| Previous changeset 9:d1107fb17398 (2024-11-19) Next changeset 11:c3284ce6eae1 (2024-11-20) |
|
Commit message:
planemo upload commit 7cdcb5fe86852dcb4096216097af9cd914813d6d |
|
modified:
generate_biomart_options.R macros.xml |
|
added:
tool-data/macros.xml |
| b |
| diff -r d1107fb17398 -r 99a0841e3360 generate_biomart_options.R --- a/generate_biomart_options.R Tue Nov 19 13:03:37 2024 +0000 +++ b/generate_biomart_options.R Tue Nov 19 15:11:41 2024 +0000 |
| [ |
| @@ -1,12 +1,13 @@ #!/usr/bin/env Rscript # Load necessary packages +install.packages("readr") library(readr) # Read the TSV file biomart_datasets <- read_tsv("tool-data/biomart_datasets.tsv", col_names = TRUE) # biomart_datasets <- read_tsv("planemo/GREAT_tool/tool-data/biomart_datasets.tsv", col_names = TRUE) - +biomart_datasets <- biomart_datasets[!duplicated(biomart_datasets$description), ] # biomart_datasets <- biomart_datasets[,c(1,4)] # biomart_datasets <- biomart_datasets[,c(1,4)] |
| b |
| diff -r d1107fb17398 -r 99a0841e3360 macros.xml --- a/macros.xml Tue Nov 19 13:03:37 2024 +0000 +++ b/macros.xml Tue Nov 19 15:11:41 2024 +0000 |
| b |
| @@ -241,7 +241,6 @@ <option value="sbboliviensis_gene_ensembl">Bolivian squirrel monkey genes (SaiBol1.0)</option> <option value="scanaria_gene_ensembl">Common canary genes (SCA1)</option> <option value="scaustralis_gene_ensembl">African ostrich genes (ASM69896v1)</option> - <option value="scerevisiae_gene_ensembl">Saccharomyces cerevisiae genes (R64-1-1)</option> <option value="sdumerili_gene_ensembl">Greater amberjack genes (Sdu_1.0)</option> <option value="sformosus_gene_ensembl">Asian bonytongue genes (fSclFor1.1)</option> <option value="sgrahami_gene_ensembl">Golden-line barbel genes (SAMN03320097.WGS_v1.1)</option> @@ -376,7 +375,6 @@ <option value="dggca004324835v1_eg_gene">Dendronephthya gigantea (Carnation coral, DGI-Jeju-01) genes (DenGig_1.0)</option> <option value="dggca904063045v1_eg_gene">Dimorphilus gyrociliatus (Segmented worms) genes (Dgyrociliatus_assembly)</option> <option value="dgrimshawi_eg_gene">Drosophila grimshawi (Fruit fly, TSC#15287-2541.00) genes (dgri_caf1)</option> - <option value="dmelanogaster_eg_gene">Drosophila melanogaster (Fruit fly) genes (BDGP6.46)</option> <option value="dmgca020631705v2_eg_gene">Daphnia magna (Fresh water planktonic, NIES) genes (ASM2063170v1.1)</option> <option value="dmojavensis_eg_gene">Drosophila mojavensis (Fruit fly, TSC#15081-1352.22) genes (dmoj_caf1)</option> <option value="dngca001186385v1_eg_gene">Diuraphis noxia (Russian wheat aphid, RWA2) genes (Dnoxia_1.0)</option> @@ -718,5 +716,5 @@ <option value="tgondii_eg_gene">Toxoplasma gondii ME49 genes (TGA4)</option> <option value="tpseudonana_eg_gene">Thalassiosira pseudonana genes (ASM14940v2)</option> <option value="tthermophila_eg_gene">Tetrahymena thermophila genes (JCVI-TTA1-2.2)</option> - </xml> -</macros> + </xml> +</macros> \ No newline at end of file |
| b |
| diff -r d1107fb17398 -r 99a0841e3360 tool-data/macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/macros.xml Tue Nov 19 15:11:41 2024 +0000 |
| [ |
| b'@@ -0,0 +1,643 @@\n+<option value="aastaci_eg_gene">Saccharomyces pastorianus</option>\n+<option value="aclavatus_eg_gene">Aspergillus clavatus NRRL 1</option>\n+<option value="aflavus_eg_gene">Aspergillus flavus NRRL3357</option>\n+<option value="afumigatus_eg_gene">Aspergillus fumigatus Af293</option>\n+<option value="afumigatusa1163_eg_gene">Aspergillus fumigatus A1163</option>\n+<option value="agossypii_eg_gene">Ashbya gossypii</option>\n+<option value="ainvadans_eg_gene">Talaromyces marneffei</option>\n+<option value="anidulans_eg_gene">Aspergillus nidulans</option>\n+<option value="aniger_eg_gene">Aspergillus niger</option>\n+<option value="aoryzae_eg_gene">Aspergillus oryzae RIB40</option>\n+<option value="aterreus_eg_gene">Aspergillus terreus NIH2624</option>\n+<option value="bbassiana_eg_gene">Beauveria bassiana</option>\n+<option value="bcinerea_eg_gene">Botrytis cinerea B05.10</option>\n+<option value="bgraminis_eg_gene">Blumeria graminis</option>\n+<option value="calbicans_eg_gene">Candida albicans</option>\n+<option value="cauris_eg_gene">Candida auris</option>\n+<option value="cduobushaemulonis_eg_gene">Candida duobushaemulonis</option>\n+<option value="cglabrata_eg_gene">Candida glabrata</option>\n+<option value="cgloeosporioides_eg_gene">Colletotrichum gloeosporioides Cg-14</option>\n+<option value="cgraminicola_eg_gene">Colletotrichum graminicola</option>\n+<option value="chaemuloni_eg_gene">[Candida] haemuloni</option>\n+<option value="chigginsianum_eg_gene">Colletotrichum higginsianum</option>\n+<option value="cneoformans_eg_gene">Cryptococcus neoformans var. neoformans JEC21</option>\n+<option value="corbiculare_eg_gene">Colletotrichum orbiculare</option>\n+<option value="cparapsilosis_eg_gene">Candida parapsilosis</option>\n+<option value="cpseudohaemulonis_eg_gene">[Candida] pseudohaemulonii</option>\n+<option value="ctropicalis_eg_gene">Candida tropicalis</option>\n+<option value="dseptosporum_eg_gene">Dothistroma septosporum</option>\n+<option value="fculmorum_eg_gene">Fusarium culmorum UK99</option>\n+<option value="ffujikuroi_eg_gene">Fusarium fujikuroi</option>\n+<option value="fgraminearum_eg_gene">Fusarium graminearum str. PH-1</option>\n+<option value="foxysporum_eg_gene">Fusarium oxysporum</option>\n+<option value="fsolani_eg_gene">Fusarium solani</option>\n+<option value="fverticillioides_eg_gene">Fusarium verticillioides</option>\n+<option value="ggraminis_eg_gene">Gaeumannomyces tritici R3-111a-1</option>\n+<option value="gultimum_eg_gene">Sporisorium reilianum</option>\n+<option value="hcapsulatum_eg_gene">Histoplasma capsulatum</option>\n+<option value="kpastoris_eg_gene">Komagataella pastoris</option>\n+<option value="lmaculans_eg_gene">Leptosphaeria maculans</option>\n+<option value="mlaricipopulina_eg_gene">Melampsora larici-populina</option>\n+<option value="moryzae_eg_gene">Magnaporthe oryzae</option>\n+<option value="mpoae_eg_gene">Magnaporthe poae</option>\n+<option value="mviolaceum_eg_gene">Microbotryum violaceum</option>\n+<option value="ncrassa_eg_gene">Neurospora crassa</option>\n+<option value="nfischeri_eg_gene">Aspergillus fischeri NRRL 181</option>\n+<option value="pchrysosporium_eg_gene">Phanerochaete chrysosporium</option>\n+<option value="pgraminis_eg_gene">Puccinia graminis</option>\n+<option value="pgraminisug99_eg_gene">Puccinia graminis Ug99</option>\n+<option value="pnodorum_eg_gene">Phaeosphaeria nodorum</option>\n+<option value="poryzae_eg_gene">Magnaporthe oryzae</option>\n+<option value="pstriiformis_eg_gene">Puccinia striiformis f. sp. tritici PST-130 str. Race 130</option>\n+<option value="pteres_eg_gene">Pyrenophora teres f. teres</option>\n+<option value="ptriticina_eg_gene">Puccinia triticina</option>\n+<option value="ptriticirepentis_eg_gene">Pyrenophora tritici-repentis Pt-1C-BFP</option>\n+<option value="scerevisiae_eg_gene">Saccharomyces cerevisiae</option>\n+<option value="scryophilus_eg_gene">Schizosaccharomyces cryophilus</option>\n+<option value="sjaponicus_eg_gene">Schizosaccharomyces japonicus</option>\n+'..b'ca</option>\n+<option value="psativum_eg_gene">Pisum sativum</option>\n+<option value="psomniferum_eg_gene">Papaver somniferum</option>\n+<option value="ptrichocarpa_eg_gene">Populus trichocarpa</option>\n+<option value="pvera_eg_gene">Pistacia vera</option>\n+<option value="pvulgaris_eg_gene">Phaseolus vulgaris</option>\n+<option value="qlobata_eg_gene">Quercus lobata</option>\n+<option value="qsuber_eg_gene">Quercus suber</option>\n+<option value="rchinensis_eg_gene">Rosa chinensis</option>\n+<option value="sbicolor_eg_gene">Sorghum bicolor</option>\n+<option value="scereale_eg_gene">Secale cereale</option>\n+<option value="sindicum_eg_gene">Sesamum indicum</option>\n+<option value="sitalica_eg_gene">Setaria italica</option>\n+<option value="slycopersicum_eg_gene">Solanum lycopersicum</option>\n+<option value="smoellendorffii_eg_gene">Selaginella moellendorffii</option>\n+<option value="sspontaneum_eg_gene">Saccharum spontaneum</option>\n+<option value="strh8903916_eg_gene">Solanum tuberosum RH89-039-16</option>\n+<option value="sviridis_eg_gene">Setaria viridis</option>\n+<option value="taarinalrfor_eg_gene">Triticum aestivum Arinalrfor</option>\n+<option value="tcacao_eg_gene">Theobroma cacao Matina 1-6</option>\n+<option value="tdicoccoides_eg_gene">Triticum dicoccoides</option>\n+<option value="tpratense_eg_gene">Trifolium pratense</option>\n+<option value="tspelta_eg_gene">Triticum spelta</option>\n+<option value="tturgidum_eg_gene">Triticum turgidum</option>\n+<option value="turartu_eg_gene">Triticum urartu</option>\n+<option value="vangularis_eg_gene">Vigna angularis</option>\n+<option value="vradiata_eg_gene">Vigna radiata</option>\n+<option value="vunguiculata_eg_gene">Vigna unguiculata</option>\n+<option value="vvinifera_eg_gene">Vitis vinifera</option>\n+<option value="zmays_eg_gene">Zea mays</option>\n+<option value="alaibachii_eg_gene">Albugo laibachii</option>\n+<option value="bnatans_eg_gene">Bigelowiella natans</option>\n+<option value="ddiscoideum_eg_gene">Dictyostelium discoideum</option>\n+<option value="ehistolytica_eg_gene">Entamoeba histolytica</option>\n+<option value="ehuxleyi_eg_gene">Emiliania huxleyi</option>\n+<option value="glamblia_eg_gene">Giardia lamblia</option>\n+<option value="gtheta_eg_gene">Guillardia theta CCMP2712</option>\n+<option value="harabidopsidis_eg_gene">Hyaloperonospora arabidopsidis</option>\n+<option value="lmajor_eg_gene">Leishmania major</option>\n+<option value="paphanidermatum_eg_gene">Pythium aphanidermatum</option>\n+<option value="parrhenomanes_eg_gene">Pythium arrhenomanes</option>\n+<option value="pberghei_eg_gene">Plasmodium berghei</option>\n+<option value="pchabaudi_eg_gene">Plasmodium chabaudi</option>\n+<option value="pfalciparum_eg_gene">Plasmodium falciparum 3D7</option>\n+<option value="pinfestans_eg_gene">Phytophthora infestans</option>\n+<option value="pirregulare_eg_gene">Pythium irregulare</option>\n+<option value="piwayamai_eg_gene">Pythium iwayamai</option>\n+<option value="pkernoviae_eg_gene">Phytophthora kernoviae</option>\n+<option value="pknowlesi_eg_gene">Plasmodium knowlesi</option>\n+<option value="plateralis_eg_gene">Phytophthora lateralis</option>\n+<option value="pmultistriata_eg_gene">Pseudo-nitzschia multistriata</option>\n+<option value="pparasitica_eg_gene">Phytophthora parasitica</option>\n+<option value="pramorum_eg_gene">Phytophthora ramorum</option>\n+<option value="psojae_eg_gene">Phytophthora sojae</option>\n+<option value="ptetraurelia_eg_gene">Paramecium tetraurelia</option>\n+<option value="ptricornutum_eg_gene">Phaeodactylum tricornutum</option>\n+<option value="pultimum_eg_gene">Pythium ultimum</option>\n+<option value="pvexans_eg_gene">Pythium vexans</option>\n+<option value="pvivax_eg_gene">Plasmodium vivax</option>\n+<option value="tbrucei_eg_gene">Trypanosoma brucei</option>\n+<option value="tgondii_eg_gene">Toxoplasma gondii ME49</option>\n+<option value="tpseudonana_eg_gene">Thalassiosira pseudonana</option>\n+<option value="tthermophila_eg_gene">Tetrahymena thermophila</option>\n+\n' |