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changeset 1:8e8dc9a1e3e5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 47ad236b09eaf7541fbd7dd5b95e970800d545a5
author iuc
date Mon, 30 Oct 2017 05:40:10 -0400
parents 735872ff8222
children 253b7a1cf87e
files mlst.xml mlst_list.xml test-data/output_list.txt test-data/output_longlist.txt tool_dependencies.xml
diffstat 5 files changed, 15 insertions(+), 131 deletions(-) [+]
line wrap: on
line diff
--- a/mlst.xml	Mon Dec 12 15:07:38 2016 -0500
+++ b/mlst.xml	Mon Oct 30 05:40:10 2017 -0400
@@ -1,6 +1,6 @@
-<tool id="mlst" name="MLST" version="0.1.0">
+<tool id="mlst" name="MLST" version="2.9">
     <requirements>
-        <requirement type="package" version="2.6">mlst</requirement>
+        <requirement type="package" version="2.9">mlst</requirement>
     </requirements>
 
     <version_command>mlst --version</version_command>
@@ -117,6 +117,7 @@
 |  *-*   | Allele missing            |
 +--------+---------------------------+
 
+Galaxy wrapper maintained by Simon Gladman.
     ]]></help>
 
     <citations>
--- a/mlst_list.xml	Mon Dec 12 15:07:38 2016 -0500
+++ b/mlst_list.xml	Mon Oct 30 05:40:10 2017 -0400
@@ -1,6 +1,6 @@
-<tool id="mlst_list" name="MLST List" version="0.1.0">
+<tool id="mlst_list" name="MLST List" version="2.9">
     <requirements>
-        <requirement type="package" version="2.6">mlst</requirement>
+        <requirement type="package" version="2.9">mlst</requirement>
     </requirements>
 
     <version_command>mlst --version</version_command>
@@ -22,13 +22,21 @@
         <!-- Test the longlist option -->
         <test>
             <param name="list_type" value="true" />
-            <output name="report" ftype="txt" file="output_longlist.txt" />
+            <output name="report" ftype="txt" >
+                <assert_contents>
+                    <has_text text="saureus" />
+                </assert_contents>
+            </output>
         </test>
 
         <!-- Test the list option -->
         <test>
             <param name="list_type" value="false" />
-            <output name="report" ftype="txt" file="output_list.txt" />
+            <output name="report" ftype="txt" >
+                <assert_contents>
+                    <has_text text="saureus" />
+                </assert_contents>
+            </output>
         </test>
     </tests>
 
--- a/test-data/output_list.txt	Mon Dec 12 15:07:38 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-abaumannii abaumannii_2 achromobacter aeromonas afumigatus aphagocytophilum arcobacter bcc bcereus bhampsonii bhenselae bhyodysenteriae bintermedia blicheniformis bordetella borrelia bpilosicoli bpseudomallei brachyspira bsubtilis calbicans campylobacter cbotulinum cconcisus cdifficile cdiphtheriae cfetus cfreundii cglabrata chelveticus chlamydiales chyointestinalis cinsulaenigrae ckrusei clanienae clari cmaltaromaticum cronobacter csepticum csinensis csputorum ctropicalis cupsaliensis ecloacae ecoli ecoli_2 efaecalis efaecium fpsychrophilum hcinaedi hinfluenzae hparasuis hpylori hsuis kkingae koxytoca kpneumoniae kseptempunctata leptospira leptospira_2 leptospira_3 lmonocytogenes lsalivarius mabscessus magalactiae mbovis mcatarrhalis mhaemolytica mhyorhinis mmassiliense mplutonius neisseria orhinotracheale otsutsugamushi pacnes paeruginosa pfluorescens pgingivalis plarvae pmultocida_multihost pmultocida_rirdc ppentosaceus ranatipestifer sagalactiae saureus scanis sdysgalactiae senterica sepidermidis sgallolyticus shaemolyticus shominis sinorhizobium slugdunensis smaltophilia soralis spneumoniae spseudintermedius spyogenes ssuis sthermophilus sthermophilus_2 streptomyces suberis szooepidemicus taylorella tenacibaculum tvaginalis vcholerae vibrio vparahaemolyticus vtapetis vvulnificus wolbachia xfastidiosa yersinia ypseudotuberculosis yruckeri
--- a/test-data/output_longlist.txt	Mon Dec 12 15:07:38 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,118 +0,0 @@
-abaumannii	Oxf_gltA	Oxf_gyrB	Oxf_gdhB	Oxf_recA	Oxf_cpn60	Oxf_gpi	Oxf_rpoD
-abaumannii_2	Pas_cpn60	Pas_fusA	Pas_gltA	Pas_pyrG	Pas_recA	Pas_rplB	Pas_rpoB
-achromobacter	nusA	rpoB	eno	gltB	lepA	nuoL	nrdA
-aeromonas	gyrB	groL	gltA	metG	ppsA	recA
-afumigatus	ANX4	BGT1	CAT1	LIP	MAT1_2	SODB	ZRF2
-aphagocytophilum	pheS	glyA	fumC	mdh	sucA	dnaN	atpA
-arcobacter	aspA	atpA	glnA	gltA	glyA	pgm	tkt
-bcc	atpD	gltB	gyrB	recA	lepA	phaC	trpB
-bcereus	glp	gmk	ilv	pta	pur	pyc	tpi
-bhampsonii	Bha_adh	Bha_est	Bha_gdh	Bha_glpK	Bha_pgm	Bha_thi
-bhenselae	_16S	batR	ftsZ	gltA	groEL	nlpD	ribC	rpoB
-bhyodysenteriae	Bhy_adh	Bhy_alp	Bhy_est	Bhy_gdh	Bhy_glpK	Bhy_pgm	Bhy_thi
-bintermedia	Bin_adh	Bin_alp	Bin_est	Bin_gdh	Bin_glpK	Bin_pgm	Bin_thi
-blicheniformis	adk	ccpA	recF	rpoB	spo0A	sucC
-bordetella	adk	fumC	glyA	tyrB	icd	pepA	pgm
-borrelia	clpA	clpX	nifS	pepX	pyrG	recG	rplB	uvrA
-bpilosicoli	Bpi_adh	Bpi_alp	Bpi_est	Bpi_gdh	Bpi_glpK	Bpi_pgm	Bpi_thi
-bpseudomallei	ace	gltB	gmhD	lepA	lipA	narK	ndh
-brachyspira	Bra_adh	Bra_alp	Bra_est	Bra_gdh	Bra_glp	Bra_pgm	Bra_thi
-bsubtilis	glpF	ilvD	pta	purH	pycA	rpoD	tpiA
-calbicans	AAT1a	ACC1	ADP1	MPIb	SYA1	VPS13	ZWF1b
-campylobacter	aspA	glnA	gltA	glyA	pgm	tkt	uncA
-cbotulinum	aroE	mdh	aceK	oppB	rpoB	recA	hsp
-cconcisus	Cco_aspA	Cco_atpA	Cco_glnA	Cco_gltA	Cco_glyA	Cco_ilvD	Cco_pgm
-cdifficile	adk	atpA	dxr	glyA	recA	sodA	tpi
-cdiphtheriae	atpA	dnaE	dnaK	fusA	leuA	odhA	rpoB
-cfetus	Cfe_aspA	Cfe_glnA	Cfe_gltA	Cfe_glyA	Cfe_pgm	Cfe_tkt	Cfe_uncA
-cfreundii	aspC	clpX	fadD	mdh	arcA	dnaG	lysP
-cglabrata	FKS	LEU2	NMT1	TRP1	UGP1	URA3
-chelveticus	Che_aspA	Che_atpA	Che_glnA	Che_gltA	Che_glyA	Che_pgm	Che_tkt
-chlamydiales	gatA	oppA	hflX	gidA	enoA	hemN	fumC
-chyointestinalis	Chy_aspA	Chy_atpA	Chy_glnA	Chy_gltA	Chy_glyA	Chy_pgm	Chy_tkt
-cinsulaenigrae	Cin_aspA	Cin_atpA	Cin_glnA	Cin_glyA	Cin_pgi	Cin_pgm	Cin_tkt
-ckrusei	HIS3	LEU2	NMT1	TRP1	ADE2	LYS2D
-clanienae	Cln_aspA	Cln_atpA	Cln_glnA	Cln_gltA	Cln_glyA	Cln_pgm	Cln_tkt
-clari	Cla_adk	Cla_atpA	Cla_glnA	Cla_glyA	Cla_pgi	Cla_pgm	Cla_tkt
-cmaltaromaticum	dapE	ddlA	glpQ	ilvE	leuS	pyc	pyrE
-cronobacter	atpD	fusA	glnS	gltB	gyrB	infB	pps
-csepticum	ddl	dnaK	glpK	groEL	gyrA	recA	tpi
-csinensis	Actin	Cox1	Cox3	Ef_1a	Its1	Nad4	Nad5	Tubulin
-csputorum	Csp_aspA	Csp_atpA	Csp_glnA	Csp_gltA	Csp_glyA	Csp_pgm	Csp_tkt
-ctropicalis	ICL1	MDR1	SAPT2	SAPT4	XYR1	ZWF1a
-cupsaliensis	Cup_adk	Cup_aspA	Cup_atpA	Cup_glnA	Cup_glyA	Cup_pgi	Cup_tkt
-ecloacae	dnaA	fusA	gyrB	leuS	pyrG	rplB	rpoB
-ecoli	adk	fumC	gyrB	icd	mdh	purA	recA
-ecoli_2	dinB	icdA	pabB	polB	putP	trpA	trpB	uidA
-efaecalis	gdh	gyd	pstS	gki	aroE	xpt	yqiL
-efaecium	atpA	ddl	gdh	purK	gyd	pstS	adk
-fpsychrophilum	atpA	dnaK	fumC	gyrB	murG	trpB	tuf
-hcinaedi	_23S_rRNA	ppa	aspA	aroE	atpA	tkt	cdtB
-hinfluenzae	adk	atpG	frdB	fucK	mdh	pgi	recA
-hparasuis	atpD	infB	mdh	rpoB	_6pgd	g3pd	frdB
-hpylori	atpA	efp	mutY	ppa	trpC	ureI	yphC
-hsuis	atpA	efp	mutY	ppa	trpC	ureAB	yphC
-kkingae	abcZ	adk	aroE	cpn60	gdh	recA
-koxytoca	gapA	infB	mdh	pgi	phoE	rpoB	tonB
-kpneumoniae	gapA	infB	mdh	pgi	phoE	rpoB	tonB
-kseptempunctata	cox1	rnl
-leptospira	glmU	pntA	sucA	tpiA	pfkB	mreA	caiB
-leptospira_2	adk_2	glmU_2	icdA_2	lipL32_2	lipL41_2	mreA_2	pntA_2
-leptospira_3	adk_3	icdA_3	lipL32_3	lipL41_3	rrs2_3	secY_3
-lmonocytogenes	abcZ	bglA	cat	dapE	dat	ldh	lhkA
-lsalivarius	pstB	rpsB	nrdB	rpoA	parB
-mabscessus	Mab_argH	Mab_cya	Mab_gnd	Mab_murC	Mab_pta	Mab_purH	Mab_rpoB
-magalactiae	dnaA	gltX	gyrB	metS	tufA
-mbovis	adh1	gltX	gpsA	gyrB	pta2	tdk	tkt
-mcatarrhalis	abcZ	adk	efp	fumC	glyBETA	mutY	ppa	trpE
-mhaemolytica	adk	aroE	deoD	gapDH	gnd	mdh	zwf
-mhyorhinis	dnaA	rpoB	gyrB	gltX	adk	gmk
-mmassiliense	Mma_argH	Mma_cya	Mma_gnd	Mma_murC	Mma_pta	Mma_purH	Mma_rpoB
-mplutonius	argE	galK	gbpB	purR
-neisseria	abcZ	adk	aroE	fumC	gdh	pdhC	pgm
-orhinotracheale	adk	aroE	fumC	gdhA	mdh	pgi	pmi
-otsutsugamushi	gpsA	mdh	nrdF	nuoF	ppdK	sucB	sucD
-pacnes	aroE	atpD	gmk	guaA	lepA	sodA	tly	CAMP2
-paeruginosa	acs	aro	gua	mut	nuo	pps	trp
-pfluorescens	glnS	gyrB	ileS	nuoD	recA	rpoB	rpoD
-pgingivalis	ftsQ	gpdxJ	hagB	mcmA	pepO	pga	recA
-plarvae	glpF	sigF	glpT	Natrans	rpoB	ftsA	clpC
-pmultocida_multihost	adk	aroA	deoD	gdhA	g6pd	mdh	pgi
-pmultocida_rirdc	adk	est	pmi	zwf	mdh	gdh	pgi
-ppentosaceus	gyrB	pyc	pgm	leuS	glnA	dalR	pgI
-ranatipestifer	dnaB	groEL	gyrA	mdh	gluD	gpi	rpoB
-sagalactiae	adhP	pheS	atr	glnA	sdhA	glcK	tkt
-saureus	arcC	aroE	glpF	gmk	pta	tpi	yqiL
-scanis	gki	gtr	murI	mutS	recP	xpt	yqiZ
-sdysgalactiae	gki	gtr	murI	mutS	recP	xpt	atoB
-senterica	aroC	dnaN	hemD	hisD	purE	sucA	thrA
-sepidermidis	arcC	aroE	gtr	mutS	pyrR	tpiA	yqiL
-sgallolyticus	aroE	glgB	nifS	p20	tkt	trpD	uvrA
-shaemolyticus	arcC	SH_1200	hemH	leuB	SH1431	cfxE	Ribose_ABC
-shominis	arcC	glpK	gtr	pta	tpiA	tuf
-sinorhizobium	asd	edd	gap	glnD	gnd	nuoE1	ordL2	recA	sucA	zwf
-slugdunensis	aroE	dat	ddl	gmk	ldh	recA	yqiL
-smaltophilia	atpD	gapA	guaA	mutM	nuoD	ppsA	recA
-soralis	aroE	ddl	gdh	gki	hexB	recP	xpt
-spneumoniae	aroE	gdh	gki	recP	spi	xpt	ddl
-spseudintermedius	ack	cpn60	fdh	pta	purA	sar	tuf
-spyogenes	gki	gtr	murI	mutS	recP	xpt	yqiL
-ssuis	aroA	cpn60	dpr	gki	mutS	recA	thrA
-sthermophilus	ddlA	glcK	proA	ptsI	serB	tkt
-sthermophilus_2	carB	clpX	dnaA	murC	murE	pepN	pepX	pyrG	recA	rpoB
-streptomyces	_16S	atpD	gyrB	recA	rpoB	trpB
-suberis	arcC	ddl	gki	recP	tdk	tpi	yqiL
-szooepidemicus	arcC	nrdE	proS	spi	tdk	tpi	yqiL
-taylorella	gltA	gyrB	fh	shmt	tyrB	adk	txn
-tenacibaculum	atpA	dnaK	glyA	gyrB	infB	rlmN	tgt
-tvaginalis	TRYP	GLUT	FT2A	ALTS	DMRP	SHMT	M6PI
-vcholerae	adk	gyrB	mdh	metE	pntA	purM	pyrC
-vibrio	gyrB	pyrH	recA	atpA
-vparahaemolyticus	dnaE	gyrB	recA	dtdS	pntA	pyrC	tnaA
-vtapetis	atpA	fstZ	gapA	hsp60	pyrH	rctB	recA	rpoA	rpoD	topA
-vvulnificus	glp	gyrB	mdh	metG	purM	dtdS	lysA	pntA	pyrC	tnaA
-wolbachia	gatB	coxA	hcpA	ftsZ	fbpA
-xfastidiosa	leuA	petC	malF	cysG	holC	nuoL	gltT
-yersinia	aarF	dfp	galR	glnS	hemA	rfaE	speA
-ypseudotuberculosis	adk	argA	aroA	glnA	thrA	tmk	trpE
-yruckeri	glnA	gyrB	dnaJ	thrA	hsp60	recA
--- a/tool_dependencies.xml	Mon Dec 12 15:07:38 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="mlst" version="2.6">
-        <repository changeset_revision="53b0a618e1a7" name="package_mlst_2_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>