| Next changeset 1:1bb5501a3292 (2024-11-08) |
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Commit message:
planemo upload commit bea844bbbf7c1ccbfe60af62697f89708e00522a |
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added:
macros.xml rgreat.R rgreat.xml test-data/Galaxy16-[dmrseqTest_on_data_7,_data_6,_and_others__DMRseq_results_(RDS)].rdata test-data/dmrseq_1208_1137.rdata test-data/dmrseq_output.rdata test-data/great_output.rds test-data/sim_DMRs.rds tool-data/biomart_datasets.loc tool-data/biomart_datasets.loc.sample tool-data/biomart_datasets.tsv tool-data/generated_options.xml tool_data_table_conf.xml |
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| diff -r 000000000000 -r 3700c6ff0eee macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Nov 07 14:24:33 2024 +0000 |
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| b'@@ -0,0 +1,729 @@\n+<macros>\n+ <xml name="biomart">\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="fpseudograminearum_eg_gene">Fusarium graminearum</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="pstriifor'..b'n value="tanorin61_eg_gene">Triticum aestivum Norin61</option>\n+ <option value="taparagon_eg_gene">Triticum aestivum Paragon</option>\n+ <option value="tarefseqv2_eg_gene">Triticum aestivum Refseqv2</option>\n+ <option value="tarenan_eg_gene">Triticum aestivum Renan</option>\n+ <option value="tarobigus_eg_gene">Triticum aestivum Robigus</option>\n+ <option value="tastanley_eg_gene">Triticum aestivum Stanley</option>\n+ <option value="taweebil_eg_gene">Triticum aestivum Weebill</option>\n+ <option value="tcacao_eg_gene">Theobroma cacao Matina 1-6</option>\n+ <option value="tccriollo_eg_gene">Theobroma cacao Belizian Criollo B97-61/B2</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+ </xml>\n+ <!--\n+ <xml name="citations">\n+ <citations>\n+ <yield />\n+ </citations>\n+ </xml>\n+ -->\n+</macros>\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r 3700c6ff0eee rgreat.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rgreat.R Thu Nov 07 14:24:33 2024 +0000 |
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| b'@@ -0,0 +1,272 @@\n+#!/usr/bin/env Rscript\n+\n+## Command to run tool (without galaxy; for testing):\n+# Rscript Kmer_enumerate_tool.R --input Kmer_enumerate_test_input.fq --input 2 --output Kmer_enumerate_test_output.txt\n+# Rscript dmrseq.R --input 2.fastq --output Kmer_enumerate_test_output.txt\n+# Rscript \'${__tool_directory__}/dmrseq_tool/dmrseq_test.R\' --input \'$input1\' --output \'$output1\'\n+# Rscript /Users/admin_urpp/Desktop/methylator-galaxy/planemo/dmrseq_tool/dmrseq_test.R --input \'$input1\' --output \'$output1\'\n+\n+# Set up R error handling to go to stderr\n+options(show.error.messages=F, error=function(){cat(geterrmessage(),file=stderr());q("no",1,F)})\n+\n+# Avoid crashing Galaxy with an UTF8 error on German LC settings\n+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")\n+\n+## Import required libraries\n+# General:\n+library("getopt")\n+library("tools")\n+library("data.table")\n+\n+# Tool-specific\n+library("rGREAT")\n+library("KEGGREST")\n+library("biomaRt")\n+library("BioMartGOGeneSets")\n+library("GenomicFeatures")\n+library("biomartr") # for getGO\n+library("GenomicRanges")\n+# library("genomation") # annotation of DML/R\n+library("GenomeInfoDb")\n+\n+### create biomart table/file\n+# biomart_datasets <- BioMartGOGeneSets::supportedOrganisms(html=FALSE)\n+# write.table(biomart_datasets, "./planemo/GREAT_tool/tool-data/biomart_datasets.tsv", row.names = FALSE, col.names = TRUE, quote = FALSE, sep = "\\t")\n+# write.table(biomart_datasets[,c(1,4)], "./planemo/GREAT_tool/tool-data/biomart_datasets.loc", row.names = FALSE, col.names = TRUE, quote = FALSE, sep = "\\t")\n+\n+# <tables>\n+# <table name="biomart_datasets" comment_char="#">\n+# <columns>value, name</columns>\n+# <file path="tool-data/biomart_datasets.loc"/>\n+# </table>\n+# </tables>\n+# \n+# <configfiles>\n+# <configfile name="generated_options" from_file="tool-data/generated_options.xml" />\n+# </configfiles>\n+\n+\n+# Take in trailing command line arguments\n+# args <- commandArgs(trailingOnly = TRUE) # maybe use later again if not working\n+\n+#source_local <- function(fname) {\n+# argv <- commandArgs(trailingOnly = FALSE)\n+# base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))\n+# source(paste(base_dir, fname, sep = "/"))\n+#}\n+\n+#source_local("get_deseq_dataset.R")\n+\n+#suppressPackageStartupMessages({\n+# library("DESeq2")\n+# library("RColorBrewer")\n+# library("gplots")\n+#})\n+\n+# Get options using the spec as defined by the enclosed list\n+# Read the options from the default: commandArgs(TRUE)\n+# Define option specification\n+option_specification <- matrix(c(\n+ \'input\', \'i\', 1, \'character\',\n+ \'output_hypo\', \'o\', 1, \'character\',\n+ \'output_hyper\', \'r\', 1, \'character\',\n+ \'biomart_dataset\', \'b\', 1, \'character\',\n+ \'min_gene_set_size\', \'s\', 2, \'integer\', # Optional\n+ \'mode\', \'m\', 2, \'character\', # Optional\n+ \'basal_upstream\', \'u\', 2, \'integer\', # Optional\n+ \'basal_downstream\', \'d\', 2, \'integer\', # Optional\n+ \'extend_from\', \'f\', 2, \'character\', # Optional\n+ \'extension\', \'e\', 2, \'integer\', # Optional\n+ \'exclude\', \'x\', 2, \'character\' # Optional\n+), byrow=TRUE, ncol=4)\n+\n+# Parse options\n+opt <- getopt(option_specification)\n+\n+# Set defaults for parameters if not provided\n+min_gene_set_size <- if (!is.null(opt$min_gene_set_size)) opt$min_gene_set_size else 10\n+mode <- if (!is.null(opt$mode)) opt$mode else \'twoClosest\'\n+extend_from <- if (!is.null(opt$extend_from)) opt$extend_from else \'TSS\'\n+extension <- if (!is.null(opt$extension)) opt$extension else 1000000\n+\n+# Conditional handling for basalUpstream and basalDownstream only if mode == \'basalPlusExt\'\n+if (mode == \'basalPlusExt\') {\n+ basal_upstream <- if (!is.null(opt$basal_upstream)) opt$basal_upstream else 5000\n+ basal_downstream <- if (!is.null(opt$basal_downstream)) opt$basal_downstream else 1000\n+} else {\n+ basal_upstream <- NULL\n+ basal_downstream <- NULL\n+}\n+\n+# Handle optional exclude parameter\n+exclude <- if (!is.null(opt$exclude)) opt$exclude else NULL\n+\n+# Debugging: Print options to ve'..b' = dmRegions, cores = param$cores)\n+# greatResult_CC <- great(gr = significantRegions, gene_sets = "CC", biomart_dataset = param$biomart_selection,\n+# background = dmRegions, cores = param$cores)\n+# greatResult_MF <- great(gr = significantRegions, gene_sets = "MF", biomart_dataset = param$biomart_selection,\n+# background = dmRegions, cores = param$cores)\n+# \n+# # enrichmentTable_BP <- getEnrichmentTable(greatResult_BP)\n+# # enrichmentTable_CC <- getEnrichmentTable(greatResult_CC)\n+# # enrichmentTable_MF <- getEnrichmentTable(greatResult_MF)\n+# \n+# if(param$biomart_selection=="athaliana_eg_gene") {\n+# reactome <- "https://plantreactome.gramene.org/download/current/gene_ids_by_pathway_and_species.tab"\n+# react <- data.frame(data.table::fread(input = reactome, header = F, nThread = 16))\n+# rdb <- react[grep(pattern = "^R-ATH", x = react$V1), ]\n+# reactome_pathways <- split(rdb$V4, paste(rdb$V1, rdb$V2, sep = ": "))\n+# \n+# ## KEGG pathways\n+# kg <- keggList("organism")\n+# \n+# pathway2gene <- keggLink("pathway", "ath")\n+# pathwayName <- keggList("pathway", "ath")\n+# df1 <- data.frame(\n+# gene = gsub("ath:", "", names(pathway2gene)),\n+# pathID = gsub("path:", "", pathway2gene)\n+# )\n+# \n+# df2 <- data.frame(\n+# pathID = gsub("path:", "", names(pathwayName)),\n+# name = pathwayName\n+# )\n+# \n+# df_kegg <- merge(df2, df1)\n+# kegg_pathways <- split(df_kegg$gene, paste(df_kegg$pathID, df_kegg$name,\n+# sep = ": "\n+# ))\n+# \n+# greatResult_RE <- great(gr = significantRegions, gene_sets = reactome_pathways, tss_source = "TxDb.Athaliana.BioMart.plantsmart51",\n+# background = dmRegions, cores = param$cores)\n+# greatResult_KE <- great(gr = significantRegions, gene_sets = kegg_pathways, tss_source = "TxDb.Athaliana.BioMart.plantsmart51",\n+# background = dmRegions, cores = param$cores)\n+# \n+# # enrichmentTable_RE <- getEnrichmentTable(greatResult_RE)\n+# # enrichmentTable_KE <- getEnrichmentTable(greatResult_KE)\n+# saveRDS(greatResult_RE, file = file.path(type, paste0("greatResultRE", ".rds")))\n+# saveRDS(greatResult_KE, file = file.path(type, paste0("greatResultKE", ".rds")))\n+# }\n+# saveRDS(greatResult_BP, file = file.path(type, paste0("greatResultBP", ".rds")))\n+# saveRDS(greatResult_CC, file = file.path(type, paste0("greatResultCC", ".rds")))\n+# saveRDS(greatResult_MF, file = file.path(type, paste0("greatResultMF", ".rds")))\n+# }\n+\n+# Print options to stdout\n+# Useful for debugging\n+#cat("\\n input file: ",opt$input1)\n+#cat("\\n kmer: ",opt$input2)\n+#cat("\\n output file: ",opt$output)\n+\n+\n+\n+######----- Output -----######\n+# saveRDS(list(bs_combined = bs_combined, \n+# bs_filtered = bs_filtered, \n+# sample_info = sample_info,\n+# dmRegions = dmRegions,\n+# significantRegions = significantRegions,\n+# significantRegions_hypo = significantRegions_hypo,\n+# significantRegions_hyper = significantRegions_hyper\n+# ), \n+# # file = opt$output)\n+# file = "output.rds")\n+\n+# write.csv(dmrs, "dmr_results.csv", row.names = FALSE)\n+# write.csv(summary_stats, "summary_stats.csv", row.names = FALSE)\n+# pdf("diagnostic_plot.pdf")\n+# # plotting code here\n+# dev.off()\n+\n+# data(BS.chr21)\n+# pData <- pData(BS.chr21)\n+\n+# Output (...)\n+# write.csv(pData, file = opt$output1)\n+# write.table(pData, file = "/Users/admin_urpp/Desktop/methylator-galaxy/planemo/dmrseq_tool/test-data/pData.txt", quote = F, col.names = F)\n+# write.csv(pData, file = "/Users/admin_urpp/Desktop/methylator-galaxy/planemo/dmrseq_tool/test-data/pData.csv")\n+\n+# \\Users\\admin_urpp\\Desktop\\methylator-galaxy\\planemo\\dmrseq_tool\\test-data\n+cat("\\n Successfully ran great \\n")\n+\n+cat("Session information:\\n\\n")\n+\n+sessionInfo()\n' |
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| diff -r 000000000000 -r 3700c6ff0eee rgreat.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rgreat.xml Thu Nov 07 14:24:33 2024 +0000 |
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| @@ -0,0 +1,133 @@ +<tool id="rgreat" name="Genomic Regions Enrichment of Annotations Tool" version="0.1.0+galaxy0" profile="21.05"> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="4.3.0">r-base</requirement> + <requirement type="package" version="1.20.3">r-getopt</requirement> + <requirement type="package" version="1.15.4">r-data.table</requirement> + <requirement type="package" version="2.4.0">bioconductor-rgreat</requirement> + <requirement type="package" version="1.42.0">bioconductor-keggrest</requirement> + <requirement type="package" version="1.0.7">r-biomartr</requirement> + <requirement type="package" version="0.99.11">bioconductor-biomartgogenesets</requirement> + <requirement type="package" version="1.54.1">bioconductor-genomicranges</requirement> + <requirement type="package" version="1.2.11">bioconductor-genomeinfodbdata</requirement> + <requirement type="package" version="1.34.0">bioconductor-genomationdata</requirement> + </requirements> + + <required_files> + <include path="rgreat.R" /> + </required_files> + + <stdio> + <exit_code range="1:" /> + </stdio> + + <command detect_errors="exit_code"><![CDATA[ + + Rscript '$__tool_directory__/rgreat.R' + --input '$input' + --output_hypo '$output_hypo' + --output_hyper '$output_hyper' + --biomart_dataset '$biomart_dataset' + #if $advanced_parameters.advanced_options + --min_gene_set_size $advanced_parameters.min_gene_set_size + --mode $advanced_parameters.gene_extension_mode.mode + #if $advanced_parameters.gene_extension_mode.mode == 'basalPlusExt' + --basal_upstream $advanced_parameters.gene_extension_mode.basal_upstream + --basal_downstream $advanced_parameters.gene_extension_mode.basal_downstream + #end if + --extend_from $advanced_parameters.extend_from + --extension $advanced_parameters.extension + #if $advanced_parameters.exclude + --exclude '$advanced_parameters.exclude' + #end if + #end if + + ]]></command> + + + <inputs> + <param type="data" name="input" format="rds" /> + <param name="cytosine_context" type="select" value="CG" label="Cytosine context" help="Cytosine methylation context to analyse" > + <option value="CG">C(p)G</option> + <option value="CHG">CHG</option> + <option value="CHH">CHH</option> + </param> + <!-- + <param name="biomart_dataset" type="select" label="Select organism and dataset" help="Choose the organism and corresponding dataset from BioMartGOGeneSets"> + <expand macro="biomart" /> + </param> + --> + <param name="biomart_dataset" type="select" data_table="biomart_datasets" label="Select organism and dataset" help="Choose the organism and corresponding dataset from BioMartGOGeneSets"> + <conditional name="advanced_parameters"> + <param name="advanced_options" type="boolean" label="Show advanced options?" help="Check this box to set additional advanced parameters." checked="false" /> + <when value="true"> + <param name="min_gene_set_size" type="integer" value="10" min="1" label="Minimal size of gene sets" help="Minimal size of gene sets to be considered in the analysis." /> + + <conditional name="gene_extension_mode"> + <param name="mode" type="select" label="Mode to extend genes"> + <option value="basalPlusExt">Basal Plus Extension</option> + <option value="twoClosest">Two Closest</option> + <option value="oneClosest">One Closest</option> + </param> + <when value="basalPlusExt"> + <param name="basal_upstream" type="integer" value="5000" min="0" label="Basal upstream extension" help="Number of base pairs extending to the upstream of TSS to form the basal domains." /> + <param name="basal_downstream" type="integer" value="1000" min="0" label="Basal downstream extension" help="Number of base pairs extending to the downstream of TSS to form the basal domains." /> + </when> + <when value="twoClosest" /> + <when value="oneClosest" /> + </conditional> + + <param name="extend_from" type="select" label="Extend gene from"> + <option value="tss">TSS only</option> + <option value="complete">Complete gene</option> + </param> + + <param name="extension" type="integer" value="1000000" min="0" label="Extension from basal domains" help="Extensions from the basal domains." /> + + <param name="exclude" type="text" area="true" optional="true" label="Excluded regions" help="Regions that are excluded from analysis such as gap regions. The value can also be a vector of chromosome names. Use 'gap' to remove gap regions for the corresponding organism." > + <validator type="regex" message="Use 'gap' or provide a list of chromosome names"> + ^(gap|(\w+,?\s*)+)$ + </validator> + </param> + </when> + <when value="false" /> + </conditional> + + </inputs> + <outputs> + <data name="output_hypo" format="rds" label="Output hypo-methyla: ${cytosine_context} context" /> + <data name="output_hyper" format="rds" label="Output hyper: ${cytosine_context} context" /> + </outputs> + <tests> + <test> + <param name="input" value="dmrseq_output.rdata"/> + <param name="cytosine_context" value="CG"/> + <param name="biomart_dataset" value="hsapiens_gene_ensembl"/> + <param name="advanced_options" value="true"/> + <param name="min_gene_set_size" value="15"/> + <param name="mode" value="basalPlusExt"/> + <param name="basal_upstream" value="5000"/> + <param name="basal_downstream" value="1000"/> + <param name="extend_from" value="tss"/> + <param name="extension" value="1000000"/> + <param name="exclude" value="gap"/> + <output name="output_hypo" file="output_hypo.rds"/> + <output name="output_hyper" file="output_hyper.rds"/> + </test> + </tests> + <help><![CDATA[ + scream for help + + ]]></help> + <citations> + <citation type="bibtex">@Article{, + title = {rGREAT: an R/Bioconductor package for functional enrichment on genomic regions}, + author = {Zuguang Gu and Daniel Huebschmann}, + journal = {Bioinformatics}, + year = {2022}, + doi = {10.1093/bioinformatics/btac745}, + }</citation> + </citations> +</tool> |
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| Binary file test-data/sim_DMRs.rds has changed |
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| diff -r 000000000000 -r 3700c6ff0eee tool-data/biomart_datasets.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/biomart_datasets.loc Thu Nov 07 14:24:33 2024 +0000 |
| [ |
| b"@@ -0,0 +1,719 @@\n+#value\tname\n+aastaci_eg_gene\tSaccharomyces pastorianus\n+aclavatus_eg_gene\tAspergillus clavatus NRRL 1\n+aflavus_eg_gene\tAspergillus flavus NRRL3357\n+afumigatus_eg_gene\tAspergillus fumigatus Af293\n+afumigatusa1163_eg_gene\tAspergillus fumigatus A1163\n+agossypii_eg_gene Ashbya gossypii\n+ainvadans_eg_gene\tTalaromyces marneffei\n+anidulans_eg_gene\tAspergillus nidulans\n+aniger_eg_gene\tAspergillus niger\n+aoryzae_eg_gene\tAspergillus oryzae RIB40\n+aterreus_eg_gene\tAspergillus terreus NIH2624\n+bbassiana_eg_gene\tBeauveria bassiana\n+bcinerea_eg_gene\tBotrytis cinerea B05.10\n+bgraminis_eg_gene\tBlumeria graminis\n+calbicans_eg_gene\tCandida albicans\n+cauris_eg_gene\tCandida auris\n+cduobushaemulonis_eg_gene\tCandida duobushaemulonis\n+cglabrata_eg_gene\tCandida glabrata\n+cgloeosporioides_eg_gene\tColletotrichum gloeosporioides Cg-14\n+cgraminicola_eg_gene\tColletotrichum graminicola\n+chaemuloni_eg_gene\t[Candida] haemuloni\n+chigginsianum_eg_gene\tColletotrichum higginsianum\n+cneoformans_eg_gene\tCryptococcus neoformans var. neoformans JEC21\n+corbiculare_eg_gene\tColletotrichum orbiculare\n+cparapsilosis_eg_gene\tCandida parapsilosis\n+cpseudohaemulonis_eg_gene\t[Candida] pseudohaemulonii\n+ctropicalis_eg_gene\tCandida tropicalis\n+dseptosporum_eg_gene\tDothistroma septosporum\n+fculmorum_eg_gene\tFusarium culmorum UK99\n+ffujikuroi_eg_gene\tFusarium fujikuroi\n+fgraminearum_eg_gene\tFusarium graminearum str. PH-1\n+foxysporum_eg_gene\tFusarium oxysporum\n+fpseudograminearum_eg_gene\tFusarium graminearum\n+fsolani_eg_gene\tFusarium solani\n+fverticillioides_eg_gene\tFusarium verticillioides\n+ggraminis_eg_gene\tGaeumannomyces tritici R3-111a-1\n+gultimum_eg_gene\tSporisorium reilianum\n+hcapsulatum_eg_gene\tHistoplasma capsulatum\n+kpastoris_eg_gene\tKomagataella pastoris\n+lmaculans_eg_gene\tLeptosphaeria maculans\n+mlaricipopulina_eg_gene\tMelampsora larici-populina\n+moryzae_eg_gene\tMagnaporthe oryzae\n+mpoae_eg_gene\tMagnaporthe poae\n+mviolaceum_eg_gene\tMicrobotryum violaceum\n+ncrassa_eg_gene\tNeurospora crassa\n+nfischeri_eg_gene\tAspergillus fischeri NRRL 181\n+pchrysosporium_eg_gene\tPhanerochaete chrysosporium\n+pgraminis_eg_gene\tPuccinia graminis\n+pgraminisug99_eg_gene\tPuccinia graminis Ug99\n+pnodorum_eg_gene\tPhaeosphaeria nodorum\n+poryzae_eg_gene\tMagnaporthe oryzae\n+pstriiformis_eg_gene\tPuccinia striiformis f. sp. tritici PST-130 str. Race 130\n+pteres_eg_gene\tPyrenophora teres f. teres\n+ptriticina_eg_gene\tPuccinia triticina\n+ptriticirepentis_eg_gene\tPyrenophora tritici-repentis Pt-1C-BFP\n+scerevisiae_eg_gene\tSaccharomyces cerevisiae\n+scryophilus_eg_gene\tSchizosaccharomyces cryophilus\n+sjaponicus_eg_gene\tSchizosaccharomyces japonicus\n+soctosporus_eg_gene\tSchizosaccharomyces octosporus\n+spombe_eg_gene\tSchizosaccharomyces pombe\n+sreilianum_eg_gene\tSporisorium reilianum\n+ssclerotiorum_eg_gene\tSclerotinia sclerotiorum\n+tmelanosporum_eg_gene\tTuber melanosporum\n+treesei_eg_gene\tTrichoderma parareesei\n+tvirens_eg_gene\tTrichoderma virens\n+umaydis_eg_gene\tUstilago maydis\n+vdahliae_eg_gene\tVerticillium dahliae\n+vdahliaejr2_eg_gene\tVerticillium dahliae JR2\n+ylipolytica_eg_gene\tYarrowia lipolytica\n+ztritici_eg_gene\tZymoseptoria tritici\n+abrachyrhynchus_gene_ensembl\tAnser brachyrhynchus (Pink-footed goose)\n+acalliptera_gene_ensembl\tAstatotilapia calliptera (Eastern happy)\n+acarolinensis_gene_ensembl\tAnolis carolinensis (Green anole)\n+acchrysaetos_gene_ensembl\tAquila chrysaetos chrysaetos (Golden eagle)\n+acitrinellus_gene_ensembl\tAmphilophus citrinellus (Midas cichlid)\n+amelanoleuca_gene_ensembl\tAiluropoda melanoleuca (Giant panda)\n+amexicanus_gene_ensembl\tAstyanax mexicanus (Mexican tetra)\n+anancymaae_gene_ensembl\tAotus nancymaae (Ma's night monkey)\n+aocellaris_gene_ensembl\tAmphiprion ocellaris (Clown anemonefish)\n+apercula_gene_ensembl\tAmphiprion percula (Orange clownfish)\n+aplatyrhynchos_gene_ensembl\tAnas platyrhynchos (Mallard)\n+apolyacanthus_gene_ensembl\tAcanthochromis polyacanthus (Spiny chromis)\n+applatyrhynchos_gene_ensembl\tAnas platyrhynchos platyrhynchos (Duck)\n+atestudineu"..b'Indica-3B1 var. Khao Yai Guang)\n+oslarhamugad_eg_gene\tOryza sativa (Xian/Indica-2B var. Larha Mugad)\n+oslima_eg_gene\tOryza sativa (Xian/Indica-3A var. Lima)\n+osliuxu_eg_gene\tOryza sativa (Xian/Indica-3B2 var. Liu Xu)\n+osmh63_eg_gene\tOryza sativa (Xian/Indica-adm var. Minghui 63)\n+osn22_eg_gene\tOryza sativa (circum-Aus1 var. N22)\n+osnatelboro_eg_gene\tOryza sativa (circum-Aus2 var. Natel Boro)\n+ospr106_eg_gene\tOryza sativa (Xian/Indica-1B2 var. PR106)\n+oszs97_eg_gene\tOryza sativa (Xian/Indica-1A var. Zhenshan 97)\n+pavium_eg_gene\tPrunus avium\n+pdulcis_eg_gene\tPrunus dulcis\n+phallii_eg_gene\tPanicum hallii HAL2\n+phfil2_eg_gene\tPanicum hallii FIL2\n+ppatens_eg_gene\tPhyscomitrium patens\n+ppersica_eg_gene\tPrunus persica\n+psativum_eg_gene\tPisum sativum\n+psomniferum_eg_gene\tPapaver somniferum\n+ptrichocarpa_eg_gene\tPopulus trichocarpa\n+pvera_eg_gene\tPistacia vera\n+pvulgaris_eg_gene\tPhaseolus vulgaris\n+qlobata_eg_gene\tQuercus lobata\n+qsuber_eg_gene\tQuercus suber\n+rchinensis_eg_gene\tRosa chinensis\n+sbicolor_eg_gene\tSorghum bicolor\n+scereale_eg_gene\tSecale cereale\n+sindicum_eg_gene\tSesamum indicum\n+sitalica_eg_gene\tSetaria italica\n+slycopersicum_eg_gene\tSolanum lycopersicum\n+smoellendorffii_eg_gene\tSelaginella moellendorffii\n+sspontaneum_eg_gene\tSaccharum spontaneum\n+strh8903916_eg_gene\tSolanum tuberosum RH89-039-16\n+stuberosum_eg_gene\tSolanum tuberosum\n+sviridis_eg_gene\tSetaria viridis\n+taarinalrfor_eg_gene\tTriticum aestivum Arinalrfor\n+tacadenza_eg_gene\tTriticum aestivum Cadenza\n+taclaire_eg_gene\tTriticum aestivum Claire\n+taestivum_eg_gene\tTriticum aestivum\n+tajagger_eg_gene\tTriticum aestivum Jagger\n+tajulius_eg_gene\tTriticum aestivum Julius\n+takariega_eg_gene\tTriticum aestivum Kariega\n+talancer_eg_gene\tTriticum aestivum Lancer\n+talandmark_eg_gene\tTriticum aestivum Landmark\n+tamace_eg_gene\tTriticum aestivum Mace\n+tamattis_eg_gene\tTriticum aestivum Sy Mattis\n+tanorin61_eg_gene\tTriticum aestivum Norin61\n+taparagon_eg_gene\tTriticum aestivum Paragon\n+tarefseqv2_eg_gene\tTriticum aestivum Refseqv2\n+tarenan_eg_gene\tTriticum aestivum Renan\n+tarobigus_eg_gene\tTriticum aestivum Robigus\n+tastanley_eg_gene\tTriticum aestivum Stanley\n+taweebil_eg_gene\tTriticum aestivum Weebill\n+tcacao_eg_gene\tTheobroma cacao Matina 1-6\n+tccriollo_eg_gene\tTheobroma cacao Belizian Criollo B97-61/B2\n+tdicoccoides_eg_gene\tTriticum dicoccoides\n+tpratense_eg_gene\tTrifolium pratense\n+tspelta_eg_gene\tTriticum spelta\n+tturgidum_eg_gene\tTriticum turgidum\n+turartu_eg_gene\tTriticum urartu\n+vangularis_eg_gene\tVigna angularis\n+vradiata_eg_gene\tVigna radiata\n+vunguiculata_eg_gene\tVigna unguiculata\n+vvinifera_eg_gene\tVitis vinifera\n+zmays_eg_gene\tZea mays\n+alaibachii_eg_gene\tAlbugo laibachii\n+bnatans_eg_gene\tBigelowiella natans\n+ddiscoideum_eg_gene\tDictyostelium discoideum\n+ehistolytica_eg_gene\tEntamoeba histolytica\n+ehuxleyi_eg_gene\tEmiliania huxleyi\n+glamblia_eg_gene\tGiardia lamblia\n+gtheta_eg_gene\tGuillardia theta CCMP2712\n+harabidopsidis_eg_gene\tHyaloperonospora arabidopsidis\n+lmajor_eg_gene\tLeishmania major\n+paphanidermatum_eg_gene\tPythium aphanidermatum\n+parrhenomanes_eg_gene\tPythium arrhenomanes\n+pberghei_eg_gene\tPlasmodium berghei\n+pchabaudi_eg_gene\tPlasmodium chabaudi\n+pfalciparum_eg_gene\tPlasmodium falciparum 3D7\n+pinfestans_eg_gene\tPhytophthora infestans\n+pirregulare_eg_gene\tPythium irregulare\n+piwayamai_eg_gene\tPythium iwayamai\n+pkernoviae_eg_gene\tPhytophthora kernoviae\n+pknowlesi_eg_gene\tPlasmodium knowlesi\n+plateralis_eg_gene\tPhytophthora lateralis\n+pmultistriata_eg_gene\tPseudo-nitzschia multistriata\n+pparasitica_eg_gene\tPhytophthora parasitica\n+pramorum_eg_gene\tPhytophthora ramorum\n+psojae_eg_gene\tPhytophthora sojae\n+ptetraurelia_eg_gene\tParamecium tetraurelia\n+ptricornutum_eg_gene\tPhaeodactylum tricornutum\n+pultimum_eg_gene\tPythium ultimum\n+pvexans_eg_gene\tPythium vexans\n+pvivax_eg_gene\tPlasmodium vivax\n+tbrucei_eg_gene\tTrypanosoma brucei\n+tgondii_eg_gene\tToxoplasma gondii ME49\n+tpseudonana_eg_gene\tThalassiosira pseudonana\n+tthermophila_eg_gene\tTetrahymena thermophila\n' |
| b |
| diff -r 000000000000 -r 3700c6ff0eee tool-data/biomart_datasets.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/biomart_datasets.loc.sample Thu Nov 07 14:24:33 2024 +0000 |
| [ |
| b"@@ -0,0 +1,719 @@\n+#value\tname\n+aastaci_eg_gene\tSaccharomyces pastorianus\n+aclavatus_eg_gene\tAspergillus clavatus NRRL 1\n+aflavus_eg_gene\tAspergillus flavus NRRL3357\n+afumigatus_eg_gene\tAspergillus fumigatus Af293\n+afumigatusa1163_eg_gene\tAspergillus fumigatus A1163\n+agossypii_eg_gene Ashbya gossypii\n+ainvadans_eg_gene\tTalaromyces marneffei\n+anidulans_eg_gene\tAspergillus nidulans\n+aniger_eg_gene\tAspergillus niger\n+aoryzae_eg_gene\tAspergillus oryzae RIB40\n+aterreus_eg_gene\tAspergillus terreus NIH2624\n+bbassiana_eg_gene\tBeauveria bassiana\n+bcinerea_eg_gene\tBotrytis cinerea B05.10\n+bgraminis_eg_gene\tBlumeria graminis\n+calbicans_eg_gene\tCandida albicans\n+cauris_eg_gene\tCandida auris\n+cduobushaemulonis_eg_gene\tCandida duobushaemulonis\n+cglabrata_eg_gene\tCandida glabrata\n+cgloeosporioides_eg_gene\tColletotrichum gloeosporioides Cg-14\n+cgraminicola_eg_gene\tColletotrichum graminicola\n+chaemuloni_eg_gene\t[Candida] haemuloni\n+chigginsianum_eg_gene\tColletotrichum higginsianum\n+cneoformans_eg_gene\tCryptococcus neoformans var. neoformans JEC21\n+corbiculare_eg_gene\tColletotrichum orbiculare\n+cparapsilosis_eg_gene\tCandida parapsilosis\n+cpseudohaemulonis_eg_gene\t[Candida] pseudohaemulonii\n+ctropicalis_eg_gene\tCandida tropicalis\n+dseptosporum_eg_gene\tDothistroma septosporum\n+fculmorum_eg_gene\tFusarium culmorum UK99\n+ffujikuroi_eg_gene\tFusarium fujikuroi\n+fgraminearum_eg_gene\tFusarium graminearum str. PH-1\n+foxysporum_eg_gene\tFusarium oxysporum\n+fpseudograminearum_eg_gene\tFusarium graminearum\n+fsolani_eg_gene\tFusarium solani\n+fverticillioides_eg_gene\tFusarium verticillioides\n+ggraminis_eg_gene\tGaeumannomyces tritici R3-111a-1\n+gultimum_eg_gene\tSporisorium reilianum\n+hcapsulatum_eg_gene\tHistoplasma capsulatum\n+kpastoris_eg_gene\tKomagataella pastoris\n+lmaculans_eg_gene\tLeptosphaeria maculans\n+mlaricipopulina_eg_gene\tMelampsora larici-populina\n+moryzae_eg_gene\tMagnaporthe oryzae\n+mpoae_eg_gene\tMagnaporthe poae\n+mviolaceum_eg_gene\tMicrobotryum violaceum\n+ncrassa_eg_gene\tNeurospora crassa\n+nfischeri_eg_gene\tAspergillus fischeri NRRL 181\n+pchrysosporium_eg_gene\tPhanerochaete chrysosporium\n+pgraminis_eg_gene\tPuccinia graminis\n+pgraminisug99_eg_gene\tPuccinia graminis Ug99\n+pnodorum_eg_gene\tPhaeosphaeria nodorum\n+poryzae_eg_gene\tMagnaporthe oryzae\n+pstriiformis_eg_gene\tPuccinia striiformis f. sp. tritici PST-130 str. Race 130\n+pteres_eg_gene\tPyrenophora teres f. teres\n+ptriticina_eg_gene\tPuccinia triticina\n+ptriticirepentis_eg_gene\tPyrenophora tritici-repentis Pt-1C-BFP\n+scerevisiae_eg_gene\tSaccharomyces cerevisiae\n+scryophilus_eg_gene\tSchizosaccharomyces cryophilus\n+sjaponicus_eg_gene\tSchizosaccharomyces japonicus\n+soctosporus_eg_gene\tSchizosaccharomyces octosporus\n+spombe_eg_gene\tSchizosaccharomyces pombe\n+sreilianum_eg_gene\tSporisorium reilianum\n+ssclerotiorum_eg_gene\tSclerotinia sclerotiorum\n+tmelanosporum_eg_gene\tTuber melanosporum\n+treesei_eg_gene\tTrichoderma parareesei\n+tvirens_eg_gene\tTrichoderma virens\n+umaydis_eg_gene\tUstilago maydis\n+vdahliae_eg_gene\tVerticillium dahliae\n+vdahliaejr2_eg_gene\tVerticillium dahliae JR2\n+ylipolytica_eg_gene\tYarrowia lipolytica\n+ztritici_eg_gene\tZymoseptoria tritici\n+abrachyrhynchus_gene_ensembl\tAnser brachyrhynchus (Pink-footed goose)\n+acalliptera_gene_ensembl\tAstatotilapia calliptera (Eastern happy)\n+acarolinensis_gene_ensembl\tAnolis carolinensis (Green anole)\n+acchrysaetos_gene_ensembl\tAquila chrysaetos chrysaetos (Golden eagle)\n+acitrinellus_gene_ensembl\tAmphilophus citrinellus (Midas cichlid)\n+amelanoleuca_gene_ensembl\tAiluropoda melanoleuca (Giant panda)\n+amexicanus_gene_ensembl\tAstyanax mexicanus (Mexican tetra)\n+anancymaae_gene_ensembl\tAotus nancymaae (Ma's night monkey)\n+aocellaris_gene_ensembl\tAmphiprion ocellaris (Clown anemonefish)\n+apercula_gene_ensembl\tAmphiprion percula (Orange clownfish)\n+aplatyrhynchos_gene_ensembl\tAnas platyrhynchos (Mallard)\n+apolyacanthus_gene_ensembl\tAcanthochromis polyacanthus (Spiny chromis)\n+applatyrhynchos_gene_ensembl\tAnas platyrhynchos platyrhynchos (Duck)\n+atestudineu"..b'Indica-3B1 var. Khao Yai Guang)\n+oslarhamugad_eg_gene\tOryza sativa (Xian/Indica-2B var. Larha Mugad)\n+oslima_eg_gene\tOryza sativa (Xian/Indica-3A var. Lima)\n+osliuxu_eg_gene\tOryza sativa (Xian/Indica-3B2 var. Liu Xu)\n+osmh63_eg_gene\tOryza sativa (Xian/Indica-adm var. Minghui 63)\n+osn22_eg_gene\tOryza sativa (circum-Aus1 var. N22)\n+osnatelboro_eg_gene\tOryza sativa (circum-Aus2 var. Natel Boro)\n+ospr106_eg_gene\tOryza sativa (Xian/Indica-1B2 var. PR106)\n+oszs97_eg_gene\tOryza sativa (Xian/Indica-1A var. Zhenshan 97)\n+pavium_eg_gene\tPrunus avium\n+pdulcis_eg_gene\tPrunus dulcis\n+phallii_eg_gene\tPanicum hallii HAL2\n+phfil2_eg_gene\tPanicum hallii FIL2\n+ppatens_eg_gene\tPhyscomitrium patens\n+ppersica_eg_gene\tPrunus persica\n+psativum_eg_gene\tPisum sativum\n+psomniferum_eg_gene\tPapaver somniferum\n+ptrichocarpa_eg_gene\tPopulus trichocarpa\n+pvera_eg_gene\tPistacia vera\n+pvulgaris_eg_gene\tPhaseolus vulgaris\n+qlobata_eg_gene\tQuercus lobata\n+qsuber_eg_gene\tQuercus suber\n+rchinensis_eg_gene\tRosa chinensis\n+sbicolor_eg_gene\tSorghum bicolor\n+scereale_eg_gene\tSecale cereale\n+sindicum_eg_gene\tSesamum indicum\n+sitalica_eg_gene\tSetaria italica\n+slycopersicum_eg_gene\tSolanum lycopersicum\n+smoellendorffii_eg_gene\tSelaginella moellendorffii\n+sspontaneum_eg_gene\tSaccharum spontaneum\n+strh8903916_eg_gene\tSolanum tuberosum RH89-039-16\n+stuberosum_eg_gene\tSolanum tuberosum\n+sviridis_eg_gene\tSetaria viridis\n+taarinalrfor_eg_gene\tTriticum aestivum Arinalrfor\n+tacadenza_eg_gene\tTriticum aestivum Cadenza\n+taclaire_eg_gene\tTriticum aestivum Claire\n+taestivum_eg_gene\tTriticum aestivum\n+tajagger_eg_gene\tTriticum aestivum Jagger\n+tajulius_eg_gene\tTriticum aestivum Julius\n+takariega_eg_gene\tTriticum aestivum Kariega\n+talancer_eg_gene\tTriticum aestivum Lancer\n+talandmark_eg_gene\tTriticum aestivum Landmark\n+tamace_eg_gene\tTriticum aestivum Mace\n+tamattis_eg_gene\tTriticum aestivum Sy Mattis\n+tanorin61_eg_gene\tTriticum aestivum Norin61\n+taparagon_eg_gene\tTriticum aestivum Paragon\n+tarefseqv2_eg_gene\tTriticum aestivum Refseqv2\n+tarenan_eg_gene\tTriticum aestivum Renan\n+tarobigus_eg_gene\tTriticum aestivum Robigus\n+tastanley_eg_gene\tTriticum aestivum Stanley\n+taweebil_eg_gene\tTriticum aestivum Weebill\n+tcacao_eg_gene\tTheobroma cacao Matina 1-6\n+tccriollo_eg_gene\tTheobroma cacao Belizian Criollo B97-61/B2\n+tdicoccoides_eg_gene\tTriticum dicoccoides\n+tpratense_eg_gene\tTrifolium pratense\n+tspelta_eg_gene\tTriticum spelta\n+tturgidum_eg_gene\tTriticum turgidum\n+turartu_eg_gene\tTriticum urartu\n+vangularis_eg_gene\tVigna angularis\n+vradiata_eg_gene\tVigna radiata\n+vunguiculata_eg_gene\tVigna unguiculata\n+vvinifera_eg_gene\tVitis vinifera\n+zmays_eg_gene\tZea mays\n+alaibachii_eg_gene\tAlbugo laibachii\n+bnatans_eg_gene\tBigelowiella natans\n+ddiscoideum_eg_gene\tDictyostelium discoideum\n+ehistolytica_eg_gene\tEntamoeba histolytica\n+ehuxleyi_eg_gene\tEmiliania huxleyi\n+glamblia_eg_gene\tGiardia lamblia\n+gtheta_eg_gene\tGuillardia theta CCMP2712\n+harabidopsidis_eg_gene\tHyaloperonospora arabidopsidis\n+lmajor_eg_gene\tLeishmania major\n+paphanidermatum_eg_gene\tPythium aphanidermatum\n+parrhenomanes_eg_gene\tPythium arrhenomanes\n+pberghei_eg_gene\tPlasmodium berghei\n+pchabaudi_eg_gene\tPlasmodium chabaudi\n+pfalciparum_eg_gene\tPlasmodium falciparum 3D7\n+pinfestans_eg_gene\tPhytophthora infestans\n+pirregulare_eg_gene\tPythium irregulare\n+piwayamai_eg_gene\tPythium iwayamai\n+pkernoviae_eg_gene\tPhytophthora kernoviae\n+pknowlesi_eg_gene\tPlasmodium knowlesi\n+plateralis_eg_gene\tPhytophthora lateralis\n+pmultistriata_eg_gene\tPseudo-nitzschia multistriata\n+pparasitica_eg_gene\tPhytophthora parasitica\n+pramorum_eg_gene\tPhytophthora ramorum\n+psojae_eg_gene\tPhytophthora sojae\n+ptetraurelia_eg_gene\tParamecium tetraurelia\n+ptricornutum_eg_gene\tPhaeodactylum tricornutum\n+pultimum_eg_gene\tPythium ultimum\n+pvexans_eg_gene\tPythium vexans\n+pvivax_eg_gene\tPlasmodium vivax\n+tbrucei_eg_gene\tTrypanosoma brucei\n+tgondii_eg_gene\tToxoplasma gondii ME49\n+tpseudonana_eg_gene\tThalassiosira pseudonana\n+tthermophila_eg_gene\tTetrahymena thermophila\n' |
| b |
| diff -r 000000000000 -r 3700c6ff0eee tool-data/biomart_datasets.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/biomart_datasets.tsv Thu Nov 07 14:24:33 2024 +0000 |
| b |
| b'@@ -0,0 +1,719 @@\n+dataset\tdescription\tversion\tname\ttaxon_id\tgenbank_accession\tmart\tn_gene\tn_bp_genesets\tn_cc_genesets\tn_mf_genesets\tncbi_genome_link\n+aastaci_eg_gene\tAphanomyces astaci genes (GCA000520075v1)\tGCA000520075v1\tSaccharomyces pastorianus\t27292\tGCA_011022315.1\tfungi_mart\t19584\t2210\t534\t1516\thttps://ftp.ncbi.nih.gov/genomes/all/GCA/011/022/315//GCA_011022315.1_ASM1102231v1/GCA_011022315.1_ASM1102231v1_assembly_report.txt\n+aclavatus_eg_gene\tAspergillus clavatus NRRL 1 genes (ASM271v1)\tASM271v1\tAspergillus clavatus NRRL 1\t344612\tGCA_000002715.1\tfungi_mart\t9356\t4100\t894\t2120\thttps://ftp.ncbi.nih.gov/genomes/all/GCA/000/002/715//GCA_000002715.1_ASM271v1/GCA_000002715.1_ASM271v1_assembly_report.txt\n+aflavus_eg_gene\tAspergillus flavus NRRL3357 genes (JCVI-afl1-v2.0)\tJCVI-afl1-v2.0\tAspergillus flavus NRRL3357\t332952\tGCA_000006275.2\tfungi_mart\t13485\t4083\t883\t2073\thttps://ftp.ncbi.nih.gov/genomes/all/GCA/000/006/275//GCA_000006275.2_JCVI-afl1-v2.0/GCA_000006275.2_JCVI-afl1-v2.0_assembly_report.txt\n+afumigatus_eg_gene\tAspergillus fumigatus Af293 genes (ASM265v1)\tASM265v1\tAspergillus fumigatus Af293\t330879\tGCA_000002655.1\tfungi_mart\t9859\t4809\t1026\t2623\thttps://ftp.ncbi.nih.gov/genomes/all/GCA/000/002/655//GCA_000002655.1_ASM265v1/GCA_000002655.1_ASM265v1_assembly_report.txt\n+afumigatusa1163_eg_gene\tAspergillus fumigatus A1163 genes (ASM15014v1)\tASM15014v1\tAspergillus fumigatus A1163\t451804\tGCA_000150145.1\tfungi_mart\t10109\t3840\t866\t2015\thttps://ftp.ncbi.nih.gov/genomes/all/GCA/000/150/145//GCA_000150145.1_ASM15014v1/GCA_000150145.1_ASM15014v1_assembly_report.txt\n+agossypii_eg_gene\tAshbya gossypii genes (ASM9102v1)\tASM9102v1\tAshbya gossypii\t284811\tGCA_000091025.3\tfungi_mart\t5520\t4969\t1061\t2320\thttps://ftp.ncbi.nih.gov/genomes/all/GCA/000/091/025//GCA_000091025.3_ASM9102v3/GCA_000091025.3_ASM9102v3_assembly_report.txt\n+ainvadans_eg_gene\tAphanomyces invadans genes (GCA000520115v1)\tGCA000520115v1\tTalaromyces marneffei\t37727\tGCA_009556855.1\tfungi_mart\t15416\t2236\t525\t1519\thttps://ftp.ncbi.nih.gov/genomes/all/GCA/009/556/855//GCA_009556855.1_ASM955685v1/GCA_009556855.1_ASM955685v1_assembly_report.txt\n+anidulans_eg_gene\tAspergillus nidulans genes (ASM1142v1)\tASM1142v1\tAspergillus nidulans\t227321\tGCA_000011425.1\tfungi_mart\t10828\t4989\t1063\t2568\thttps://ftp.ncbi.nih.gov/genomes/all/GCA/000/011/425//GCA_000011425.1_ASM1142v1/GCA_000011425.1_ASM1142v1_assembly_report.txt\n+aniger_eg_gene\tAspergillus niger genes (ASM285v2)\tASM285v2\tAspergillus niger\t5061\tGCA_000002855.2\tfungi_mart\t14772\t4815\t987\t2588\thttps://ftp.ncbi.nih.gov/genomes/all/GCA/000/002/855//GCA_000002855.2_ASM285v2/GCA_000002855.2_ASM285v2_assembly_report.txt\n+aoryzae_eg_gene\tAspergillus oryzae RIB40 genes (ASM18445v3)\tASM18445v3\tAspergillus oryzae RIB40\t510516\tGCA_000184455.3\tfungi_mart\t12376\t4168\t890\t2100\thttps://ftp.ncbi.nih.gov/genomes/all/GCA/000/184/455//GCA_000184455.3_ASM18445v3/GCA_000184455.3_ASM18445v3_assembly_report.txt\n+aterreus_eg_gene\tAspergillus terreus NIH2624 genes (ASM14961v1)\tASM14961v1\tAspergillus terreus NIH2624\t341663\tGCA_000149615.1\tfungi_mart\t10551\t4048\t882\t2088\thttps://ftp.ncbi.nih.gov/genomes/all/GCA/000/149/615//GCA_000149615.1_ASM14961v1/GCA_000149615.1_ASM14961v1_assembly_report.txt\n+bbassiana_eg_gene\tBeauveria bassiana genes (ASM168263v1)\tASM168263v1\tBeauveria bassiana\t176275\tGCA_001682635.1\tfungi_mart\t10286\t3871\t859\t2119\thttps://ftp.ncbi.nih.gov/genomes/all/GCA/001/682/635//GCA_001682635.1_ASM168263v1/GCA_001682635.1_ASM168263v1_assembly_report.txt\n+bcinerea_eg_gene\tBotrytis cinerea B05.10 genes (ASM83294v1)\tASM83294v1\tBotrytis cinerea B05.10\t332648\tGCA_000143535.4\tfungi_mart\t12194\t3897\t862\t1992\thttps://ftp.ncbi.nih.gov/genomes/all/GCA/000/143/535//GCA_000143535.4_ASM14353v4/GCA_000143535.4_ASM14353v4_assembly_report.txt\n+bgraminis_eg_gene\tBlumeria graminis genes (EF2)\tEF2\tBlumeria graminis\t546991\tGCA_000151065.2\tfungi_mart\t7659\t3808\t851\t1886\thttps://ftp.ncbi.nih.gov/genomes/all/GCA/000/151/065//GCA_000151065.2_BGH_DH14_v2.0/GCA_000151065.2_BGH_DH'..b'ASM635v1/GCA_000006355.1_ASM635v1_assembly_report.txt\n+plateralis_eg_gene\tPhytophthora lateralis genes (MPF4_v1.0)\tMPF4_v1.0\tPhytophthora lateralis\t1254522\tGCA_000318465.1\tprotists_mart\t12339\t1742\t421\t1173\thttps://ftp.ncbi.nih.gov/genomes/all/GCA/000/318/465//GCA_000318465.1_MPF4_v1.0/GCA_000318465.1_MPF4_v1.0_assembly_report.txt\n+pmultistriata_eg_gene\tPseudo-nitzschia multistriata genes (ASM90066040v1)\tASM90066040v1\tPseudo-nitzschia multistriata\t183589\tGCA_900660405.1\tprotists_mart\t11895\t1743\t451\t1292\thttps://ftp.ncbi.nih.gov/genomes/all/GCA/900/660/405//GCA_900660405.1_ASM90066040v1/GCA_900660405.1_ASM90066040v1_assembly_report.txt\n+pparasitica_eg_gene\tPhytophthora parasitica genes (Phyt_para_P1569_V1)\tPhyt_para_P1569_V1\tPhytophthora parasitica\t1317065\tGCA_000365505.1\tprotists_mart\t23305\t2100\t520\t1466\thttps://ftp.ncbi.nih.gov/genomes/all/GCA/000/365/505//GCA_000365505.1_Phyt_para_P1569_V1/GCA_000365505.1_Phyt_para_P1569_V1_assembly_report.txt\n+pramorum_eg_gene\tPhytophthora ramorum genes (ASM14973v1)\tASM14973v1\tPhytophthora ramorum\t164328\tGCA_000149735.1\tprotists_mart\t15955\t1975\t482\t1367\thttps://ftp.ncbi.nih.gov/genomes/all/GCA/000/149/735//GCA_000149735.1_ASM14973v1/GCA_000149735.1_ASM14973v1_assembly_report.txt\n+psojae_eg_gene\tPhytophthora sojae genes (P.sojae V3.0)\tP.sojae V3.0\tPhytophthora sojae\t67593\tGCA_000149755.2\tprotists_mart\t28145\t2059\t511\t1422\thttps://ftp.ncbi.nih.gov/genomes/all/GCA/000/149/755//GCA_000149755.2_P.sojae_V3.0/GCA_000149755.2_P.sojae_V3.0_assembly_report.txt\n+ptetraurelia_eg_gene\tParamecium tetraurelia genes (ASM16542v1)\tASM16542v1\tParamecium tetraurelia\t5888\tGCA_000165425.1\tprotists_mart\t39910\t1820\t429\t1123\thttps://ftp.ncbi.nih.gov/genomes/all/GCA/000/165/425//GCA_000165425.1_ASM16542v1/GCA_000165425.1_ASM16542v1_assembly_report.txt\n+ptricornutum_eg_gene\tPhaeodactylum tricornutum genes (ASM15095v2)\tASM15095v2\tPhaeodactylum tricornutum\t556484\tGCA_000150955.2\tprotists_mart\t12392\t1928\t461\t1485\thttps://ftp.ncbi.nih.gov/genomes/all/GCA/000/150/955//GCA_000150955.2_ASM15095v2/GCA_000150955.2_ASM15095v2_assembly_report.txt\n+pultimum_eg_gene\tPythium ultimum genes (pug)\tpug\tPythium ultimum\t431595\tGCA_000143045.1\tprotists_mart\t15839\t2115\t494\t1446\thttps://ftp.ncbi.nih.gov/genomes/all/GCA/000/143/045//GCA_000143045.1_pug/GCA_000143045.1_pug_assembly_report.txt\n+pvexans_eg_gene\tPythium vexans genes (pve_scaffolds_v1)\tpve_scaffolds_v1\tPythium vexans\t1223560\tGCA_000387545.2\tprotists_mart\t11991\t1842\t459\t1305\thttps://ftp.ncbi.nih.gov/genomes/all/GCA/000/387/545//GCA_000387545.2_pve_scaffolds_v1/GCA_000387545.2_pve_scaffolds_v1_assembly_report.txt\n+pvivax_eg_gene\tPlasmodium vivax genes (ASM241v2)\tASM241v2\tPlasmodium vivax\t5855\tGCA_000002415.2\tprotists_mart\t5499\t1404\t381\t928\thttps://ftp.ncbi.nih.gov/genomes/all/GCA/000/002/415//GCA_000002415.2_ASM241v2/GCA_000002415.2_ASM241v2_assembly_report.txt\n+tbrucei_eg_gene\tTrypanosoma brucei genes (TryBru_Apr2005_chr11)\tTryBru_Apr2005_chr11\tTrypanosoma brucei\t5691\tGCA_000209005.1\tprotists_mart\t9456\t1510\t359\t971\thttps://ftp.ncbi.nih.gov/genomes/all/GCA/000/209/005//GCA_000209005.1_TryBru_Apr2005_chr11/GCA_000209005.1_TryBru_Apr2005_chr11_assembly_report.txt\n+tgondii_eg_gene\tToxoplasma gondii ME49 genes (TGA4)\tTGA4\tToxoplasma gondii ME49\t508771\tGCA_000006565.2\tprotists_mart\t8920\t1612\t426\t1409\thttps://ftp.ncbi.nih.gov/genomes/all/GCA/000/006/565//GCA_000006565.2_TGA4/GCA_000006565.2_TGA4_assembly_report.txt\n+tpseudonana_eg_gene\tThalassiosira pseudonana genes (ASM14940v2)\tASM14940v2\tThalassiosira pseudonana\t296543\tGCA_000149405.2\tprotists_mart\t11869\t2534\t646\t1702\thttps://ftp.ncbi.nih.gov/genomes/all/GCA/000/149/405//GCA_000149405.2_ASM14940v2/GCA_000149405.2_ASM14940v2_assembly_report.txt\n+tthermophila_eg_gene\tTetrahymena thermophila genes (JCVI-TTA1-2.2)\tJCVI-TTA1-2.2\tTetrahymena thermophila\t312017\tGCA_000189635.1\tprotists_mart\t25655\t1834\t447\t1158\thttps://ftp.ncbi.nih.gov/genomes/all/GCA/000/189/635//GCA_000189635.1_JCVI-TTA1-2.2/GCA_000189635.1_JCVI-TTA1-2.2_assembly_report.txt\n' |
| b |
| diff -r 000000000000 -r 3700c6ff0eee tool-data/generated_options.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/generated_options.xml Thu Nov 07 14:24:33 2024 +0000 |
| [ |
| b'@@ -0,0 +1,719 @@\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="fpseudograminearum_eg_gene">Fusarium graminearum</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+<'..b'iticum aestivum Claire</option>\n+<option value="taestivum_eg_gene">Triticum aestivum</option>\n+<option value="tajagger_eg_gene">Triticum aestivum Jagger</option>\n+<option value="tajulius_eg_gene">Triticum aestivum Julius</option>\n+<option value="takariega_eg_gene">Triticum aestivum Kariega</option>\n+<option value="talancer_eg_gene">Triticum aestivum Lancer</option>\n+<option value="talandmark_eg_gene">Triticum aestivum Landmark</option>\n+<option value="tamace_eg_gene">Triticum aestivum Mace</option>\n+<option value="tamattis_eg_gene">Triticum aestivum Sy Mattis</option>\n+<option value="tanorin61_eg_gene">Triticum aestivum Norin61</option>\n+<option value="taparagon_eg_gene">Triticum aestivum Paragon</option>\n+<option value="tarefseqv2_eg_gene">Triticum aestivum Refseqv2</option>\n+<option value="tarenan_eg_gene">Triticum aestivum Renan</option>\n+<option value="tarobigus_eg_gene">Triticum aestivum Robigus</option>\n+<option value="tastanley_eg_gene">Triticum aestivum Stanley</option>\n+<option value="taweebil_eg_gene">Triticum aestivum Weebill</option>\n+<option value="tcacao_eg_gene">Theobroma cacao Matina 1-6</option>\n+<option value="tccriollo_eg_gene">Theobroma cacao Belizian Criollo B97-61/B2</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' |
| b |
| diff -r 000000000000 -r 3700c6ff0eee tool_data_table_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml Thu Nov 07 14:24:33 2024 +0000 |
| b |
| @@ -0,0 +1,7 @@ +<?xml version="1.0"?> +<tables> + <table name="biomart_datasets" comment_char="#"> + <columns>value, name</columns> + <file path="tool-data/biomart_datasets.loc"/> + </table> +</tables> \ No newline at end of file |