| Next changeset 1:3ab168143b69 (2016-02-25) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 85e0f34aec3045f48ca9b1a00db02de199a99c95-dirty |
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added:
goseq.r goseq.xml tool-data/gene_ids.loc.sample tool-data/genomes.loc.sample tool_dependencies.xml |
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| diff -r 000000000000 -r fe71b97cc1a5 goseq.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/goseq.r Wed Feb 24 15:54:37 2016 -0500 |
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| @@ -0,0 +1,71 @@ +sink(stdout(), type = "message") +library(goseq) +library(optparse) + +option_list <- list( + make_option(c("-d", "--dge_file"), type="character", help="Path to file with differential gene expression result"), + make_option(c("-w","--wallenius_tab"), type="character", help="Path to output file with P-values estimated using wallenius distribution."), + make_option(c("-s","--sampling_tab"), type="character", default=FALSE, help="Path to output file with P-values estimated using wallenius distribution."), + make_option(c("-n","--nobias_tab"), type="character", default=FALSE, help="Path to output file with P-values estimated using wallenius distribution and no correction for gene length bias."), + make_option(c("-l","--length_bias_plot"), type="character", default=FALSE, help="Path to length-bias plot."), + make_option(c("-sw","--sample_vs_wallenius_plot"), type="character", default=FALSE, help="Path to plot comparing sampling with wallenius p-values."), + make_option(c("-padj", "--p_adj_column"), type="integer",help="Column that contains p. adjust values"), + make_option(c("-c", "--cutoff"), type="double",dest="p_adj_cutoff", + help="Genes with p.adjust below cutoff are considered not differentially expressed and serve as control genes"), + make_option(c("-r", "--repcnt"), type="integer", default=100, help="Number of repeats for sampling"), + make_option(c("-g", "--genome"), type="character", help = "Genome [used for looking up correct gene length]"), + make_option(c("-i", "--gene_id"), type="character", help="Gene ID of gene column in DGE file") + ) +parser <- OptionParser(usage = "%prog [options] file", option_list=option_list) +args = parse_args(parser) + +# Vars: +dge_file = args$dge_file +p_adj_column = args$p_adj_colum +p_adj_cutoff = args$p_adj_cutoff +genome = args$genome +gene_id = args$gene_id +wallenius_tab = args$wallenius_tab +sampling_tab = args$sampling_tab +nobias_tab = args$nobias_tab +length_bias_plot = args$length_bias_plot +sample_vs_wallenius_plot = args$sample_vs_wallenius_plot +repcnt = args$repcnt + + +# format DE genes into vector suitable for use with goseq +dge_table = read.delim(dge_file, header = TRUE, sep="\t", check.names = FALSE) +genes = as.integer(dge_table[,p_adj_column]<p_adj_cutoff) +names(genes) = dge_table[,1] # Assuming first row contains gene names + +# Estimate PWF + +pdf(length_bias_plot) +pwf=nullp(genes, genome , gene_id) +dev.off() +# Null dstribution wallenius +GO.wall=goseq(pwf, genome, gene_id) + +GO.nobias=goseq(pwf, genome, gene_id, method="Hypergeometric") + +# Sampling dsitribution +GO.samp=goseq(pwf,genome, gene_id, method="Sampling",repcnt=repcnt) + +# Compare sampling with wallenius +pdf(sample_vs_wallenius_plot) +plot(log10(GO.wall[,2]), log10(GO.samp[match(GO.samp[,1],GO.wall[,1]),2]), + xlab="log10(Wallenius p-values)",ylab="log10(Sampling p-values)", + xlim=c(-3,0)) +abline(0,1,col=3,lty=2) +dev.off() + + +write.table(GO.wall, wallenius_tab, sep="\t", row.names = FALSE, quote = FALSE) +write.table(GO.samp, sampling_tab, sep="\t", row.names = FALSE, quote = FALSE) +write.table(GO.nobias, nobias_tab, sep="\t", row.names = FALSE, quote = FALSE) + +# Use the following to get a list of supported genomes / gene ids + +# write.table(supportedGenomes(), "available_genomes.tab", row.names = FALSE, quote=FALSE) +# write.table(supportedGeneIDs(), "supported_gene_ids.tab", row.name = FALSE, quote = FALSE) +# write.table(table.summary, "input_gene_count_matrix.tab", row.names = FALSE, quote = FALSE) |
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| diff -r 000000000000 -r fe71b97cc1a5 goseq.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/goseq.xml Wed Feb 24 15:54:37 2016 -0500 |
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| @@ -0,0 +1,65 @@ +<tool id="goseq" name="goseq gene ontology analyser" version="0.1.1"> + <description /> + <requirements> + <requirement type="package" version="3.2.1">R</requirement> + <requirement type="package" version="1.22.0">goseq</requirement> + </requirements> + <command interpreter="Rscript"> + goseq.r --dge_file "$dge_file" + --p_adj_column "$p_adj_column" + --cutoff "$p_adj_cutoff" + --genome "$genome" + --gene_id "$gene_id" + --wallenius_tab "$wallenius_tab" + --sampling_tab "$sampling_tab" + --nobias_tab "$nobias_tab" + --length_bias_plot "$length_bias_plot" + --sample_vs_wallenius_plot "$sample_vs_wallenius_plot" + --repcnt "$repcnt" + </command> + <inputs> + <param help="deseq2/edger/limma differential gene expression list" label="DGE list" name="dge_file" type="data" format="tabular" /> + <param help="Select the column that contains the multiple-testing corrected p-value" label="p adjust column" name="p_adj_column" type="data_column" data_ref="dge_file"/> + <param help="Typically 0.05 after multiple testing correction" max="1" label="Minimum p adjust value to consider gene differentially expressed" name="p_adj_cutoff" type="float" value="0.05" /> + <param help="Needed to retrive gene length for length correction" label="Select the genome source" name="genome" size="3" type="select"> + <options from_file="genomes.loc"> + <column name="value" index="0"/> + <column name="name" index="1"/> + </options> + </param> + <param help="Needed for GO analysis" label="Select gene identifier" name="gene_id" type="select"> + <options from_file="gene_ids.loc"> + <column name="value" index="0"/> + <column name="name" index="1"/> + </options> + </param> + <param help="Do this many random samplings. Larger values take a long time" label="Number of random sampling" name="repcnt" size="3" type="integer" min="100" max="10000" value="1000" /> + </inputs> + <outputs> + <data format="tabular" label="Ranked category list - wallenius" name="wallenius_tab" /> + <data format="tabular" label="Ranked category list - sampling" name="sampling_tab" /> + <data format="tabular" label="Ranked category list - no length bias correction" name="nobias_tab" /> + <data format="pdf" label="length bias plot" name="length_bias_plot" /> + <data format="pdf" label="Plot P-value from sampling against wallenius distribution" name="sample_vs_wallenius_plot" /> + </outputs> + <tests> + <test> + + </test> + </tests> + <help> + + **What it does** + + Detects Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. + + Options map closely to the excellent manual_ + + .. _manual: https://bioconductor.org/packages/release/bioc/vignettes/goseq/inst/doc/goseq.pdf + + + </help> + <citations> + <citation type="doi">10.1186/gb-2010-11-2-r14</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r fe71b97cc1a5 tool-data/gene_ids.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/gene_ids.loc.sample Wed Feb 24 15:54:37 2016 -0500 |
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| @@ -0,0 +1,42 @@ +knownGene knownGene, UCSC Genes, NA, Entrez Gene ID +knownGeneOld3 knownGeneOld3, Old UCSC Genes, NA, +ccdsGene ccdsGene, CCDS, NA, +refGene refGene, RefSeq Genes, NA, Entrez Gene ID +xenoRefGene xenoRefGene, Other RefSeq, NA, +vegaGene vegaGene, Vega Genes, Vega Protein Genes, HAVANA Pseudogene ID +vegaPseudoGene vegaPseudoGene, Vega Genes, Vega Pseudogenes, HAVANA Pseudogene ID +ensGene ensGene, Ensembl Genes, NA, Ensembl gene ID +acembly acembly, AceView Genes, NA, +sibGene sibGene, SIB Genes, NA, +nscanPasaGene nscanPasaGene, N-SCAN, N-SCAN PASA-EST, +nscanGene nscanGene, N-SCAN, N-SCAN, +sgpGene sgpGene, SGP Genes, NA, +geneid geneid, Geneid Genes, NA, +genscan genscan, Genscan Genes, NA, +exoniphy exoniphy, Exoniphy, NA, +augustusHints augustusHints, Augustus, Augustus Hints, +augustusXRA augustusXRA, Augustus, Augustus De Novo, +augustusAbinitio augustusAbinitio, Augustus, Augustus Ab Initio, +acescan acescan, ACEScan, NA, +lincRNAsTranscripts lincRNAsTranscripts, lincRNAsTranscripts, NA, Name of gene +wgEncodeGencodeManualV3 wgEncodeGencodeManualV3, Gencode Genes, Gencode Manual, Ensembl gene ID +wgEncodeGencodeAutoV3 wgEncodeGencodeAutoV3, Gencode Genes, Gencode Auto, Ensembl gene ID +wgEncodeGencodePolyaV3 wgEncodeGencodePolyaV3, Gencode Genes, Gencode PolyA, Ensembl gene ID +wgEncodeGencodeBasicV17 wgEncodeGencodeBasicV17, GENCODE Genes V17, NA, Ensembl gene ID +wgEncodeGencodeCompV17 wgEncodeGencodeCompV17, GENCODE Genes V17, NA, Ensembl gene ID +wgEncodeGencodePseudoGeneV17 wgEncodeGencodePseudoGeneV17, GENCODE Genes V17, NA, Ensembl gene ID +wgEncodeGencode2wayConsPseudoV17 wgEncodeGencode2wayConsPseudoV17, GENCODE Genes V17, NA, Ensembl gene ID +wgEncodeGencodePolyaV17 wgEncodeGencodePolyaV17, GENCODE Genes V17, NA, Ensembl gene ID +wgEncodeGencodeBasicV14 wgEncodeGencodeBasicV14, GENCODE Genes V14, NA, Ensembl gene ID +wgEncodeGencodeCompV14 wgEncodeGencodeCompV14, GENCODE Genes V14, NA, Ensembl gene ID +wgEncodeGencodePseudoGeneV14 wgEncodeGencodePseudoGeneV14, GENCODE Genes V14, NA, Ensembl gene ID +wgEncodeGencode2wayConsPseudoV14 wgEncodeGencode2wayConsPseudoV14, GENCODE Genes V14, NA, Ensembl gene ID +wgEncodeGencodePolyaV14 wgEncodeGencodePolyaV14, GENCODE Genes V14, NA, Ensembl gene ID +wgEncodeGencodeBasicV7 wgEncodeGencodeBasicV7, GENCODE Genes V7, NA, Ensembl gene ID +wgEncodeGencodeCompV7 wgEncodeGencodeCompV7, GENCODE Genes V7, NA, Ensembl gene ID +wgEncodeGencodePseudoGeneV7 wgEncodeGencodePseudoGeneV7, GENCODE Genes V7, NA, Ensembl gene ID +wgEncodeGencode2wayConsPseudoV7 wgEncodeGencode2wayConsPseudoV7, GENCODE Genes V7, NA, Ensembl gene ID +wgEncodeGencodePolyaV7 wgEncodeGencodePolyaV7, GENCODE Genes V7, NA, Ensembl gene ID +flyBaseGene flyBaseGene, FlyBase Genes, NA, Name of canonical transcript in cluster +sgdGene sgdGene, SGD Genes, NA, Name of canonical transcript in cluster +geneSymbol geneSymbol, refGene, refFlat, Gene Symbol |
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| diff -r 000000000000 -r fe71b97cc1a5 tool-data/genomes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/genomes.loc.sample Wed Feb 24 15:54:37 2016 -0500 |
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| b'@@ -0,0 +1,170 @@\n+hg38\thg38, Human, Dec. 2013, Genome Reference Consortium GRCh38\n+hg19\thg19, Human, Feb. 2009, Genome Reference Consortium GRCh37\n+hg18\thg18, Human, Mar. 2006, NCBI Build 36.1\n+hg17\thg17, Human, May 2004, NCBI Build 35\n+hg16\thg16, Human, Jul. 2003, NCBI Build 34\n+vicPac2\tvicPac2, Alpaca, Mar. 2013, Broad Institute Vicugna_pacos-2.0.1\n+vicPac1\tvicPac1, Alpaca, Jul. 2008, Broad Institute VicPac1.0\n+dasNov3\tdasNov3, Armadillo, Dec. 2011, Broad Institute DasNov3\n+otoGar3\totoGar3, Bushbaby, Mar. 2011, Broad Institute OtoGar3\n+papHam1\tpapHam1, Baboon, Nov. 2008, Baylor College of Medicine HGSC Pham_1.0\n+papAnu2\tpapAnu2, Baboon, Mar. 2012, Baylor College of Medicine Panu_2.0\n+felCat8\tfelCat8, Cat, Nov. 2014, ICGSC Felis_catus_8.0\n+felCat5\tfelCat5, Cat, Sep. 2011, ICGSC Felis_catus-6.2\n+felCat4\tfelCat4, Cat, Dec. 2008, NHGRI catChrV17e\n+felCat3\tfelCat3, Cat, Mar. 2006, Broad Institute Release 3\n+panTro4\tpanTro4, Chimp, Feb. 2011, CGSC Build 2.1.4\n+panTro3\tpanTro3, Chimp, Oct. 2010, CGSC Build 2.1.3\n+panTro2\tpanTro2, Chimp, Mar. 2006, CGSC Build 2.1\n+panTro1\tpanTro1, Chimp, Nov. 2003, CGSC Build 1.1\n+criGri1\tcriGri1, Chinese hamster, Jul. 2013, Beijing Genomics Institution-Shenzhen C_griseus_v1.0\n+bosTau8\tbosTau8, Cow, Jun. 2014, University of Maryland v3.1.1\n+bosTau7\tbosTau7, Cow, Oct. 2011, Baylor College of Medicine HGSC Btau_4.6.1\n+bosTau6\tbosTau6, Cow, Nov. 2009, University of Maryland v3.1\n+bosTau4\tbosTau4, Cow, Oct. 2007, Baylor College of Medicine HGSC Btau_4.0\n+bosTau3\tbosTau3, Cow, Aug. 2006, Baylor College of Medicine HGSC Btau_3.1\n+bosTau2\tbosTau2, Cow, Mar. 2005, Baylor College of Medicine HGSC Btau_2.0\n+canFam3\tcanFam3, Dog, Sep. 2011, Broad Institute v3.1\n+canFam2\tcanFam2, Dog, May 2005, Broad Institute v2.0\n+canFam1\tcanFam1, Dog, Jul. 2004, Broad Institute v1.0\n+turTru2\tturTru2, Dolphin, Oct. 2011, Baylor College of Medicine Ttru_1.4\n+loxAfr3\tloxAfr3, Elephant, Jul. 2009, Broad Institute LoxAfr3\n+musFur1\tmusFur1, Ferret, Apr. 2011, Ferret Genome Sequencing Consortium MusPutFur1.0\n+nomLeu3\tnomLeu3, Gibbon, Oct. 2012, Gibbon Genome Sequencing Consortium Nleu3.0\n+nomLeu2\tnomLeu2, Gibbon, Jun. 2011, Gibbon Genome Sequencing Consortium Nleu1.1\n+nomLeu1\tnomLeu1, Gibbon, Jan. 2010, Gibbon Genome Sequencing Consortium Nleu1.0\n+gorGor3\tgorGor3, Gorilla, May 2011, Wellcome Trust Sanger Institute gorGor3.1\n+cavPor3\tcavPor3, Guinea pig, Feb. 2008, Broad Institute cavPor3\n+eriEur2\teriEur2, Hedgehog, May 2012, Broad Institute EriEur2.0\n+eriEur1\teriEur1, Hedgehog, Jun. 2006, Broad Institute Draft_v1\n+equCab2\tequCab2, Horse, Sep. 2007, Broad Institute EquCab2\n+equCab1\tequCab1, Horse, Jan. 2007, Broad Institute EquCab1\n+dipOrd1\tdipOrd1, Kangaroo rat, Jul. 2008, Baylor/Broad Institute DipOrd1.0\n+triMan1\ttriMan1, Manatee, Oct. 2011, Broad Institute TriManLat1.0\n+calJac3\tcalJac3, Marmoset, Mar. 2009, WUSTL Callithrix_jacchus-v3.2\n+calJac1\tcalJac1, Marmoset, Jun. 2007, WUSTL Callithrix_jacchus-v2.0.2\n+pteVam1\tpteVam1, Megabat, Jul. 2008, Broad Institute Ptevap1.0\n+myoLuc2\tmyoLuc2, Microbat, Jul. 2010, Broad Institute MyoLuc2.0\n+balAcu1\tbalAcu1, Minke whale, Oct. 2013, KORDI BalAcu1.0\n+mm10\tmm10, Mouse, Dec. 2011, Genome Reference Consortium GRCm38\n+mm9\tmm9, Mouse, Jul. 2007, NCBI Build 37\n+mm8\tmm8, Mouse, Feb. 2006, NCBI Build 36\n+mm7\tmm7, Mouse, Aug. 2005, NCBI Build 35\n+micMur2\tmicMur2, Mouse lemur, May 2015, Baylor/Broad Institute Mmur_2.0\n+micMur1\tmicMur1, Mouse lemur, Jul. 2007, Broad Institute MicMur1.0\n+hetGla2\thetGla2, Naked mole-rat, Jan. 2012, Broad Institute HetGla_female_1.0\n+hetGla1\thetGla1, Naked mole-rat, Jul. 2011, Beijing Genomics Institute HetGla_1.0\n+monDom5\tmonDom5, Opossum, Oct. 2006, Broad Institute release MonDom5\n+monDom4\tmonDom4, Opossum, Jan. 2006, Broad Institute release MonDom4\n+monDom1\tmonDom1, Opossum, Oct. 2004, Broad Institute release MonDom1\n+ponAbe2\tponAbe2, Orangutan, Jul. 2007, WUSTL Pongo_albelii-2.0.2\n+ailMel1\tailMel1, Panda, Dec. 2009, BGI-Shenzhen AilMel 1.0\n+susScr3\tsusScr3, Pig, A'..b'r1\tanoCar1, Lizard, Feb. 2007, Broad Institute AnoCar1\n+oryLat2\toryLat2, Medaka, Oct. 2005, NIG v1.0\n+geoFor1\tgeoFor1, Medium ground finch, Apr. 2012, BGI GeoFor_1.0 / NCBI 13302\n+oreNil2\toreNil2, Nile tilapia, Jan. 2011, Broad Institute Release OreNil1.1\n+chrPic1\tchrPic1, Painted turtle, Dec. 2011, IPTGSC Chrysemys_picta_bellii-3.0.1\n+gasAcu1\tgasAcu1, Stickleback, Feb. 2006, Broad Institute Release 1.0\n+tetNig2\ttetNig2, Tetraodon, Mar. 2007, Genoscope v7\n+tetNig1\ttetNig1, Tetraodon, Feb. 2004, Genoscope v7\n+melGal1\tmelGal1, Turkey, Dec. 2009, Turkey Genome Consortium v2.01\n+xenTro7\txenTro7, X. tropicalis, Sep. 2012, JGI v.7.0\n+xenTro3\txenTro3, X. tropicalis, Nov. 2009, JGI v.4.2\n+xenTro2\txenTro2, X. tropicalis, Aug. 2005, JGI v.4.1\n+xenTro1\txenTro1, X. tropicalis, Oct. 2004, JGI v.3.0\n+taeGut2\ttaeGut2, Zebra finch, Feb. 2013, WashU taeGut324\n+taeGut1\ttaeGut1, Zebra finch, Jul. 2008, WUSTL v3.2.4\n+danRer10\tdanRer10, Zebrafish, Sep. 2014, Genome Reference Consortium GRCz10 \n+danRer7\tdanRer7, Zebrafish, Jul. 2010, Sanger Institute Zv9 \n+danRer6\tdanRer6, Zebrafish, Dec. 2008, Sanger Institute Zv8 \n+danRer5\tdanRer5, Zebrafish, Jul. 2007, Sanger Institute Zv7 \n+danRer4\tdanRer4, Zebrafish, Mar. 2006, Sanger Institute Zv6 \n+danRer3\tdanRer3, Zebrafish, May 2005, Sanger Institute Zv5 \n+ci2\tci2, C. intestinalis, Mar. 2005, JGI v2.0\n+ci1\tci1, C. intestinalis, Dec. 2002, JGI v1.0\n+braFlo1\tbraFlo1, Lancelet, Mar. 2006, JGI v1.0\n+strPur2\tstrPur2, S. purpuratus, Sep. 2006, Baylor College of Medicine HGSC v. Spur 2.1\n+strPur1\tstrPur1, S. purpuratus, Apr. 2005, Baylor College of Medicine HGSC v. Spur_0.5\n+apiMel2\tapiMel2, A. mellifera, Jan. 2005, Baylor College of Medicine HGSC v.Amel_2.0 \n+apiMel1\tapiMel1, A. mellifera, Jul. 2004, Baylor College of Medicine HGSC v.Amel_1.2 \n+anoGam1\tanoGam1, A. gambiae, Feb. 2003, IAGP v.MOZ2\n+droAna2\tdroAna2, D. ananassae, Aug. 2005, Agencourt Arachne release\n+droAna1\tdroAna1, D. ananassae, Jul. 2004, TIGR Celera release\n+droEre1\tdroEre1, D. erecta, Aug. 2005, Agencourt Arachne release\n+droGri1\tdroGri1, D. grimshawi, Aug. 2005, Agencourt Arachne release\n+dm6\tdm6, D. melanogaster, Aug. 2014, BDGP Release 6 + ISO1 MT\n+dm3\tdm3, D. melanogaster, Apr. 2006, BDGP Release 5\n+dm2\tdm2, D. melanogaster, Apr. 2004, BDGP Release 4\n+dm1\tdm1, D. melanogaster, Jan. 2003, BDGP Release 3\n+droMoj2\tdroMoj2, D. mojavensis, Aug. 2005, Agencourt Arachne release\n+droMoj1\tdroMoj1, D. mojavensis, Aug. 2004, Agencourt Arachne release\n+droPer1\tdroPer1, D. persimilis, Oct. 2005, Broad Institute release\n+dp3\tdp3, D. pseudoobscura, Nov. 2004, Flybase Release 1.0\n+dp2\tdp2, D. pseudoobscura, Aug. 2003, Baylor College of Medicine HGSC Freeze 1\n+droSec1\tdroSec1, D. sechellia, Oct. 2005, Broad Institute Release 1.0\n+droSim1\tdroSim1, D. simulans, Apr. 2005, WUSTL Release 1.0\n+droVir2\tdroVir2, D. virilis, Aug. 2005, Agencourt Arachne release\n+droVir1\tdroVir1, D. virilis, Jul. 2004, Agencourt Arachne release\n+droYak2\tdroYak2, D. yakuba, Nov. 2005, WUSTL Release 2.0\n+droYak1\tdroYak1, D. yakuba, Apr. 2004, WUSTL Release 1.0\n+caePb2\tcaePb2, C. brenneri, Feb. 2008, WUSTL 6.0.1\n+caePb1\tcaePb1, C. brenneri, Jan. 2007, WUSTL 4.0\n+cb3\tcb3, C. briggsae, Jan. 2007, WUSTL Cb3\n+cb1\tcb1, C. briggsae, Jul. 2002, WormBase v. cb25.agp8\n+ce10\tce10, C. elegans, Oct. 2010, WormBase v. WS220\n+ce6\tce6, C. elegans, May 2008, WormBase v. WS190\n+ce4\tce4, C. elegans, Jan. 2007, WormBase v. WS170\n+ce2\tce2, C. elegans, Mar. 2004, WormBase v. WS120\n+caeJap1\tcaeJap1, C. japonica, Mar. 2008, WUSTL 3.0.2\n+caeRem3\tcaeRem3, C. remanei, May 2007, WUSTL 15.0.1\n+caeRem2\tcaeRem2, C. remanei, Mar. 2006, WUSTL 1.0\n+priPac1\tpriPac1, P. pacificus, Feb. 2007, WUSTL 5.0\n+aplCal1\taplCal1, Sea Hare, Sep. 2008, Broad Release Aplcal2.0\n+sacCer3\tsacCer3, Yeast, April 2011, SGD April 2011 sequence\n+sacCer2\tsacCer2, Yeast, June 2008, SGD June 2008 sequence\n+sacCer1\tsacCer1, Yeast, Oct. 2003, SGD 1 Oct 2003 sequence\n+eboVir3\teboVir3, Ebola Virus, June 2014, Sierra Leone 2014 (G3683/KM034562.1)\n' |
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| diff -r 000000000000 -r fe71b97cc1a5 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Feb 24 15:54:37 2016 -0500 |
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| @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="R" version="3.2.1"> + <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="goseq" version="1.22.0"> + <repository changeset_revision="0552aea78457" name="package_r_3_2_1_goseq_1_22_0" owner="mvdbeek" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |