diff admin_scripts/species @ 20:2cafc729b2ae draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/admin_scripts/species	Sun May 31 09:05:57 2015 -0400
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+>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
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