test>
 
-        <!-- Advanced test 4 - Min DNA ID 100 -->
+        <!-- Advanced test 4 - Changed DB to megares -->
+        <test>
+            <param name="file_input" value="MRSA0252.fna"/>
+            <param name="db" value="megares"/>
+            <output name="report" ftype="tabular" file="output_db-megares.txt" compare="contains"/>
+        </test>
+
+        <!-- Advanced test 5 - Min DNA ID 100 -->
         <test>
             <param name="file_input" value="MRSA0252.fna"/>
             <param name="min_dna_id" value="100"/>
             <output name="report" ftype="tabular" file="output_minid100.txt" compare="contains"/>
         </test>
 
-        <!-- Filetype test 5 - input a gbk -->
+        <!-- Advanced test 6 - Min Coverage 100 -->
+        <test>
+            <param name="file_input" value="MRSA0252.fna"/>
+            <param name="min_cov" value="100"/>
+            <output name="report" ftype="tabular" file="output_mincov100.txt" compare="contains"/>
+        </test>
+
+        <!-- Filetype test 7 - input a gbk -->
         <test>
             <param name="file_input" value="test.gbk"/>
             <output name="report" ftype="tabular" file="output_gbk.txt" compare="contains"/>
diff -r 4efdca267d51 -r b734db305578 macros.xml
--- a/macros.xml	Tue Oct 29 19:24:59 2019 -0400
+++ b/macros.xml	Wed Apr 22 18:44:06 2020 -0400
@@ -10,7 +10,7 @@
         <version_command><![CDATA[abricate --version]]></version_command>
     </xml>
 
-    <token name="@VERSION@">0.9.8</token>
+    <token name="@VERSION@">1.0.1</token>
 
     <xml name="citations">
       <citations>
diff -r 4efdca267d51 -r b734db305578 test-data/output_db-card.txt
--- a/test-data/output_db-card.txt	Tue Oct 29 19:24:59 2019 -0400
+++ b/test-data/output_db-card.txt	Wed Apr 22 18:44:06 2020 -0400
@@ -1,18 +1,17 @@
 #FILE	SEQUENCE	START	END	STRAND	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION	PRODUCT	RESISTANCE
-MRSA0252.fna	gi|49482253|ref|NC_002952.2|	40786	41547	-	ANT(4')-Ib	1-762/762	===============	0/0	100.00	100.00	card	GQ900432.1:26738-27500	Kanamycin nucleotidyltransferase sequence from Staphylococcus aureus plasmid. Confers resistance to kanamycin neomycin and other aminoglycosides	aminoglycoside
-MRSA0252.fna	gi|49482253|ref|NC_002952.2|	44919	46925	-	mecA	1-2007/2007	===============	0/0	100.00	99.90	card	KC243783:1-2008	A foreign PBP2a acquired by lateral gene transfer that able to perform peptidoglycan synthesis in the presence of beta-lactams.	penam
-MRSA0252.fna	gi|49482253|ref|NC_002952.2|	47025	48782	+	mecR1	1-1758/1758	===============	0/0	100.00	99.94	card	CP000703.1:40849-42607	mecR1 is a transmembrane spanning and signal transducing protein which in response to interaction with beta-lactam antibiotics results in upregulation of the mecA/mecR1/mecI operon.	penam
-MRSA0252.fna	gi|49482253|ref|NC_002952.2|	48782	49153	+	mecI	1-372/372	===============	0/0	100.00	99.73	card	BA000018.3:48894-49266	mecI acts as a repressor of transcription of the mecA/mecR1/mecI operon.	penam
-MRSA0252.fna	gi|49482253|ref|NC_002952.2|	55890	56621	+	ErmA	1-732/732	===============	0/0	100.00	100.00	card	X03216.1:4551-5283	ErmA confers the MLSb phenotype. Similar to ErmC Expression of ErmA is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmA.	streptogramin/macrolide/lincosamide
-MRSA0252.fna	gi|49482253|ref|NC_002952.2|	152865	154217	+	tet(38)	1-1353/1353	===============	0/0	100.00	98.52	card	AY825285:1-1354	Tet38 is a tetracycline efflux pump found in the Gram-positive Staphylococcus aureus. It is regulated by mgrA which also regulates NorB.	benzalkonium_chloride/isoniazid/lincosamide/diaminopyrimidine/antibacterial_free_fatty_acids/bicyclomycin/penam/macrolide/nucleoside/nitroimidazole/rifamycin/peptide/rhodamine/tetracycline/oxazolidinone/acridine_dye/fluoroquinolone/cephalosporin/phenicol/glycylcycline/fosfomycin
-MRSA0252.fna	gi|49482253|ref|NC_002952.2|	376045	376464	+	mepR	1-420/420	===============	0/0	100.00	99.05	card	BA000017.4:379932-380352	MepR is an upstream repressor of MepA in Staphylococcus aureus. It is part of the mepRAB operon.	glycylcycline/acridine_dye/tetracycline/fluoroquinolone
-MRSA0252.fna	gi|49482253|ref|NC_002952.2|	376571	377926	+	mepA	1-1356/1356	===============	0/0	100.00	98.53	card	AY661734.1:840-2196	MepA is an efflux protein regulated by MepR and part of the MepRAB cluster. Its presence in Staphylococcus aureus led to multidrug resistance while it has also been shown to decrease tigecycline susceptibility.	glycylcycline/acridine_dye/tetracycline/fluoroquinolone
-MRSA0252.fna	gi|49482253|ref|NC_002952.2|	774312	774755	-	mgrA	1-444/444	===============	0/0	100.00	99.78	card	BA000018.3:735417-735861	MgrA also known as NorR is a regulator for norA norB and tet38. It is a positive regulator for norA expression but is a direct repressor for norB and an indirect repressor of tet38.	antibacterial_free_fatty_acids/bicyclomycin/diaminopyrimidine/isoniazid/lincosamide/benzalkonium_chloride/rifamycin/pleuromutilin/nitroimidazole/nucleoside/macrolide/penam/rhodamine/peptide/fosfomycin/glycylcycline/phenicol/cephalosporin/fluoroquinolone/tetracycline/acridine_dye/oxazolidinone
-MRSA0252.fna	gi|49482253|ref|NC_002952.2|	782414	783579	+	Staphylococcus_aureus_norA	1-1166/1167	===============	0/0	99.91	91.51	card	D90119.1:478-1645	NorA gene cloned from Staphylococcus aureus conferred relatively high resistance to hydrophilic quinolones such as norfloxacin enoxacin ofloxacin and ciprofloxacin in S. aureus and Escherichia coli. Had low or no resistance at all to hydrophobic ones such as nalidixic acid oxolinic acid and sparfloxacin in S. aureus and Escherichia coli.	macrolide/penam/nucleoside/rifamycin/nitroimidazole/isoniazid/lincosamide/benzalkonium_chloride/diaminopyrimidine/antibacterial_free_fatty_acids/bicyclomycin/tetracycline/oxazolidinone/acridine_dye/cephalosporin/fluoroquinolone/glycylcycline/phenicol/fosfomycin/peptide/rhodamine
-MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1486310	1487665	-	arlS	1-1356/1356	===============	0/0	100.00	98.38	card	CP000253.1:1360281-1361637	ArlS is a protein histidine kinase that phosphorylates ArlR a promoter for norA expression.	antibacterial_free_fatty_acids/bicyclomycin/diaminopyrimidine/benzalkonium_chloride/isoniazid/lincosamide/nitroimidazole/rifamycin/nucleoside/penam/macrolide/rhodamine/peptide/fosfomycin/phenicol/glycylcycline/fluoroquinolone/cephalosporin/tetracycline/oxazolidinone/acridine_dye
-MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1487662	1488321	-	arlR	1-660/660	===============	0/0	100.00	99.09	card	NC_009641.1:1461589-1462249	ArlR is a response regulator that binds to the norA promoter to activate expression. ArlR must first be phosphorylated by ArlS.	fosfomycin/phenicol/glycylcycline/fluoroquinolone/cephalosporin/tetracycline/acridine_dye/oxazolidinone/rhodamine/peptide/nitroimidazole/rifamycin/nucleoside/penam/macrolide/antibacterial_free_fatty_acids/bicyclomycin/diaminopyrimidine/benzalkonium_chloride/lincosamide/isoniazid
-MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1796513	1797244	+	ErmA	1-732/732	===============	0/0	100.00	100.00	card	X03216.1:4551-5283	ErmA confers the MLSb phenotype. Similar to ErmC Expression of ErmA is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmA.	streptogramin/macrolide/lincosamide
-MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1913827	1914672	+	PC1_beta-lactamase_(blaZ)	1-846/846	===============	0/0	100.00	97.16	card	CP000732.1:9683-10529	The blaZ beta-lactamase is found in Bacillus subtilis and Staphylococcus aureus.	penam
-MRSA0252.fna	gi|49482253|ref|NC_002952.2|	2338959	2340402	-	Staphylococcys_aureus_LmrS	1-1443/1443	========/======	1/1	100.00	91.41	card	CP000046.1:2235375-2236818	MFS transporters are secondary active transporters with single-polypeptide chains containing 400-600 amino acids that transport small solutes across the membrane by using electrochemical gradients. LmrS has 14 transmembrane helices and when expressed in E. coli is capable of extruding a variety of antibiotics inclinding linezolid trimethoprim florfenicol chlorampheniocol erythromycin streptomycin kanamycin and fusidic acid	nucleoside/rifamycin/nitroimidazole/macrolide/penam/diaminopyrimidine/bicyclomycin/antibacterial_free_fatty_acids/isoniazid/lincosamide/benzalkonium_chloride/glycylcycline/phenicol/fosfomycin/acridine_dye/oxazolidinone/tetracycline/cephalosporin/fluoroquinolone/aminoglycoside/peptide/rhodamine
-MRSA0252.fna	gi|49482253|ref|NC_002952.2|	2488459	2488878	+	Staphylococcus_aureus_FosB	1-420/420	===============	0/0	100.00	98.81	card	AHLO01000073.1:63139-63559	The Bacillus subtilis fosB gene encodes a fosfomycin resistance protein	fosfomycin
-MRSA0252.fna	gi|49482253|ref|NC_002952.2|	2622988	2624175	-	DHA-1	1-1188/1188	===============	0/0	100.00	99.16	card	BA000018.3:2517801-2518989	DHA-1 is a class C beta-lactamase found in Morganella morganii and Salmonella enterica	cephamycin/cephalosporin
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	40786	41547	-	ANT(4')-Ib	1-762/762	===============	0/0	100.00	100.00	card	GQ900432.1:27499-26737	Kanamycin nucleotidyltransferase sequence from Staphylococcus aureus plasmid. Confers resistance to kanamycin neomycin and other aminoglycosides	aminoglycoside
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	44919	46925	-	mecA	1-2007/2007	===============	0/0	100.00	99.90	card	KC243783:0-2007	A foreign PBP2a acquired by lateral gene transfer that able to perform peptidoglycan synthesis in the presence of beta-lactams.	penam
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	47025	48782	+	mecR1	1-1758/1758	===============	0/0	100.00	99.94	card	CP000703.1:40848-42606	mecR1 is a transmembrane spanning and signal transducing protein which in response to interaction with beta-lactam antibiotics results in upregulation of the mecA/mecR1/mecI operon.	penam
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	48782	49153	+	mecI	1-372/372	===============	0/0	100.00	99.73	card	BA000018.3:48893-49265	mecI acts as a repressor of transcription of the mecA/mecR1/mecI operon.	penam
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	55890	56621	+	ErmA	1-732/732	===============	0/0	100.00	100.00	card	X03216.1:5282-4550	ErmA confers the MLSb phenotype. Similar to ErmC Expression of ErmA is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmA.	lincosamide;macrolide;streptogramin
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	152865	154217	+	tet(38)	1-1353/1353	===============	0/0	100.00	98.52	card	AY825285:0-1353	Tet38 is a tetracycline efflux pump found in the Gram-positive Staphylococcus aureus. It is regulated by mgrA which also regulates NorB.	tetracycline
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	376045	376464	+	mepR	1-420/420	===============	0/0	100.00	99.05	card	BA000017.4:379931-380351	MepR is an upstream repressor of MepA in Staphylococcus aureus. It is part of the mepRAB operon.	glycylcycline;tetracycline
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	376571	377926	+	mepA	1-1356/1356	===============	0/0	100.00	98.53	card	AY661734.1:839-2195	MepA is an efflux protein regulated by MepR and part of the MepRAB cluster. Its presence in Staphylococcus aureus led to multidrug resistance while it has also been shown to decrease tigecycline susceptibility.	glycylcycline;tetracycline
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	774312	774755	-	mgrA	1-444/444	===============	0/0	100.00	99.78	card	BA000018.3:735860-735416	MgrA also known as NorR is a regulator for norA norB and tet38. It is a positive regulator for norA expression but is a direct repressor for norB and an indirect repressor of tet38.	acridine_dye;cephalosporin;fluoroquinolone;penam;peptide;tetracycline
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	782414	783579	+	Staphylococcus_aureus_norA	1-1166/1167	===============	0/0	99.91	91.51	card	D90119.1:477-1644	NorA gene cloned from Staphylococcus aureus conferred relatively high resistance to hydrophilic quinolones such as norfloxacin enoxacin ofloxacin and ciprofloxacin in S. aureus and Escherichia coli. Had low or no resistance at all to hydrophobic ones such as nalidixic acid oxolinic acid and sparfloxacin in S. aureus and Escherichia coli.	fluoroquinolone
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1486310	1487665	-	arlS	1-1356/1356	===============	0/0	100.00	98.38	card	CP000253.1:1361636-1360280	ArlS is a protein histidine kinase that phosphorylates ArlR a promoter for norA expression.	acridine_dye;fluoroquinolone
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1487662	1488321	-	arlR	1-660/660	===============	0/0	100.00	99.09	card	CP023390.1:1462248-1461588	ArlR is a response regulator that binds to the norA promoter to activate expression. ArlR must first be phosphorylated by ArlS.	acridine_dye;fluoroquinolone
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1796513	1797244	+	ErmA	1-732/732	===============	0/0	100.00	100.00	card	X03216.1:5282-4550	ErmA confers the MLSb phenotype. Similar to ErmC Expression of ErmA is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmA.	lincosamide;macrolide;streptogramin
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1913827	1914672	+	PC1_beta-lactamase_(blaZ)	1-846/846	===============	0/0	100.00	97.16	card	CP000732.1:10528-9682	The blaZ beta-lactamase is found in Bacillus subtilis and Staphylococcus aureus.	penam
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	2338959	2340402	-	Staphylococcys_aureus_LmrS	1-1443/1443	========/======	1/1	100.00	91.41	card	CP000046.1:2236817-2235374	MFS transporters are secondary active transporters with single-polypeptide chains containing 400-600 amino acids that transport small solutes across the membrane by using electrochemical gradients. LmrS has 14 transmembrane helices and when expressed in E. coli is capable of extruding a variety of antibiotics inclinding linezolid trimethoprim florfenicol chlorampheniocol erythromycin streptomycin kanamycin and fusidic acid	aminoglycoside;diaminopyrimidine;macrolide;oxazolidinone;phenicol
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	2488459	2488878	+	Staphylococcus_aureus_FosB	1-420/420	===============	0/0	100.00	98.81	card	AHLO01000073.1:63138-63558	The Bacillus subtilis fosB gene encodes a fosfomycin resistance protein	fosfomycin
diff -r 4efdca267d51 -r b734db305578 test-data/output_db-megares.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_db-megares.txt	Wed Apr 22 18:44:06 2020 -0400
@@ -0,0 +1,28 @@
+#FILE	SEQUENCE	START	END	STRAND	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION	PRODUCT	RESISTANCE
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	33660	34139	+	RLMH	1-480/480	===============	0/0	100.00	99.17	megares	MEG_6058	Drugs:MLS:23S_rRNA_methyltransferases:RLMH	
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	40165	40569	-	BLE	1-405/405	===============	0/0	100.00	100.00	megares	MEG_1460	Drugs:Glycopeptides:Bleomycin_resistance_protein:BLE	
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	40786	41556	-	ANT4-PRIME	1-771/771	===============	0/0	100.00	99.87	megares	MEG_978	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT4-PRIME	
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	44919	46928	-	MECA	1-2010/2010	===============	0/0	100.00	100.00	megares	MEG_3785	Drugs:betalactams:Penicillin_binding_protein:MECA	
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	47025	48782	+	MECA	1-1758/1758	===============	0/0	100.00	100.00	megares	MEG_3786	Drugs:betalactams:Penicillin_binding_protein:MECA	
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	48782	49153	+	MECI	1-372/372	===============	0/0	100.00	99.73	megares	MEG_3804	Drugs:betalactams:Penicillin_binding_protein_regulator:MECI	
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	55890	56621	+	ERMA	1-732/732	===============	0/0	100.00	100.00	megares	MEG_2785	Drugs:MLS:23S_rRNA_methyltransferases:ERMA	
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	56747	57529	-	ANT3-DPRIME	1-783/783	===============	0/0	100.00	100.00	megares	MEG_925	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	152865	154217	+	TET38	1-1353/1353	===============	0/0	100.00	100.00	megares	MEG_6981	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TET38	
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	376045	376464	+	MEPR	1-420/420	===============	0/0	100.00	99.05	megares	MEG_3836	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_regulator:MEPR	
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	376556	377926	+	MEPA	1-1371/1371	===============	0/0	100.00	98.54	megares	MEG_3834	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MEPA	
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	378032	378472	+	MEPB	1-441/441	===============	0/0	100.00	88.89	megares	MEG_3835	Drugs:Multi-drug_resistance:Multi-drug_MATE_efflux_pump:MEPB	
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	765853	766296	+	AAC3	1-444/444	===============	0/0	100.00	100.00	megares	MEG_47	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	774312	774755	-	MGRA	1-444/444	===============	0/0	100.00	99.78	megares	MEG_3943	Drugs:Multi-drug_resistance:MDR_regulator:MGRA	
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	782414	783580	+	NORA	1-1167/1167	===============	0/0	100.00	91.69	megares	MEG_4209	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:NORA	
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1486310	1487665	-	ARLS	1-1356/1356	===============	0/0	100.00	98.38	megares	MEG_1118	Drugs:Multi-drug_resistance:MDR_regulator:ARLS	
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1487662	1488321	-	ARLR	1-660/660	===============	0/0	100.00	100.00	megares	MEG_1114	Drugs:Multi-drug_resistance:MDR_regulator:ARLR	
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1535528	1536919	-	NORB	1-1392/1392	===============	0/0	100.00	98.20	megares	MEG_4210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:NORB	
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1796513	1797244	+	ERMA	1-732/732	===============	0/0	100.00	100.00	megares	MEG_2785	Drugs:MLS:23S_rRNA_methyltransferases:ERMA	
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1797370	1798152	-	ANT3-DPRIME	1-783/783	===============	0/0	100.00	100.00	megares	MEG_925	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1911593	1911973	-	BLAI	1-381/381	===============	0/0	100.00	100.00	megares	MEG_1287	Drugs:betalactams:Penicillin_binding_protein_regulator:BLAI	
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1911963	1913720	-	BLAR	1-1758/1758	===============	0/0	100.00	99.83	megares	MEG_1302	Drugs:betalactams:Penicillin_binding_protein_regulator:BLAR	
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1913785	1914672	+	BLAZ	1-888/888	===============	0/0	100.00	99.66	megares	MEG_1408	Drugs:betalactams:Class_A_betalactamases:BLAZ	
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1915805	1916605	-	APH3-PRIME	1-801/801	===============	0/0	100.00	99.00	megares	MEG_1060	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-PRIME	
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	2338959	2340402	-	LMRS	1-1443/1443	========/======	1/1	100.00	91.41	megares	MEG_3599	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:LMRS	
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	2488459	2488878	+	FOSB	1-420/420	===============	0/0	100.00	98.81	megares	MEG_3009	Drugs:Fosfomycin:Fosfomycin_thiol_transferases:FOSB	
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	2622988	2624175	-	DHAP	1-1188/1188	===============	0/0	100.00	99.16	megares	MEG_2614	Drugs:Phenicol:Phenicol_resistance_MFS_efflux_pumps:DHAP	
diff -r 4efdca267d51 -r b734db305578 test-data/output_list.txt
--- a/test-data/output_list.txt	Tue Oct 29 19:24:59 2019 -0400
+++ b/test-data/output_list.txt	Wed Apr 22 18:44:06 2020 -0400
@@ -1,9 +1,10 @@
 DATABASE	SEQUENCES	DBTYPE	DATE
-ncbi	5029	nucl	2019-Sep-10
-resfinder	3077	nucl	2019-Sep-10
-card	2594	nucl	2019-Sep-10
-vfdb	2597	nucl	2019-Sep-10
-argannot	2223	nucl	2019-Sep-10
-plasmidfinder	460	nucl	2019-Sep-10
-ecoli_vf	2701	nucl	2019-Sep-10
-ecoh	597	nucl	2019-Sep-10
+ecoh	597	nucl	2020-Apr-19
+vfdb	2597	nucl	2020-Apr-19
+resfinder	3077	nucl	2020-Apr-19
+argannot	2223	nucl	2020-Apr-19
+card	2631	nucl	2020-Apr-19
+ncbi	5386	nucl	2020-Apr-19
+plasmidfinder	460	nucl	2020-Apr-19
+megares	6635	nucl	2020-Apr-19
+ecoli_vf	2701	nucl	2020-Apr-19
diff -r 4efdca267d51 -r b734db305578 test-data/output_mincov100.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_mincov100.txt	Wed Apr 22 18:44:06 2020 -0400
@@ -0,0 +1,8 @@
+#FILE	SEQUENCE	START	END	STRAND	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION	PRODUCT	RESISTANCE
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	40786	41556	-	aadD_1	1-771/771	===============	0/0	100.00	99.74	resfinder	AF181950	aadD	Amikacin;Tobramycin
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	44919	46925	-	mecA_6	1-2007/2007	===============	0/0	100.00	100.00	resfinder	BX571856	mecA	Amoxicillin;Amoxicillin+Clavulanic_acid;Ampicillin;Ampicillin+Clavulanic_acid;Cefepime;Cefixime;Cefotaxime;Cefoxitin;Ceftazidime;Ertapenem;Imipenem;Meropenem;Piperacillin;Piperacillin+Tazobactam
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	55890	56621	+	erm(A)_1	1-732/732	===============	0/0	100.00	100.00	resfinder	X03216	erm(A)	Erythromycin;Lincomycin;Clindamycin;Quinupristin;Pristinamycin_IA;Virginiamycin_S
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	56747	57529	-	ant(9)-Ia_1	1-783/783	===============	0/0	100.00	100.00	resfinder	X02588	ant(9)-Ia	
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1796513	1797244	+	erm(A)_1	1-732/732	===============	0/0	100.00	100.00	resfinder	X03216	erm(A)	Erythromycin;Lincomycin;Clindamycin;Quinupristin;Pristinamycin_IA;Virginiamycin_S
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1797370	1798152	-	ant(9)-Ia_1	1-783/783	===============	0/0	100.00	100.00	resfinder	X02588	ant(9)-Ia	
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1913785	1914672	+	blaZ_78	1-888/888	===============	0/0	100.00	99.66	resfinder	KU607301	blaZ	Amoxicillin;Ampicillin;Penicillin;Piperacillin
diff -r 4efdca267d51 -r b734db305578 test-data/output_mrsa.txt
--- a/test-data/output_mrsa.txt	Tue Oct 29 19:24:59 2019 -0400
+++ b/test-data/output_mrsa.txt	Wed Apr 22 18:44:06 2020 -0400
@@ -0,0 +1,8 @@
+#FILE	SEQUENCE	START	END	STRAND	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION	PRODUCT	RESISTANCE
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	40786	41556	-	aadD_1	1-771/771	===============	0/0	100.00	99.74	resfinder	AF181950	aadD	Amikacin;Tobramycin
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	44919	46925	-	mecA_6	1-2007/2007	===============	0/0	100.00	100.00	resfinder	BX571856	mecA	Amoxicillin;Amoxicillin+Clavulanic_acid;Ampicillin;Ampicillin+Clavulanic_acid;Cefepime;Cefixime;Cefotaxime;Cefoxitin;Ceftazidime;Ertapenem;Imipenem;Meropenem;Piperacillin;Piperacillin+Tazobactam
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	55890	56621	+	erm(A)_1	1-732/732	===============	0/0	100.00	100.00	resfinder	X03216	erm(A)	Erythromycin;Lincomycin;Clindamycin;Quinupristin;Pristinamycin_IA;Virginiamycin_S
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	56747	57529	-	ant(9)-Ia_1	1-783/783	===============	0/0	100.00	100.00	resfinder	X02588	ant(9)-Ia	
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1796513	1797244	+	erm(A)_1	1-732/732	===============	0/0	100.00	100.00	resfinder	X03216	erm(A)	Erythromycin;Lincomycin;Clindamycin;Quinupristin;Pristinamycin_IA;Virginiamycin_S
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1797370	1798152	-	ant(9)-Ia_1	1-783/783	===============	0/0	100.00	100.00	resfinder	X02588	ant(9)-Ia	
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1913785	1914672	+	blaZ_78	1-888/888	===============	0/0	100.00	99.66	resfinder	KU607301	blaZ	Amoxicillin;Ampicillin;Penicillin;Piperacillin
diff -r 4efdca267d51 -r b734db305578 test-data/output_noheader.txt
--- a/test-data/output_noheader.txt	Tue Oct 29 19:24:59 2019 -0400
+++ b/test-data/output_noheader.txt	Wed Apr 22 18:44:06 2020 -0400
@@ -5,4 +5,3 @@
 MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1796513	1797244	+	erm(A)_1	1-732/732	===============	0/0	100.00	100.00	resfinder	X03216	erm(A)	Erythromycin;Lincomycin;Clindamycin;Quinupristin;Pristinamycin_IA;Virginiamycin_S
 MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1797370	1798152	-	ant(9)-Ia_1	1-783/783	===============	0/0	100.00	100.00	resfinder	X02588	ant(9)-Ia	
 MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1913785	1914672	+	blaZ_78	1-888/888	===============	0/0	100.00	99.66	resfinder	KU607301	blaZ	Amoxicillin;Ampicillin;Penicillin;Piperacillin
-MRSA0252.fna	gi|49482253|ref|NC_002952.2|	2488459	2488878	+	fosD_1	1-420/420	===============	0/0	100.00	79.05	resfinder	KC989517	fosD	Fosfomycin