# HG changeset patch
# User mvdbeek
# Date 1456494599 18000
# Node ID 1b03f62329005f2ff65fefe31add83a45ae8674d
# Parent 8ce9513136889da65a0cfa64c69ed256afae9530
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
diff -r 8ce951313688 -r 1b03f6232900 get_length_and_gc_content.xml
--- a/get_length_and_gc_content.xml Thu Feb 25 08:49:20 2016 -0500
+++ b/get_length_and_gc_content.xml Fri Feb 26 08:49:59 2016 -0500
@@ -33,10 +33,7 @@
-
-
-
-
+
**What it does**
diff -r 8ce951313688 -r 1b03f6232900 goseq.r
--- a/goseq.r Thu Feb 25 08:49:20 2016 -0500
+++ b/goseq.r Fri Feb 26 08:49:59 2016 -0500
@@ -46,35 +46,34 @@
length_table = read.delim(length_file, header=TRUE, sep="\t", check.names=FALSE, row.names=TRUE)
gene_lengths = length_table[names(genes),]$length
} else {
- gene_lengths = getlength(names(genes),genome, gene_id)
+ gene_lengths = getlength(names(genes), genome, gene_id)
}
# Estimate PWF
-print(gene_lengths)
-
pdf(length_bias_plot)
pwf=nullp(genes, genome, gene_id, gene_lengths)
dev.off()
-# Null dstribution wallenius
+# wallenius approximation of p-values
GO.wall=goseq(pwf, genome, gene_id)
GO.nobias=goseq(pwf, genome, gene_id, method="Hypergeometric")
-# Sampling dsitribution
-GO.samp=goseq(pwf,genome, gene_id, method="Sampling",repcnt=repcnt)
-
-# Compare sampling with wallenius
-pdf(sample_vs_wallenius_plot)
-plot(log10(GO.wall[,2]), log10(GO.samp[match(GO.samp[,1],GO.wall[,1]),2]),
+# Sampling distribution
+if (repcnt > 0) {
+ GO.samp=goseq(pwf,genome, gene_id, method="Sampling", repcnt=repcnt)
+ # Compare sampling with wallenius
+ pdf(sample_vs_wallenius_plot)
+ plot(log10(GO.wall[,2]), log10(GO.samp[match(GO.samp[,1],GO.wall[,1]),2]),
xlab="log10(Wallenius p-values)",ylab="log10(Sampling p-values)",
xlim=c(-3,0))
-abline(0,1,col=3,lty=2)
-dev.off()
+ abline(0,1,col=3,lty=2)
+ dev.off()
+ write.table(GO.samp, sampling_tab, sep="\t", row.names = FALSE, quote = FALSE)
+}
write.table(GO.wall, wallenius_tab, sep="\t", row.names = FALSE, quote = FALSE)
-write.table(GO.samp, sampling_tab, sep="\t", row.names = FALSE, quote = FALSE)
write.table(GO.nobias, nobias_tab, sep="\t", row.names = FALSE, quote = FALSE)
sessionInfo()
diff -r 8ce951313688 -r 1b03f6232900 goseq.xml
--- a/goseq.xml Thu Feb 25 08:49:20 2016 -0500
+++ b/goseq.xml Fri Feb 26 08:49:59 2016 -0500
@@ -1,4 +1,4 @@
-
+
R
@@ -8,6 +8,9 @@
goseq.r --dge_file "$dge_file"
--p_adj_column "$p_adj_column"
--cutoff "$p_adj_cutoff"
+ #if $source.use_length_file == "yes":
+ --length_file "$length_file"
+ #end if
--genome "$genome"
--gene_id "$gene_id"
--wallenius_tab "$wallenius_tab"
@@ -19,32 +22,46 @@
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
-
-
-
-
+
-
+
+
+
+ repcnt != 0
+
-
+
+ repcnt != 0
+
-
-
-
+
+
+
+
+
+ />
@@ -58,8 +75,8 @@
.. _manual: https://bioconductor.org/packages/release/bioc/vignettes/goseq/inst/doc/goseq.pdf
-
+
- 10.1186/gb-2010-11-2-r14
+ 10.1186/gb-2010-11-2-r14
diff -r 8ce951313688 -r 1b03f6232900 test-data/dge_list.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dge_list.tab Fri Feb 26 08:49:59 2016 -0500
@@ -0,0 +1,1001 @@
+Name adj.p.value
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+ENSG00000226637 0.808666563269323
+ENSG00000213092 0.658698634912749
+ENSG00000116209 0.0072223349585748
+ENSG00000241923 0.303289893139539
+ENSG00000092208 0.142441040143205
+ENSG00000161692 0.868354248252297
+ENSG00000018699 0.734374788514334
+ENSG00000134765 0.00650215110876595
+ENSG00000232943 0.701549702363261
+ENSG00000171055 0.00148466914736854
+ENSG00000170412 0.88891990694387
+ENSG00000180884 0.458441720542912
+ENSG00000213066 0.80547549639133
+ENSG00000189343 0.690305853891637
+ENSG00000152377 7.4292956255214e-06
+ENSG00000137642 0.268435747292594
+ENSG00000230406 0.13401701674262
+ENSG00000027697 0.002840466182828
+ENSG00000138685 0.548466549084201
+ENSG00000125691 1.15003598686071e-07
+ENSG00000139192 0.649756977698652
+ENSG00000170142 6.38922101876979e-14
+ENSG00000236735 0.848420495778619
+ENSG00000127226 0.899320127523039
+ENSG00000213033 0.360884039315709
+ENSG00000174483 0.260193846869692
+ENSG00000232676 0.560624855234317
+ENSG00000181359 0.592517124081931
+ENSG00000114735 0.535010072830088
+ENSG00000084073 0.923914050086403
+ENSG00000132879 0.0393568923556353
+ENSG00000187504 0.0441101602396413
+ENSG00000131100 0.000106436767813105
+ENSG00000022556 0.27883485650015
+ENSG00000128590 1.73800036802318e-21
+ENSG00000214029 0.917064559966224
+ENSG00000163322 0.675001698592716
+ENSG00000164332 0.20454326671199
+ENSG00000188529 0.0161433556599521
+ENSG00000164930 0.984153316362751
+ENSG00000188863 0.233043132401159
+ENSG00000198746 0.721379469500436
+ENSG00000231434 0.725608381839331
+ENSG00000168916 0.00589024091625099
+ENSG00000203837 1.76892833362719e-07
+ENSG00000118507 0.449912308591957
+ENSG00000184319 0.366678423622579
+ENSG00000130349 0.0160421479898614
+ENSG00000100478 0.119406328267409
+ENSG00000185189 0.624428577795196
+ENSG00000113621 0.000222224973480795
+ENSG00000238251 0.874940743959374
+ENSG00000198250 2.74474802092663e-05
+ENSG00000232905 0.20532113298844
+ENSG00000206560 1.18683304929125e-05
+ENSG00000225374 0.894456494069142
+ENSG00000236330 0.315576488077443
+ENSG00000136048 0.750473149432026
+ENSG00000146574 0.772807530778178
+ENSG00000129518 0.0459798175019202
+ENSG00000111652 0.634193344204788
+ENSG00000136709 0.554407246784547
+ENSG00000159259 0.262366605763669
+ENSG00000205628 0.798268587926075
+ENSG00000236739 0.382890111338818
+ENSG00000118680 4.1968818844451e-05
+ENSG00000174799 0.742300334521863
+ENSG00000227376 0.996194084342179
+ENSG00000079215 0.162453281378504
+ENSG00000224628 0.191864473181457
+ENSG00000197121 0.290794059600547
+ENSG00000151690 0.00537072754790089
+ENSG00000230531 0.906787427531995
+ENSG00000126226 0.311778628629739
+ENSG00000074071 0.00113433808990478
+ENSG00000100577 0.957727988445661
+ENSG00000086289 0.968664254628913
+ENSG00000205208 0.0550710401653758
+ENSG00000134326 0.748712777850785
+ENSG00000157423 0.999510507884463
+ENSG00000239569 0.328888885510785
+ENSG00000164241 0.876441153890778
+ENSG00000161040 0.831091903231873
+ENSG00000174705 0.244064101688463
+ENSG00000197888 0.00134653046466952
+ENSG00000141448 0.236835594384422
+ENSG00000181690 0.326440628237822
+ENSG00000166788 0.411378011058103
+ENSG00000101473 0.0171413081804384
+ENSG00000204396 0.0483007758935841
+ENSG00000168826 0.552443415574652
+ENSG00000155729 0.0991597147747372
+ENSG00000142082 0.638923880981661
+ENSG00000143727 0.750662288343334
+ENSG00000203995 0.984084091008067
+ENSG00000165055 0.812569903475227
+ENSG00000213971 0.627749833317985
+ENSG00000224453 0.976708700408519
+ENSG00000108960 0.911297258283906
+ENSG00000183506 0.848060111100076
+ENSG00000099139 0.676269590957853
+ENSG00000111331 0.0182585761489983
+ENSG00000133226 0.993938540221067
+ENSG00000217801 0.542666342284879
+ENSG00000130227 0.832276261107283
+ENSG00000164144 0.265975159558312
+ENSG00000128731 0.629112082740044
+ENSG00000079785 0.94307244855189
+ENSG00000106948 0.05112788313254
+ENSG00000115107 0.00183983255792611
+ENSG00000236696 0.193376341017005
+ENSG00000198482 0.37380351144772
+ENSG00000173681 0.0716154000382221
+ENSG00000204164 0.985737910608511
+ENSG00000228612 0.748712777850785
+ENSG00000003096 0.00042794028375702
+ENSG00000180881 0.136030933129489
+ENSG00000205084 0.90764052404365
+ENSG00000159173 0.2498290003939
+ENSG00000197535 0.107477968331359
+ENSG00000223382 0.0390812398780999
+ENSG00000183309 0.949877448246991
+ENSG00000215099 0.977533446702643
+ENSG00000116685 0.130258856790993
+ENSG00000181472 0.783562229232973
+ENSG00000132274 0.912935375903614
+ENSG00000145494 0.532946096201434
+ENSG00000122644 0.00147110292924849
+ENSG00000157107 0.000216975256848586
+ENSG00000145354 0.360340226327433
+ENSG00000158467 0.810768292961056
+ENSG00000164934 0.596506037729255
+ENSG00000134986 1.41212629180466e-07
+ENSG00000121988 0.913419273715737
+ENSG00000178996 0.10888972327876
diff -r 8ce951313688 -r 1b03f6232900 test-data/gene_ids.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_ids.loc Fri Feb 26 08:49:59 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
diff -r 8ce951313688 -r 1b03f6232900 test-data/genomes.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genomes.loc Fri Feb 26 08:49:59 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)
diff -r 8ce951313688 -r 1b03f6232900 test-data/tool_data_table_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tool_data_table_conf.xml Fri Feb 26 08:49:59 2016 -0500
@@ -0,0 +1,11 @@
+
+
+
+
+
\ No newline at end of file
diff -r 8ce951313688 -r 1b03f6232900 test-data/wall.tab
diff -r 8ce951313688 -r 1b03f6232900 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample Thu Feb 25 08:49:20 2016 -0500
+++ b/tool_data_table_conf.xml.sample Fri Feb 26 08:49:59 2016 -0500
@@ -1,7 +1,11 @@
-
-
- value, dbkey, name, path
-
+
+
+
diff -r 8ce951313688 -r 1b03f6232900 tool_data_table_conf.xml.sample.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample.test Fri Feb 26 08:49:59 2016 -0500
@@ -0,0 +1,11 @@
+
+
+
+
+