# HG changeset patch
# User iuc
# Date 1568260637 14400
# Node ID f9bf6a8d85478314362d7849242888596e7b76b3
# Parent  78c75f134c16a6b1565684d4c982186bc94320af
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit c272325e121abb0582d2a50759ee04b43f327d4d"

diff -r 78c75f134c16 -r f9bf6a8d8547 abricate.xml
--- a/abricate.xml	Mon Mar 19 10:42:19 2018 -0400
+++ b/abricate.xml	Wed Sep 11 23:57:17 2019 -0400
@@ -9,7 +9,12 @@
     <expand macro="version_command" />
 
     <command detect_errors="exit_code"><![CDATA[
-        abricate '$file_input'
+        #import re
+        #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
diff -r 78c75f134c16 -r f9bf6a8d8547 macros.xml
--- a/macros.xml	Mon Mar 19 10:42:19 2018 -0400
+++ b/macros.xml	Wed Sep 11 23:57:17 2019 -0400
@@ -10,7 +10,7 @@
         <version_command><![CDATA[abricate --version]]></version_command>
     </xml>
 
-    <token name="@VERSION@">0.8</token>
+    <token name="@VERSION@">0.9.3</token>
 
     <xml name="citations">
       <citations>
diff -r 78c75f134c16 -r f9bf6a8d8547 test-data/output_db-card.txt
--- a/test-data/output_db-card.txt	Mon Mar 19 10:42:19 2018 -0400
+++ b/test-data/output_db-card.txt	Wed Sep 11 23:57:17 2019 -0400
@@ -1,16 +1,18 @@
-#FILE	SEQUENCE	START	END	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION
-NC_002952.2	40786	41547	ANT(4')-Ib	1-762/762	===============	0/0	100.00	100.00	card	NC_013342.1:26738-27500
-NC_002952.2	44918	46925	mecA	1-2008/2008	===============	0/0	100.00	99.90	card	KC243783:1-2008
-NC_002952.2	47025	48783	mecR1	1-1759/1759	===============	0/0	100.00	99.94	card	NC_009487:40849-42607
-NC_002952.2	48782	49154	mecI	1-373/373	===============	0/0	100.00	99.73	card	NC_002745:48894-49266
-NC_002952.2	55890	56622	ErmA	1-733/733	===============	0/0	100.00	100.00	card	NC_009632:49745-50477
-NC_002952.2	152865	154217	tet(38)	1-1353/1353	===============	0/0	100.00	98.52	card	AY825285:1-1354
-NC_002952.2	376045	376465	mepR	1-421/421	===============	0/0	100.00	99.05	card	NC_009782:379935-380355
-NC_002952.2	376571	377926	mepA	1-1356/1356	===============	0/0	100.00	98.53	card	AY661734.1:840-2196
-NC_002952.2	774312	774756	mgrA	1-445/445	===============	0/0	100.00	99.78	card	NC_013450:694853-695297
-NC_002952.2	782414	783543	norA	1-1130/1165	========/======	7/14	96.39	76.08	card	AY566250:392-1556
-NC_002952.2	1486310	1487666	arlS	1-1357/1357	===============	0/0	100.00	98.38	card	NC_007795:1360281-1361637
-NC_002952.2	1487662	1488322	arlR	1-661/661	===============	0/0	100.00	99.09	card	NC_009641:1461589-1462249
-NC_002952.2	1796513	1797245	ErmA	1-733/733	===============	0/0	100.00	100.00	card	NC_009632:49745-50477
-NC_002952.2	1913826	1914672	PC1_beta-lactamase_(blaZ)	1-847/847	===============	0/0	100.00	97.17	card	NC_010066:9683-10529
-NC_002952.2	2047036	2048773	sav1866	1-1738/1738	===============	0/0	100.00	99.19	card	NC_002951:1987720-1989457
+#FILE	SEQUENCE	START	END	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION	PRODUCT
+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	card~~~ANT(4')-Ib~~~GQ900432.1:26738-27500 Kanamycin nucleotidyltransferase sequence from Staphylococcus aureus plasmid. Confers resistance to kanamycin neomycin and other aminoglycosides
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	44919	46925	mecA	1-2007/2007	===============	0/0	100.00	99.90	card	KC243783:1-2008	card~~~mecA~~~KC243783:1-2008 A foreign PBP2a acquired by lateral gene transfer that able to perform peptidoglycan synthesis in the presence of beta-lactams.
+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	card~~~mecR1~~~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.
+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	card~~~mecI~~~BA000018.3:48894-49266 mecI acts as a repressor of transcription of the mecA/mecR1/mecI operon.
+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	card~~~ErmA~~~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.
+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	card~~~tet(38)~~~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.
+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	card~~~mepR~~~BA000017.4:379932-380352 MepR is an upstream repressor of MepA in Staphylococcus aureus. It is part of the mepRAB operon.
+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	card~~~mepA~~~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.
+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	card~~~mgrA~~~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.
+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	card~~~Staphylococcus_aureus_norA~~~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.
+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	card~~~arlS~~~CP000253.1:1360281-1361637 ArlS is a protein histidine kinase that phosphorylates ArlR a promoter for norA expression.
+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	card~~~arlR~~~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.
+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	card~~~ErmA~~~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.
+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	card~~~PC1_beta-lactamase_(blaZ)~~~CP000732.1:9683-10529 The blaZ beta-lactamase is found in Bacillus subtilis and Staphylococcus aureus.
+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	card~~~Staphylococcys_aureus_LmrS~~~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
+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	card~~~Staphylococcus_aureus_FosB~~~AHLO01000073.1:63139-63559 The Bacillus subtilis fosB gene encodes a fosfomycin resistance protein
+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	card~~~DHA-1~~~BA000018.3:2517801-2518989 DHA-1 is a class C beta-lactamase found in Morganella morganii and Salmonella enterica
diff -r 78c75f134c16 -r f9bf6a8d8547 test-data/output_list.txt
--- a/test-data/output_list.txt	Mon Mar 19 10:42:19 2018 -0400
+++ b/test-data/output_list.txt	Wed Sep 11 23:57:17 2019 -0400
@@ -1,8 +1,9 @@
-DATABASE	SEQUENCES	DATE
-argannot	1749
-card	2220
-ecoh	597
-ncbi	4324
-plasmidfinder	263
-resfinder	2280
-vfdb	2597
+DATABASE	SEQUENCES	DBTYPE	DATE
+argannot	2223	nucl	2019-Aug-23
+card	2594	nucl	2019-Aug-23
+ecoh	597	nucl	2019-Aug-23
+ecoli_vf	2701	nucl	2019-Aug-23
+ncbi	4994	nucl	2019-Aug-23
+plasmidfinder	263	nucl	2019-Aug-23
+resfinder	3078	nucl	2019-Aug-23
+vfdb	2597	nucl	2019-Aug-23
diff -r 78c75f134c16 -r f9bf6a8d8547 test-data/output_minid100.txt
--- a/test-data/output_minid100.txt	Mon Mar 19 10:42:19 2018 -0400
+++ b/test-data/output_minid100.txt	Wed Sep 11 23:57:17 2019 -0400
@@ -1,7 +1,7 @@
-#FILE	SEQUENCE	START	END	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION
-NC_002952.2	44919	46928	mecA_15	1-2010/2010	===============	0/0	100.00	100.00	resfinder	AB505628
-NC_002952.2	55890	56621	erm(A)_1	1-732/732	===============	0/0	100.00	100.00	resfinder	X03216
-NC_002952.2	56747	57529	spc_1	1-783/783	===============	0/0	100.00	100.00	resfinder	X02588
-NC_002952.2	1796513	1797244	erm(A)_1	1-732/732	===============	0/0	100.00	100.00	resfinder	X03216
-NC_002952.2	1797370	1798152	spc_1	1-783/783	===============	0/0	100.00	100.00	resfinder	X02588
-NC_002952.2	1913827	1914672	blaZ_36	1-846/846	===============	0/0	100.00	100.00	resfinder	AJ400722
+#FILE	SEQUENCE	START	END	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION	PRODUCT
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	40786	41556	aadD_2	1-771/771	===============	0/0	100.00	100.00	resfinder	M19465_dupe	resfinder~~~aadD_2~~~M19465_dupe Alternate name; ant(4')-Ia and aadD2
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	44919	46925	mecA_6	1-2007/2007	===============	0/0	100.00	100.00	resfinder	BX571856	resfinder~~~mecA_6~~~BX571856 mecA_6
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	55890	56621	erm(A)_1	1-732/732	===============	0/0	100.00	100.00	resfinder	X03216	resfinder~~~erm(A)_1~~~X03216 erm(A)_1
+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	resfinder~~~ant(9)-Ia_1~~~X02588 ant(9)-Ia_1
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1796513	1797244	erm(A)_1	1-732/732	===============	0/0	100.00	100.00	resfinder	X03216	resfinder~~~erm(A)_1~~~X03216 erm(A)_1
+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	resfinder~~~ant(9)-Ia_1~~~X02588 ant(9)-Ia_1
diff -r 78c75f134c16 -r f9bf6a8d8547 test-data/output_mrsa.txt
--- a/test-data/output_mrsa.txt	Mon Mar 19 10:42:19 2018 -0400
+++ b/test-data/output_mrsa.txt	Wed Sep 11 23:57:17 2019 -0400
@@ -1,9 +1,9 @@
 #FILE	SEQUENCE	START	END	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION	PRODUCT
-	NC_002952.2	40786	41556	aadD_1	1-771/771	===============	0/0	100.00	99.74	resfinder	AF181950	Alternate name; ant(4')-Ia and aadD2
-	NC_002952.2	44919	46928	mecA_15	1-2010/2010	===============	0/0	100.00	100.00	resfinder	AB505628	mecA_15
-	NC_002952.2	55890	56621	erm(A)_1	1-732/732	===============	0/0	100.00	100.00	resfinder	X03216	erm(A)_1
-	NC_002952.2	56747	57529	spc_1	1-783/783	===============	0/0	100.00	100.00	resfinder	X02588	Alternate name; aad9 ant(9)-Ia
-	NC_002952.2	1796513	1797244	erm(A)_1	1-732/732	===============	0/0	100.00	100.00	resfinder	X03216	erm(A)_1
-	NC_002952.2	1797370	1798152	spc_1	1-783/783	===============	0/0	100.00	100.00	resfinder	X02588	Alternate name; aad9 ant(9)-Ia
-	NC_002952.2	1913827	1914672	blaZ_36	1-846/846	===============	0/0	100.00	100.00	resfinder	AJ400722	blaZ_36
-	NC_002952.2	2488459	2488878	fosD_1	1-420/420	===============	0/0	100.00	79.05	resfinder	KC989517	fosD_1
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	40786	41556	aadD_2	1-771/771	===============	0/0	100.00	100.00	resfinder	M19465_dupe	resfinder~~~aadD_2~~~M19465_dupe Alternate name; ant(4')-Ia and aadD2
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	44919	46925	mecA_6	1-2007/2007	===============	0/0	100.00	100.00	resfinder	BX571856	resfinder~~~mecA_6~~~BX571856 mecA_6
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	55890	56621	erm(A)_1	1-732/732	===============	0/0	100.00	100.00	resfinder	X03216	resfinder~~~erm(A)_1~~~X03216 erm(A)_1
+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	resfinder~~~ant(9)-Ia_1~~~X02588 ant(9)-Ia_1
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1796513	1797244	erm(A)_1	1-732/732	===============	0/0	100.00	100.00	resfinder	X03216	resfinder~~~erm(A)_1~~~X03216 erm(A)_1
+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	resfinder~~~ant(9)-Ia_1~~~X02588 ant(9)-Ia_1
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1913785	1914672	blaZ_78	1-888/888	===============	0/0	100.00	99.66	resfinder	KU607301	resfinder~~~blaZ_78~~~KU607301 blaZ_78
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	2488459	2488878	fosD_1	1-420/420	===============	0/0	100.00	79.05	resfinder	KC989517	resfinder~~~fosD_1~~~KC989517 fosD_1
diff -r 78c75f134c16 -r f9bf6a8d8547 test-data/output_noheader.txt
--- a/test-data/output_noheader.txt	Mon Mar 19 10:42:19 2018 -0400
+++ b/test-data/output_noheader.txt	Wed Sep 11 23:57:17 2019 -0400
@@ -1,8 +1,8 @@
-	NC_002952.2	40786	41556	aadD_1	1-771/771	===============	0/0	100.00	99.74	resfinder	AF181950	Alternate name; ant(4')-Ia and aadD2
-	NC_002952.2	44919	46928	mecA_15	1-2010/2010	===============	0/0	100.00	100.00	resfinder	AB505628	mecA_15
-	NC_002952.2	55890	56621	erm(A)_1	1-732/732	===============	0/0	100.00	100.00	resfinder	X03216	erm(A)_1
-	NC_002952.2	56747	57529	spc_1	1-783/783	===============	0/0	100.00	100.00	resfinder	X02588	Alternate name; aad9 ant(9)-Ia
-	NC_002952.2	1796513	1797244	erm(A)_1	1-732/732	===============	0/0	100.00	100.00	resfinder	X03216	erm(A)_1
-	NC_002952.2	1797370	1798152	spc_1	1-783/783	===============	0/0	100.00	100.00	resfinder	X02588	Alternate name; aad9 ant(9)-Ia
-	NC_002952.2	1913827	1914672	blaZ_36	1-846/846	===============	0/0	100.00	100.00	resfinder	AJ400722	blaZ_36
-	NC_002952.2	2488459	2488878	fosD_1	1-420/420	===============	0/0	100.00	79.05	resfinder	KC989517	fosD_1
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	40786	41556	aadD_2	1-771/771	===============	0/0	100.00	100.00	resfinder	M19465_dupe	resfinder~~~aadD_2~~~M19465_dupe Alternate name; ant(4')-Ia and aadD2
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	44919	46925	mecA_6	1-2007/2007	===============	0/0	100.00	100.00	resfinder	BX571856	resfinder~~~mecA_6~~~BX571856 mecA_6
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	55890	56621	erm(A)_1	1-732/732	===============	0/0	100.00	100.00	resfinder	X03216	resfinder~~~erm(A)_1~~~X03216 erm(A)_1
+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	resfinder~~~ant(9)-Ia_1~~~X02588 ant(9)-Ia_1
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1796513	1797244	erm(A)_1	1-732/732	===============	0/0	100.00	100.00	resfinder	X03216	resfinder~~~erm(A)_1~~~X03216 erm(A)_1
+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	resfinder~~~ant(9)-Ia_1~~~X02588 ant(9)-Ia_1
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1913785	1914672	blaZ_78	1-888/888	===============	0/0	100.00	99.66	resfinder	KU607301	resfinder~~~blaZ_78~~~KU607301 blaZ_78
+MRSA0252.fna	gi|49482253|ref|NC_002952.2|	2488459	2488878	fosD_1	1-420/420	===============	0/0	100.00	79.05	resfinder	KC989517	resfinder~~~fosD_1~~~KC989517 fosD_1