Mercurial > repos > mvdbeek > r_goseq_1_22_0
changeset 0:fe71b97cc1a5 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 85e0f34aec3045f48ca9b1a00db02de199a99c95-dirty
| author | mvdbeek |
|---|---|
| date | Wed, 24 Feb 2016 15:54:37 -0500 |
| parents | |
| children | 3ab168143b69 |
| files | goseq.r goseq.xml tool-data/gene_ids.loc.sample tool-data/genomes.loc.sample tool_dependencies.xml |
| diffstat | 5 files changed, 357 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/goseq.r Wed Feb 24 15:54:37 2016 -0500 @@ -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$repcnt + + +# format DE genes into vector suitable for use with goseq +dge_table = read.delim(dge_file, header = TRUE, sep="\t", check.names = FALSE) +genes = as.integer(dge_table[,p_adj_column]<p_adj_cutoff) +names(genes) = dge_table[,1] # Assuming first row contains gene names + +# Estimate PWF + +pdf(length_bias_plot) +pwf=nullp(genes, genome , gene_id) +dev.off() +# Null dstribution wallenius +GO.wall=goseq(pwf, genome, gene_id) + +GO.nobias=goseq(pwf, genome, gene_id, method="Hypergeometric") + +# Sampling dsitribution +GO.samp=goseq(pwf,genome, gene_id, method="Sampling",repcnt=repcnt) + +# Compare sampling with wallenius +pdf(sample_vs_wallenius_plot) +plot(log10(GO.wall[,2]), log10(GO.samp[match(GO.samp[,1],GO.wall[,1]),2]), + xlab="log10(Wallenius p-values)",ylab="log10(Sampling p-values)", + xlim=c(-3,0)) +abline(0,1,col=3,lty=2) +dev.off() + + +write.table(GO.wall, wallenius_tab, sep="\t", row.names = FALSE, quote = FALSE) +write.table(GO.samp, sampling_tab, sep="\t", row.names = FALSE, quote = FALSE) +write.table(GO.nobias, nobias_tab, sep="\t", row.names = FALSE, quote = FALSE) + +# Use the following to get a list of supported genomes / gene ids + +# write.table(supportedGenomes(), "available_genomes.tab", row.names = FALSE, quote=FALSE) +# write.table(supportedGeneIDs(), "supported_gene_ids.tab", row.name = FALSE, quote = FALSE) +# write.table(table.summary, "input_gene_count_matrix.tab", row.names = FALSE, quote = FALSE)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/goseq.xml Wed Feb 24 15:54:37 2016 -0500 @@ -0,0 +1,65 @@ +<tool id="goseq" name="goseq gene ontology analyser" version="0.1.1"> + <description /> + <requirements> + <requirement type="package" version="3.2.1">R</requirement> + <requirement type="package" version="1.22.0">goseq</requirement> + </requirements> + <command interpreter="Rscript"> + goseq.r --dge_file "$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>
--- /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 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/genomes.loc.sample Wed Feb 24 15:54:37 2016 -0500 @@ -0,0 +1,170 @@ +hg38 hg38, Human, Dec. 2013, Genome Reference Consortium GRCh38 +hg19 hg19, Human, Feb. 2009, Genome Reference Consortium GRCh37 +hg18 hg18, Human, Mar. 2006, NCBI Build 36.1 +hg17 hg17, Human, May 2004, NCBI Build 35 +hg16 hg16, Human, Jul. 2003, NCBI Build 34 +vicPac2 vicPac2, Alpaca, Mar. 2013, Broad Institute Vicugna_pacos-2.0.1 +vicPac1 vicPac1, Alpaca, Jul. 2008, Broad Institute VicPac1.0 +dasNov3 dasNov3, Armadillo, Dec. 2011, Broad Institute DasNov3 +otoGar3 otoGar3, Bushbaby, Mar. 2011, Broad Institute OtoGar3 +papHam1 papHam1, Baboon, Nov. 2008, Baylor College of Medicine HGSC Pham_1.0 +papAnu2 papAnu2, Baboon, Mar. 2012, Baylor College of Medicine Panu_2.0 +felCat8 felCat8, Cat, Nov. 2014, ICGSC Felis_catus_8.0 +felCat5 felCat5, Cat, Sep. 2011, ICGSC Felis_catus-6.2 +felCat4 felCat4, Cat, Dec. 2008, NHGRI catChrV17e +felCat3 felCat3, Cat, Mar. 2006, Broad Institute Release 3 +panTro4 panTro4, Chimp, Feb. 2011, CGSC Build 2.1.4 +panTro3 panTro3, Chimp, Oct. 2010, CGSC Build 2.1.3 +panTro2 panTro2, Chimp, Mar. 2006, CGSC Build 2.1 +panTro1 panTro1, Chimp, Nov. 2003, CGSC Build 1.1 +criGri1 criGri1, Chinese hamster, Jul. 2013, Beijing Genomics Institution-Shenzhen C_griseus_v1.0 +bosTau8 bosTau8, Cow, Jun. 2014, University of Maryland v3.1.1 +bosTau7 bosTau7, Cow, Oct. 2011, Baylor College of Medicine HGSC Btau_4.6.1 +bosTau6 bosTau6, Cow, Nov. 2009, University of Maryland v3.1 +bosTau4 bosTau4, Cow, Oct. 2007, Baylor College of Medicine HGSC Btau_4.0 +bosTau3 bosTau3, Cow, Aug. 2006, Baylor College of Medicine HGSC Btau_3.1 +bosTau2 bosTau2, Cow, Mar. 2005, Baylor College of Medicine HGSC Btau_2.0 +canFam3 canFam3, Dog, Sep. 2011, Broad Institute v3.1 +canFam2 canFam2, Dog, May 2005, Broad Institute v2.0 +canFam1 canFam1, Dog, Jul. 2004, Broad Institute v1.0 +turTru2 turTru2, Dolphin, Oct. 2011, Baylor College of Medicine Ttru_1.4 +loxAfr3 loxAfr3, Elephant, Jul. 2009, Broad Institute LoxAfr3 +musFur1 musFur1, Ferret, Apr. 2011, Ferret Genome Sequencing Consortium MusPutFur1.0 +nomLeu3 nomLeu3, Gibbon, Oct. 2012, Gibbon Genome Sequencing Consortium Nleu3.0 +nomLeu2 nomLeu2, Gibbon, Jun. 2011, Gibbon Genome Sequencing Consortium Nleu1.1 +nomLeu1 nomLeu1, Gibbon, Jan. 2010, Gibbon Genome Sequencing Consortium Nleu1.0 +gorGor3 gorGor3, Gorilla, May 2011, Wellcome Trust Sanger Institute gorGor3.1 +cavPor3 cavPor3, Guinea pig, Feb. 2008, Broad Institute cavPor3 +eriEur2 eriEur2, Hedgehog, May 2012, Broad Institute EriEur2.0 +eriEur1 eriEur1, Hedgehog, Jun. 2006, Broad Institute Draft_v1 +equCab2 equCab2, Horse, Sep. 2007, Broad Institute EquCab2 +equCab1 equCab1, Horse, Jan. 2007, Broad Institute EquCab1 +dipOrd1 dipOrd1, Kangaroo rat, Jul. 2008, Baylor/Broad Institute DipOrd1.0 +triMan1 triMan1, Manatee, Oct. 2011, Broad Institute TriManLat1.0 +calJac3 calJac3, Marmoset, Mar. 2009, WUSTL Callithrix_jacchus-v3.2 +calJac1 calJac1, Marmoset, Jun. 2007, WUSTL Callithrix_jacchus-v2.0.2 +pteVam1 pteVam1, Megabat, Jul. 2008, Broad Institute Ptevap1.0 +myoLuc2 myoLuc2, Microbat, Jul. 2010, Broad Institute MyoLuc2.0 +balAcu1 balAcu1, Minke whale, Oct. 2013, KORDI BalAcu1.0 +mm10 mm10, Mouse, Dec. 2011, Genome Reference Consortium GRCm38 +mm9 mm9, Mouse, Jul. 2007, NCBI Build 37 +mm8 mm8, Mouse, Feb. 2006, NCBI Build 36 +mm7 mm7, Mouse, Aug. 2005, NCBI Build 35 +micMur2 micMur2, Mouse lemur, May 2015, Baylor/Broad Institute Mmur_2.0 +micMur1 micMur1, Mouse lemur, Jul. 2007, Broad Institute MicMur1.0 +hetGla2 hetGla2, Naked mole-rat, Jan. 2012, Broad Institute HetGla_female_1.0 +hetGla1 hetGla1, Naked mole-rat, Jul. 2011, Beijing Genomics Institute HetGla_1.0 +monDom5 monDom5, Opossum, Oct. 2006, Broad Institute release MonDom5 +monDom4 monDom4, Opossum, Jan. 2006, Broad Institute release MonDom4 +monDom1 monDom1, Opossum, Oct. 2004, Broad Institute release MonDom1 +ponAbe2 ponAbe2, Orangutan, Jul. 2007, WUSTL Pongo_albelii-2.0.2 +ailMel1 ailMel1, Panda, Dec. 2009, BGI-Shenzhen AilMel 1.0 +susScr3 susScr3, Pig, Aug. 2011, Swine Genome Sequencing Consortium Sscrofa10.2 +susScr2 susScr2, Pig, Nov. 2009, Swine Genome Sequencing Consortium Sscrofa9.2 +ochPri3 ochPri3, Pika, May 2012, Broad Institute OchPri3.0 +ochPri2 ochPri2, Pika, Jul. 2008, Broad Institute OchPri2 +ornAna2 ornAna2, Platypus, Feb. 2007, WUSTL v5.0.1 +ornAna1 ornAna1, Platypus, Mar. 2007, WUSTL v5.0.1 +oryCun2 oryCun2, Rabbit, Apr. 2009, Broad Institute release OryCun2 +rn6 rn6, Rat, Jul. 2014, RGSC Rnor_6.0 +rn5 rn5, Rat, Mar. 2012, RGSC Rnor_5.0 +rn4 rn4, Rat, Nov. 2004, Baylor College of Medicine HGSC v3.4 +rn3 rn3, Rat, Jun. 2003, Baylor College of Medicine HGSC v3.1 +rheMac3 rheMac3, Rhesus, Oct. 2010, Beijing Genomics Institute CR_1.0 +rheMac2 rheMac2, Rhesus, Jan. 2006, Baylor College of Medicine HGSC v1.0 Mmul_051212 +proCap1 proCap1, Rock hyrax, Jul. 2008, Baylor College of Medicine HGSC Procap1.0 +oviAri3 oviAri3, Sheep, Aug. 2012, ISGC Oar_v3.1 +oviAri1 oviAri1, Sheep, Feb. 2010, ISGC Ovis aries 1.0 +sorAra2 sorAra2, Shrew, Aug. 2008, Broad Institute SorAra2.0 +sorAra1 sorAra1, Shrew, Jun. 2006, Broad Institute SorAra1.0 +choHof1 choHof1, Sloth, Jul. 2008, Broad Institute ChoHof1.0 +speTri2 speTri2, Squirrel, Nov. 2011, Broad Institute SpeTri2.0 +saiBol1 saiBol1, Squirrel monkey, Oct. 2011, Broad Institute SaiBol1.0 +tarSyr2 tarSyr2, Tarsier, Sep. 2013, WashU Tarsius_syrichta-2.0.1 +tarSyr1 tarSyr1, Tarsier, Aug. 2008, WUSTL/Broad Institute Tarsyr1.0 +sarHar1 sarHar1, Tasmanian devil, Feb. 2011, Wellcome Trust Sanger Institute Devil_refv7.0 +echTel2 echTel2, Tenrec, Nov. 2012, Broad Institute EchTel2.0 +echTel1 echTel1, Tenrec, Jul. 2005, Broad Institute echTel1 +tupBel1 tupBel1, Tree shrew, Dec. 2006, Broad Institute Tupbel1.0 +macEug2 macEug2, Wallaby, Sep. 2009, Tammar Wallaby Genome Sequencing Consortium Meug_1.1 +cerSim1 cerSim1, White rhinoceros, May 2012, Broad Institute CerSimSim1.0 +allMis1 allMis1, American alligator, Aug. 2012, Int. Crocodilian Genomes Working Group allMis0.2 +gadMor1 gadMor1, Atlantic cod, May 2010, Genofisk GadMor_May2010 +melUnd1 melUnd1, Budgerigar, Sep. 2011, WUSTL v6.3 +galGal4 galGal4, Chicken, Nov. +2011, ICGC Gallus-gallus-4.0 +galGal3 galGal3, Chicken, May 2006, WUSTL Gallus-gallus-2.1 +galGal2 galGal2, Chicken, Feb. 2004, WUSTL Gallus-gallus-1.0 +latCha1 latCha1, Coelacanth, Aug. 2011, Broad Institute LatCha1 +calMil1 calMil1, Elephant shark, Dec. 2013, IMCB Callorhinchus_milli_6.1.3 +fr3 fr3, Fugu, Oct. 2011, JGI v5.0 +fr2 fr2, Fugu, Oct. 2004, JGI v4.0 +fr1 fr1, Fugu, Aug. 2002, JGI v3.0 +petMar2 petMar2, Lamprey, Sep. 2010, WUGSC 7.0 +petMar1 petMar1, Lamprey, Mar. 2007, WUSTL v3.0 +anoCar2 anoCar2, Lizard, May 2010, Broad Institute AnoCar2 +anoCar1 anoCar1, Lizard, Feb. 2007, Broad Institute AnoCar1 +oryLat2 oryLat2, Medaka, Oct. 2005, NIG v1.0 +geoFor1 geoFor1, Medium ground finch, Apr. 2012, BGI GeoFor_1.0 / NCBI 13302 +oreNil2 oreNil2, Nile tilapia, Jan. 2011, Broad Institute Release OreNil1.1 +chrPic1 chrPic1, Painted turtle, Dec. 2011, IPTGSC Chrysemys_picta_bellii-3.0.1 +gasAcu1 gasAcu1, Stickleback, Feb. 2006, Broad Institute Release 1.0 +tetNig2 tetNig2, Tetraodon, Mar. 2007, Genoscope v7 +tetNig1 tetNig1, Tetraodon, Feb. 2004, Genoscope v7 +melGal1 melGal1, Turkey, Dec. 2009, Turkey Genome Consortium v2.01 +xenTro7 xenTro7, X. tropicalis, Sep. 2012, JGI v.7.0 +xenTro3 xenTro3, X. tropicalis, Nov. 2009, JGI v.4.2 +xenTro2 xenTro2, X. tropicalis, Aug. 2005, JGI v.4.1 +xenTro1 xenTro1, X. tropicalis, Oct. 2004, JGI v.3.0 +taeGut2 taeGut2, Zebra finch, Feb. 2013, WashU taeGut324 +taeGut1 taeGut1, Zebra finch, Jul. 2008, WUSTL v3.2.4 +danRer10 danRer10, Zebrafish, Sep. 2014, Genome Reference Consortium GRCz10 +danRer7 danRer7, Zebrafish, Jul. 2010, Sanger Institute Zv9 +danRer6 danRer6, Zebrafish, Dec. 2008, Sanger Institute Zv8 +danRer5 danRer5, Zebrafish, Jul. 2007, Sanger Institute Zv7 +danRer4 danRer4, Zebrafish, Mar. 2006, Sanger Institute Zv6 +danRer3 danRer3, Zebrafish, May 2005, Sanger Institute Zv5 +ci2 ci2, C. intestinalis, Mar. 2005, JGI v2.0 +ci1 ci1, C. intestinalis, Dec. 2002, JGI v1.0 +braFlo1 braFlo1, Lancelet, Mar. 2006, JGI v1.0 +strPur2 strPur2, S. purpuratus, Sep. 2006, Baylor College of Medicine HGSC v. Spur 2.1 +strPur1 strPur1, S. purpuratus, Apr. 2005, Baylor College of Medicine HGSC v. Spur_0.5 +apiMel2 apiMel2, A. mellifera, Jan. 2005, Baylor College of Medicine HGSC v.Amel_2.0 +apiMel1 apiMel1, A. mellifera, Jul. 2004, Baylor College of Medicine HGSC v.Amel_1.2 +anoGam1 anoGam1, A. gambiae, Feb. 2003, IAGP v.MOZ2 +droAna2 droAna2, D. ananassae, Aug. 2005, Agencourt Arachne release +droAna1 droAna1, D. ananassae, Jul. 2004, TIGR Celera release +droEre1 droEre1, D. erecta, Aug. 2005, Agencourt Arachne release +droGri1 droGri1, D. grimshawi, Aug. 2005, Agencourt Arachne release +dm6 dm6, D. melanogaster, Aug. 2014, BDGP Release 6 + ISO1 MT +dm3 dm3, D. melanogaster, Apr. 2006, BDGP Release 5 +dm2 dm2, D. melanogaster, Apr. 2004, BDGP Release 4 +dm1 dm1, D. melanogaster, Jan. 2003, BDGP Release 3 +droMoj2 droMoj2, D. mojavensis, Aug. 2005, Agencourt Arachne release +droMoj1 droMoj1, D. mojavensis, Aug. 2004, Agencourt Arachne release +droPer1 droPer1, D. persimilis, Oct. 2005, Broad Institute release +dp3 dp3, D. pseudoobscura, Nov. 2004, Flybase Release 1.0 +dp2 dp2, D. pseudoobscura, Aug. 2003, Baylor College of Medicine HGSC Freeze 1 +droSec1 droSec1, D. sechellia, Oct. 2005, Broad Institute Release 1.0 +droSim1 droSim1, D. simulans, Apr. 2005, WUSTL Release 1.0 +droVir2 droVir2, D. virilis, Aug. 2005, Agencourt Arachne release +droVir1 droVir1, D. virilis, Jul. 2004, Agencourt Arachne release +droYak2 droYak2, D. yakuba, Nov. 2005, WUSTL Release 2.0 +droYak1 droYak1, D. yakuba, Apr. 2004, WUSTL Release 1.0 +caePb2 caePb2, C. brenneri, Feb. 2008, WUSTL 6.0.1 +caePb1 caePb1, C. brenneri, Jan. 2007, WUSTL 4.0 +cb3 cb3, C. briggsae, Jan. 2007, WUSTL Cb3 +cb1 cb1, C. briggsae, Jul. 2002, WormBase v. cb25.agp8 +ce10 ce10, C. elegans, Oct. 2010, WormBase v. WS220 +ce6 ce6, C. elegans, May 2008, WormBase v. WS190 +ce4 ce4, C. elegans, Jan. 2007, WormBase v. WS170 +ce2 ce2, C. elegans, Mar. 2004, WormBase v. WS120 +caeJap1 caeJap1, C. japonica, Mar. 2008, WUSTL 3.0.2 +caeRem3 caeRem3, C. remanei, May 2007, WUSTL 15.0.1 +caeRem2 caeRem2, C. remanei, Mar. 2006, WUSTL 1.0 +priPac1 priPac1, P. pacificus, Feb. 2007, WUSTL 5.0 +aplCal1 aplCal1, Sea Hare, Sep. 2008, Broad Release Aplcal2.0 +sacCer3 sacCer3, Yeast, April 2011, SGD April 2011 sequence +sacCer2 sacCer2, Yeast, June 2008, SGD June 2008 sequence +sacCer1 sacCer1, Yeast, Oct. 2003, SGD 1 Oct 2003 sequence +eboVir3 eboVir3, Ebola Virus, June 2014, Sierra Leone 2014 (G3683/KM034562.1)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Feb 24 15:54:37 2016 -0500 @@ -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>