view admin_scripts/species @ 0:a9e90cdcb97a draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty

>Fungi
Ashbya gossypii	agossypii_eg_gene
Aspergillus clavatus	aclavatus_eg_gene
Aspergillus flavus	aflavus_eg_gene
Aspergillus fumigatus	afumigatus_eg_gene
Aspergillus fumigatusa1163	afumigatusa1163_eg_gene
Aspergillus nidulans	anidulans_eg_gene
Aspergillus niger	aniger_eg_gene
Aspergillus oryzae	aoryzae_eg_gene
Aspergillus terreus	aterreus_eg_gene
Blumeria graminis	bgraminis_eg_gene
Botrytis cinerea	bcinerea_eg_gene
Colletotrichum gloeosporioides	cgloeosporioides_eg_gene
Colletotrichum higginsianum	chigginsianum_eg_gene
Colletotrichum orbiculare	corbiculare_eg_gene
Cryptococcus neoformans	cneoformans_eg_gene
Dothistroma septosporum	dseptosporum_eg_gene
Fusarium fujikuroi	ffujikuroi_eg_gene
Fusarium graminearum	fgraminearum_eg_gene
Fusarium oxysporum	foxysporum_eg_gene
Fusarium pseudograminearum	fpseudograminearum_eg_gene
Fusarium solani	fsolani_eg_gene
Fusarium verticillioides	fverticillioides_eg_gene
Gaeumannomyces graminis	ggraminis_eg_gene
Colletotrichum graminicola	cgraminicola_eg_gene
Komagataella pastoris	kpastoris_eg_gene
Leptosphaeria maculans	lmaculans_eg_gene
Magnaporthe oryzae	moryzae_eg_gene
Magnaporthe poae	mpoae_eg_gene
Melampsora larici-populina	mlaricipopulina_eg_gene
Neosartorya fischeri	nfischeri_eg_gene
Neurospora crassa	ncrassa_eg_gene
Phaeosphaeria nodorum	pnodorum_eg_gene
Puccinia graminis	pgraminis_eg_gene
Puccinia graminis Ug99	pgraminisug99_eg_gene
Puccinia triticina	ptriticina_eg_gene
Pyrenophora teres	pteres_eg_gene
Pyrenophora tritici-repentis	ptriticirepentis_eg_gene
Saccharomyces cerevisiae	scerevisiae_eg_gene
Schizosaccharomyces cryophilus	scryophilus_eg_gene
Schizosaccharomyces japonicus	japonicus_eg_gene
Schizosaccharomyces octosporus	octosporus_eg_gene
Schizosaccharomyces pombe	spombe_eg_gene
Sclerotinia sclerotiorum	ssclerotiorum_eg_gene
Sporisorium reilianum	sreilianum_eg_gene
Trichoderma reesei	treesei_eg_gene
Trichoderma virens	tvirens_eg_gene
Tuber melanosporum	tmelanosporum_eg_gene
Ustilago maydis	umaydis_eg_gene
Verticillium dahliae JR2	vdahliaejr2_eg_gene
Verticillium dahliae	dahliae_eg_gene
Yarrowia lipolytica	ylipolytica_eg_gene
Zymoseptoria tritici	ztritici_eg_gene

>Metazoa
Acyrthosiphon pisum	apisum_eg_gene
Aedes aegypti (Yellow fever mosquito)	aaegypti_eg_gene
Amphimedon queenslandica	aqueenslandica_eg_gene
Anopheles darlingi	adarlingi_eg_gene
Anopheles gambiae (African malaria mosquito) 	agambiae_eg_gene
Apis mellifera 	amellifera_eg_gene
Atta cephalotes 	acephalotes_eg_gene
Bombyx mori 	bmori_eg_gene
Brugia malayi 	bmalayi_eg_gene
Caenorhabditis brenneri 	cbrenneri_eg_gene
Caenorhabditis briggsae 	cbriggsae_eg_gene
Caenorhabditis elegans 	celegans_eg_gene
Caenorhabditis japonica 	cjaponica_eg_gene
Caenorhabditis remanei 	cremanei_eg_gene
Culex quinquefasciatus (Southern house mosquito) 	cquinquefasciatus_eg_gene
Danaus plexippus 	dplexippus_eg_gene
Daphnia pulex 	dpulex_eg_gene
Dendroctonus ponderosae	ponderosae_eg_gene
Drosophila ananassae 	dananassae_eg_gene
Drosophila erecta 	derecta_eg_gene
Drosophila grimshawi 	dgrimshawi_eg_gene
Drosophila melanogaster (Fruit fly) 	dmelanogaster_eg_gene
Drosophila mojavensis 	dmojavensis_eg_gene
Drosophila persimilis 	dpersimilis_eg_gene
Drosophila pseudoobscura 	dpseudoobscura_eg_gene
Drosophila sechellia 	dsechellia_eg_gene
Drosophila simulans 	dsimulans_eg_gene
Drosophila virilis 	dvirilis_eg_gene
Drosophila willistoni 	dwillistoni_eg_gene
Drosophila yakuba 	dyakuba_eg_gene
Heliconius melpomene 	hmelpomene_eg_gene
Helobdella robusta	robusta_eg_gene
Ixodes scapularis (Black-legged tick) 	iscapularis_eg_gene
Loa loa 	lloa_eg_gene
Lottia gigantea	lgigantea_eg_gene
Megaselia scalaris 	mscalaris_eg_gene
Melitaea cinxia	mcinxia_eg_gene
Mnemiopsis leidyi	mleidyi_eg_gene
Nasonia vitripennis 	nvitripennis_eg_gene
Nematostella vectensis 	nvectensis_eg_gene
Onchocerca volvulus	ovolvulus_eg_gene
Pediculus humanus (Human louse) 	phumanus_eg_gene
Pristionchus pacificus 	ppacificus_eg_gene
Rhodnius prolixus	rprolixus_eg_gene
Schistosoma mansoni 	smansoni_eg_gene
Solenopsis invicta (Red fire ant)	sinvicta_eg_gene
Strigamia maritima 	smaritima_eg_gene
Strongylocentrotus purpuratus 	spurpuratus_eg_gene
Tetranychus urticae	turticae_eg_gene
Tribolium castaneum (red flour beetle) 	tcastaneum_eg_gene
Trichinella spiralis 	tspiralis_eg_gene
Trichoplax adhaerens 	tadhaerens_eg_gene
Zootermopsis nevadensis	znevadensis_eg_gene

>Plants
Amborella (Amborella trichopoda)	atrichopoda_eg_gene
Arabidopsis lyrata (Lyrate rockcress)	alyrata_eg_gene 
Arabidopsis thaliana (Thale-cress)	athaliana_eg_gene 
Brachypodium distachyon (False brome)	bdistachyon_eg_gene
Brassica oleracea	boleracea_eg_gene 
Brassica rapa genes (Field mustard)	brapa_eg_gene 
Chlamydomonas reinhardtii (Green algae)	creinhardtii_eg_gene 
Cyanidioschyzon merolae (Red algae)	cmerolae_eg_gene 
Glycine max (Soybean)	gmax_eg_gene 
Hordeum vulgare (Barley)	hvulgare_eg_gene 
Leersia perrieri (Leersia)	lperrieri_eg_gene
Medicago truncatula (Barrel medic)	mtruncatula_eg_gene 
Musa acuminata (Banana)	macuminata_eg_gene 
Oryza brachyantha	obrachyantha_eg_gene 
Oryza glumaepatula	oglumaepatula_eg_gene
Oryza meridionalis	omeridionalis_eg_gene
Oryza nivara	onivara_eg_gene
Oryza punctata	opunctata_eg_gene
Oryza rufipogon (Common wild rice)	orufipogon_eg_gene
Oryza sativa (Indica rice)	osativa_eg_gene 
Oryza sativa Indica Group	oindica_eg_gene 
Oryza sativa Japonica (Japonica rice)	osativa_eg_gene
Ostreococcus lucimarinus (Green algae)	olucimarinus_eg_gene
Physcomitrella patens	ppatens_eg_gene 
Physcomitrella patens (Moss)	ppatens_eg_gene
Populus trichocarpa	ptrichocarpa_eg_gene 
Populus trichocarpa (Western balsam poplar)	ptrichocarpa_eg_gene
Prunus persica (Peach)	ppersica_eg_gene
Selaginella moellendorffii (Spike moss)	smoellendorffii_eg_gene 
Setaria italica (Foxtail millet)	sitalica_eg_gene 
Solanum lycopersicum (Tomato)	slycopersicum_eg_gene 
Solanum tuberosum (Potato)	stuberosum_eg_gene 
Sorghum bicolor (Sorghum)	sbicolor_eg_gene 
Theobroma cacao (Cocoa)	tcacao_eg_gene
Triticum aestivum (Bread wheat)	taestivum_eg_gene
Triticum urartu (Einkorn)	turartu_eg_gene
Vitis vinifera (Wine grape)	vvinifera_eg_gene 
Zea mays (Maize)	zmays_eg_gene

>Protists
Albugo laibachii	alaibachii_eg_gene
Bigelowiella natans	bnatans_eg_gene
Dictyostelium discoideum	ddiscoideum_eg_gene
Emiliania huxleyi	ehuxleyi_eg_gene
Entamoeba histolytica	ehistolytica_eg_gene
Giardia lamblia	glamblia_eg_gene
Guillardia theta CCMP2712	gtheta_eg_gene
Hyaloperonospora arabidopsidis	harabidopsidis_eg_gene
Leishmania major	lmajor_eg_gene
Paramecium tetraurelia	ptetraurelia_eg_gene
Phaeodactylum tricornutum	ptricornutum_eg_gene
Phytophthora infestans	pinfestans_eg_gene
Phytophthora kernoviae	pkernoviae_eg_gene
Phytophthora lateralis	plateralis_eg_ge
Phytophthora parasitica	pparasitica_eg_gene
Phytophthora ramorum	pramorum_eg_gene
Phytophthora sojae	psojae_eg_gene
Plasmodium berghei	pberghei_eg_gene
Plasmodium chabaudi	pchabaudi_eg_gene
Plasmodium falciparum	pfalciparum_eg_gene
Plasmodium knowlesi	pknowlesi_eg_gene
Plasmodium vivax	pvivax_eg_gene
Pythium aphanidermatum	paphanidermatum_eg_gene
Pythium arrhenomanes	parrhenomanes_eg_gene
Pythium irregulare	pirregulare_eg_gene
Pythium iwayamai	piwayamai_eg_gene
Pythium ultimum	pultimum_eg_gene
Pythium vexans	pvexans_eg_gene
Tetrahymena thermophila	tthermophila_eg_gene
Thalassiosira pseudonana	tpseudonana_eg_gene
Toxoplasma gondii	tgondii_eg_gene
Trypanosoma brucei	tbrucei_eg_gene

>Vertebrates
Alpaca (Vicugna pacos)	vpacos_gene_ensembl
Amazon molly (Poecilia formosa)	pformosa_gene_ensembl
Anole lizard (Anolis carolinensis)	acarolinensis_gene_ensembl
Armadillo (Dasypus novemcinctus)	dnovemcinctus_gene_ensembl
Bushbaby (Otolemur garnettii)	ogarnettii_gene_ensembl
C. elegans (Caenorhabditis elegans)	celegans_gene_ensembl
C.intestinalis (Ciona intestinalis)	cintestinalis_gene_ensembl
C.savignyi (Ciona savignyi)	csavignyi_gene_ensembl
Cat (Felis catus)	fcatus_gene_ensembl
Cave fish (Astyanax mexicanus)	amexicanus_gene_ensembl
Chicken (Gallus gallus)	ggallus_gene_ensembl
Chimpanzee (Pan troglodytes)	ptroglodytes_gene_ensembl
Chinese softshell turtle (Pelodiscus sinensis)	psinensis_gene_ensembl
Cod (Gadus morhua)	gmorhua_gene_ensembl
Coelacanth (Latimeria chalumnae)	lchalumnae_gene_ensembl
Cow (Bos taurus)	btaurus_gene_ensembl
Dog (Canis lupus familiaris)	cfamiliaris_gene_ensembl
Dolphin (Tursiops truncatus)	ttruncatus_gene_ensembl
Duck (Anas platyrhynchos)	aplatyrhynchos_gene_ensembl
Elephant (Loxodonta africana)	lafricana_gene_ensembl
Ferret (Mustela putorius furo)	mfuro_gene_ensembl
Flycatcher (Ficedula albicollis)	falbicollis_gene_ensembl
Fruitfly (Drosophila melanogaster)	dmelanogaster_gene_ensembl
Fugu (Takifugu rubripes)	trubripes_gene_ensembl
Gibbon (Nomascus leucogenys)	nleucogenys_gene_ensembl
Gorilla (Gorilla gorilla gorilla)	ggorilla_gene_ensembl
Guinea Pig (Cavia porcellus)	cporcellus_gene_ensembl
Hedgehog (Erinaceus europaeus)	eeuropaeus_gene_ensembl
Horse (Equus caballus)	ecaballus_gene_ensembl
Human (Homo sapiens)	hsapiens_gene_ensembl
Hyrax (Procavia capensis)	pcapensis_gene_ensembl
Kangaroo rat (Dipodomys ordii)	dordii_gene_ensembl
Lamprey (Petromyzon marinus)	pmarinus_gene_ensembl
Lesser hedgehog tenrec (Echinops telfairi)	etelfairi_gene_ensembl
Macaque (Macaca mulatta)	mmulatta_gene_ensembl
Marmoset (Callithrix jacchus)	cjacchus_gene_ensembl
Medaka (Oryzias latipes)	olatipes_gene_ensembl
Megabat (Pteropus vampyrus)	pvampyrus_gene_ensembl
Microbat (Myotis lucifugus)	mlucifugus_gene_ensembl
Mouse (Mus musculus)	mmusculus_gene_ensembl
Mouse Lemur (Microcebus murinus)	mmurinus_gene_ensembl
Opossum (Monodelphis domestica)	mdomestica_gene_ensembl
Orangutan (Pongo abelii)	pabelii_gene_ensembl
Panda (Ailuropoda melanoleuca)	amelanoleuca_gene_ensembl
Pig (Sus scrofa)	sscrofa_gene_ensembl
Pika (Ochotona princeps)	oprinceps_gene_ensembl
Platyfish (Xiphophorus maculatus)	xmaculatus_gene_ensembl
Platypus (Ornithorhynchus anatinus)	oanatinus_gene_ensembl
Rabbit (Oryctolagus cuniculus)	ocuniculus_gene_ensembl
Rat (Rattus norvegicus)	rnorvegicus_gene_ensembl
S. cerevisiae (Saccharomyces cerevisiae)	scerevisiae_gene_ensembl
Sheep (Ovis aries)	oaries_gene_ensembl
Shrew (Sorex araneus)	saraneus_gene_ensembl
Sloth (Choloepus hoffmanni)	choffmanni_gene_ensembl
Spotted gar (Lepisosteus oculatus)	loculatus_gene_ensembl
Squirrel (Ictidomys tridecemlineatus)	itridecemlineatus_gene_ensembl
Stickleback (Gasterosteus aculeatus)	gaculeatus_gene_ensembl
Tarsier (Tarsius syrichta)	tsyrichta_gene_ensembl
Tasmanian devil (Sarcophilus harrisii)	sharrisii_gene_ensembl
Tetraodon (Tetraodon nigroviridis)	tnigroviridis_gene_ensembl
Tilapia (Oreochromis niloticus)	oniloticus_gene_ensembl
Tree Shrew (Tupaia belangeri)	tbelangeri_gene_ensembl
Turkey (Meleagris gallopavo)	mgallopavo_gene_ensembl
Vervet-AGM (Chlorocebus sabaeus)	csabaeus_gene_ensembl
Wallaby (Macropus eugenii)	meugenii_gene_ensembl
Xenopus (Xenopus tropicalis)	xtropicalis_gene_ensembl
Zebra Finch (Taeniopygia guttata)	tguttata_gene_ensembl
Zebrafish (Danio rerio)	drerio_gene_ensembl