| Previous changeset 16:8ce951313688 (2016-02-25) Next changeset 18:5fb82111ec62 (2016-02-26) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty |
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modified:
get_length_and_gc_content.xml goseq.r goseq.xml tool_data_table_conf.xml.sample |
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added:
test-data/dge_list.tab test-data/gene_ids.loc test-data/genomes.loc test-data/tool_data_table_conf.xml test-data/wall.tab tool_data_table_conf.xml.sample.test |
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| 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 |
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| @@ -33,10 +33,7 @@ <outputs> <data format="tabular" label="length and gc content" name="output" /> </outputs> - <tests> - <test> - </test> - </tests> + <tests></tests> <help> **What it does** |
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| 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 |
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| @@ -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),]$length } else { - gene_lengths = getlength(names(genes),genome, gene_id) + gene_lengths = getlength(names(genes), genome, gene_id) } # Estimate PWF -print(gene_lengths) - pdf(length_bias_plot) pwf=nullp(genes, genome, gene_id, gene_lengths) dev.off() -# Null dstribution wallenius +# wallenius approximation of p-values GO.wall=goseq(pwf, genome, gene_id) GO.nobias=goseq(pwf, genome, gene_id, method="Hypergeometric") -# Sampling dsitribution -GO.samp=goseq(pwf,genome, gene_id, method="Sampling",repcnt=repcnt) - -# Compare sampling with wallenius -pdf(sample_vs_wallenius_plot) -plot(log10(GO.wall[,2]), log10(GO.samp[match(GO.samp[,1],GO.wall[,1]),2]), +# Sampling distribution +if (repcnt > 0) { + GO.samp=goseq(pwf,genome, gene_id, method="Sampling", repcnt=repcnt) + # Compare sampling with wallenius + pdf(sample_vs_wallenius_plot) + plot(log10(GO.wall[,2]), log10(GO.samp[match(GO.samp[,1],GO.wall[,1]),2]), xlab="log10(Wallenius p-values)",ylab="log10(Sampling p-values)", xlim=c(-3,0)) -abline(0,1,col=3,lty=2) -dev.off() + abline(0,1,col=3,lty=2) + dev.off() + write.table(GO.samp, sampling_tab, sep="\t", row.names = FALSE, quote = FALSE) +} write.table(GO.wall, wallenius_tab, sep="\t", row.names = FALSE, quote = FALSE) -write.table(GO.samp, sampling_tab, sep="\t", row.names = FALSE, quote = FALSE) write.table(GO.nobias, nobias_tab, sep="\t", row.names = FALSE, quote = FALSE) sessionInfo() |
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| diff -r 8ce951313688 -r 1b03f6232900 goseq.xml --- a/goseq.xml Thu Feb 25 08:49:20 2016 -0500 +++ b/goseq.xml Fri Feb 26 08:49:59 2016 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="goseq" name="goseq gene ontology analyser" version="0.1.1"> +<tool id="goseq" name="goseq gene ontology analyser" version="0.1.4"> <description /> <requirements> <requirement type="package" version="3.2.1">R</requirement> @@ -8,6 +8,9 @@ goseq.r --dge_file "$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 @@ </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 help="Select the column that contains the multiple-testing corrected p-value" label="p adjust column" name="p_adj_column" type="data_column" numeric="true" data_ref="dge_file"/> + <param help="Typically 0.05 after multiple testing correction" max="1" label="Minimum p adjust value to consider genes as differentially expressed" name="p_adj_cutoff" type="float" value="0.05" /> + <conditional name="source"> + <param help="This is needed if the gene length is not available in goseq. e.g. hg38 and mm10." label="Use gene length file?" name="use_length_file" type="select"> + <option value="no">no</option> + <option value="yes">yes</option> + </param> + <when value="yes"> + <param label="Gene length file" name="length_file" type="data" format="tabular" required="false" /> + </when> + <when value="no"> + </when> + </conditional> + <param help="Needed to retrieve gene length for length correction" label="Select the genome source" name="genome" size="3" type="select"> + <options from_data_table="go_genomes"></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> + <options from_data_table="go_gene_ids"></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" /> + <param help="Draw this many random control gene sets. Set to 0 to not do sampling. Larger values take a long time" label="sampling depth" name="repcnt" size="3" type="integer" min="0" max="10000" value="0" /> </inputs> <outputs> + <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"> + <filter>repcnt != 0</filter> + </data> <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 - sampling" name="sampling_tab"> + <filter>repcnt != 0</filter> + </data> <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> - + <param name="dge_file" value="dge_list.tab" ftype="tabular"/> + <param name="use_length_file" value="no" /> + <param name="p_adj_column" value="2" /> + <param name="genome" value="hg19" /> + <param name="gene_id" value="ensGene" /> + <output name="wallenius_tab" file="wall.tab" compare="contains"/>/> </test> </tests> <help> @@ -58,8 +75,8 @@ .. _manual: https://bioconductor.org/packages/release/bioc/vignettes/goseq/inst/doc/goseq.pdf - </help> + </help> <citations> - <citation type="doi">10.1186/gb-2010-11-2-r14</citation> + <citation type="doi">10.1186/gb-2010-11-2-r14</citation> </citations> </tool> |
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| 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 |
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| b'@@ -0,0 +1,1001 @@\n+Name\tadj.p.value\n+ENSG00000140459\t0.72654265501997\n+ENSG00000236824\t0.621241793648661\n+ENSG00000162526\t0.104072112354657\n+ENSG00000090402\t0.00550590320364419\n+ENSG00000169188\t0.752973943574106\n+ENSG00000124103\t0.508292390900193\n+ENSG00000241680\t0.297679791800193\n+ENSG00000089009\t0.300444395667807\n+ENSG00000196696\t0.374747091864761\n+ENSG00000006837\t0.883750148448997\n+ENSG00000112312\t0.00157610534964364\n+ENSG00000240392\t0.302701874577034\n+ENSG00000010932\t0.118981349588869\n+ENSG00000167685\t0.076500408607647\n+ENSG00000237101\t0.748031404245103\n+ENSG00000244270\t0.567972685627182\n+ENSG00000104331\t0.00579192580215921\n+ENSG00000242858\t0.0378412177811479\n+ENSG00000148484\t0.718026595230658\n+ENSG00000057608\t0.964227972088948\n+ENSG00000182841\t0.0884209354151656\n+ENSG00000230903\t0.350797225752382\n+ENSG00000106868\t0.788981237232149\n+ENSG00000214564\t0.655009438199043\n+ENSG00000169762\t0.255621294102106\n+ENSG00000168758\t0.163373910729433\n+ENSG00000182827\t0.880121187926376\n+ENSG00000125637\t0.0396047898199658\n+ENSG00000118873\t0.259118545361492\n+ENSG00000186532\t0.884943302417759\n+ENSG00000106771\t0.107076952807406\n+ENSG00000204348\t0.38585136650363\n+ENSG00000197062\t0.244378087660012\n+ENSG00000171067\t0.860339995928752\n+ENSG00000228118\t0.837580099847927\n+ENSG00000213077\t0.0346627558595947\n+ENSG00000188549\t0.0364688234065438\n+ENSG00000135537\t0.818437150201755\n+ENSG00000173715\t0.313716721815305\n+ENSG00000227742\t0.00693864770618258\n+ENSG00000148158\t0.00356590491562172\n+ENSG00000134461\t0.0799694519824768\n+ENSG00000174442\t0.9104363820863\n+ENSG00000198648\t5.66237569853738e-54\n+ENSG00000228599\t0.171370116774069\n+ENSG00000167842\t1.68461902141834e-06\n+ENSG00000108953\t0.018535085127156\n+ENSG00000185504\t0.000252088854916783\n+ENSG00000178950\t0.374511091101791\n+ENSG00000160051\t0.837754660842895\n+ENSG00000130787\t0.627567039717229\n+ENSG00000154146\t0.21971850994087\n+ENSG00000204956\t0.922155399062633\n+ENSG00000231181\t0.798470252573313\n+ENSG00000149308\t0.205056998763193\n+ENSG00000151748\t0.960438036765227\n+ENSG00000141510\t0.843199243028581\n+ENSG00000105325\t0.256030223197636\n+ENSG00000173163\t0.307924645611919\n+ENSG00000064545\t0.0294202433903509\n+ENSG00000236946\t0.787953789147351\n+ENSG00000104450\t0.0261557859283198\n+ENSG00000174469\t0.371325165629903\n+ENSG00000010322\t0.0208260631889359\n+ENSG00000126562\t0.788271827203178\n+ENSG00000143919\t0.883536889885289\n+ENSG00000236285\t0.652881364924924\n+ENSG00000160213\t0.891666551921221\n+ENSG00000185798\t0.808815635747676\n+ENSG00000073614\t0.730900557418546\n+ENSG00000138587\t0.892556542035936\n+ENSG00000090273\t0.485697340128452\n+ENSG00000123384\t0.182965348704756\n+ENSG00000070961\t5.54110180984277e-14\n+ENSG00000159346\t0.577707704641258\n+ENSG00000141425\t0.209299850711904\n+ENSG00000072071\t0.264953967987316\n+ENSG00000057935\t0.0876841507255324\n+ENSG00000226790\t0.739812259382103\n+ENSG00000117410\t0.0991426717444789\n+ENSG00000100038\t5.5224120355487e-05\n+ENSG00000169660\t0.957344873331126\n+ENSG00000227968\t0.968126132117202\n+ENSG00000220483\t0.834400227373994\n+ENSG00000186130\t0.0886115611903655\n+ENSG00000018607\t0.892228191251005\n+ENSG00000142676\t3.05327141290058e-07\n+ENSG00000226144\t0.15035721878846\n+ENSG00000233454\t0.535010072830088\n+ENSG00000230006\t0.993550786209047\n+ENSG00000225405\t0.51182760145349\n+ENSG00000206192\t0.998818135341878\n+ENSG00000141012\t0.675869428835717\n+ENSG00000133138\t0.596116982047846\n+ENSG00000240418\t0.0414032135189338\n+ENSG00000230074\t0.176837449607711\n+ENSG00000106803\t0.110457736393565\n+ENSG00000134987\t0.419483726256258\n+ENSG00000179119\t0.90886027052608\n+ENSG00000130770\t0.797934384822854\n+ENSG00000213760\t0.733546382048368\n+ENSG00000167785\t0.819823215696948\n+ENSG00000152782\t0.187934176357927\n+ENSG00000103121\t0.000116075418643732\n+ENSG00000167614\t0.97150896023414\n+ENSG00000145990\t0.600668890368056\n+ENSG00000233846\t0.617587088091658\n+ENSG00000137285\t0.762128131856854\n+ENSG00000186743\t0.390864600953697\n+ENSG00000130717\t0.786671083021599\n+ENSG00000235363\t0.310504546625491\n+ENSG00000152642\t0.762465600065342\n+ENSG000'..b'4\n+ENSG00000236735\t0.848420495778619\n+ENSG00000127226\t0.899320127523039\n+ENSG00000213033\t0.360884039315709\n+ENSG00000174483\t0.260193846869692\n+ENSG00000232676\t0.560624855234317\n+ENSG00000181359\t0.592517124081931\n+ENSG00000114735\t0.535010072830088\n+ENSG00000084073\t0.923914050086403\n+ENSG00000132879\t0.0393568923556353\n+ENSG00000187504\t0.0441101602396413\n+ENSG00000131100\t0.000106436767813105\n+ENSG00000022556\t0.27883485650015\n+ENSG00000128590\t1.73800036802318e-21\n+ENSG00000214029\t0.917064559966224\n+ENSG00000163322\t0.675001698592716\n+ENSG00000164332\t0.20454326671199\n+ENSG00000188529\t0.0161433556599521\n+ENSG00000164930\t0.984153316362751\n+ENSG00000188863\t0.233043132401159\n+ENSG00000198746\t0.721379469500436\n+ENSG00000231434\t0.725608381839331\n+ENSG00000168916\t0.00589024091625099\n+ENSG00000203837\t1.76892833362719e-07\n+ENSG00000118507\t0.449912308591957\n+ENSG00000184319\t0.366678423622579\n+ENSG00000130349\t0.0160421479898614\n+ENSG00000100478\t0.119406328267409\n+ENSG00000185189\t0.624428577795196\n+ENSG00000113621\t0.000222224973480795\n+ENSG00000238251\t0.874940743959374\n+ENSG00000198250\t2.74474802092663e-05\n+ENSG00000232905\t0.20532113298844\n+ENSG00000206560\t1.18683304929125e-05\n+ENSG00000225374\t0.894456494069142\n+ENSG00000236330\t0.315576488077443\n+ENSG00000136048\t0.750473149432026\n+ENSG00000146574\t0.772807530778178\n+ENSG00000129518\t0.0459798175019202\n+ENSG00000111652\t0.634193344204788\n+ENSG00000136709\t0.554407246784547\n+ENSG00000159259\t0.262366605763669\n+ENSG00000205628\t0.798268587926075\n+ENSG00000236739\t0.382890111338818\n+ENSG00000118680\t4.1968818844451e-05\n+ENSG00000174799\t0.742300334521863\n+ENSG00000227376\t0.996194084342179\n+ENSG00000079215\t0.162453281378504\n+ENSG00000224628\t0.191864473181457\n+ENSG00000197121\t0.290794059600547\n+ENSG00000151690\t0.00537072754790089\n+ENSG00000230531\t0.906787427531995\n+ENSG00000126226\t0.311778628629739\n+ENSG00000074071\t0.00113433808990478\n+ENSG00000100577\t0.957727988445661\n+ENSG00000086289\t0.968664254628913\n+ENSG00000205208\t0.0550710401653758\n+ENSG00000134326\t0.748712777850785\n+ENSG00000157423\t0.999510507884463\n+ENSG00000239569\t0.328888885510785\n+ENSG00000164241\t0.876441153890778\n+ENSG00000161040\t0.831091903231873\n+ENSG00000174705\t0.244064101688463\n+ENSG00000197888\t0.00134653046466952\n+ENSG00000141448\t0.236835594384422\n+ENSG00000181690\t0.326440628237822\n+ENSG00000166788\t0.411378011058103\n+ENSG00000101473\t0.0171413081804384\n+ENSG00000204396\t0.0483007758935841\n+ENSG00000168826\t0.552443415574652\n+ENSG00000155729\t0.0991597147747372\n+ENSG00000142082\t0.638923880981661\n+ENSG00000143727\t0.750662288343334\n+ENSG00000203995\t0.984084091008067\n+ENSG00000165055\t0.812569903475227\n+ENSG00000213971\t0.627749833317985\n+ENSG00000224453\t0.976708700408519\n+ENSG00000108960\t0.911297258283906\n+ENSG00000183506\t0.848060111100076\n+ENSG00000099139\t0.676269590957853\n+ENSG00000111331\t0.0182585761489983\n+ENSG00000133226\t0.993938540221067\n+ENSG00000217801\t0.542666342284879\n+ENSG00000130227\t0.832276261107283\n+ENSG00000164144\t0.265975159558312\n+ENSG00000128731\t0.629112082740044\n+ENSG00000079785\t0.94307244855189\n+ENSG00000106948\t0.05112788313254\n+ENSG00000115107\t0.00183983255792611\n+ENSG00000236696\t0.193376341017005\n+ENSG00000198482\t0.37380351144772\n+ENSG00000173681\t0.0716154000382221\n+ENSG00000204164\t0.985737910608511\n+ENSG00000228612\t0.748712777850785\n+ENSG00000003096\t0.00042794028375702\n+ENSG00000180881\t0.136030933129489\n+ENSG00000205084\t0.90764052404365\n+ENSG00000159173\t0.2498290003939\n+ENSG00000197535\t0.107477968331359\n+ENSG00000223382\t0.0390812398780999\n+ENSG00000183309\t0.949877448246991\n+ENSG00000215099\t0.977533446702643\n+ENSG00000116685\t0.130258856790993\n+ENSG00000181472\t0.783562229232973\n+ENSG00000132274\t0.912935375903614\n+ENSG00000145494\t0.532946096201434\n+ENSG00000122644\t0.00147110292924849\n+ENSG00000157107\t0.000216975256848586\n+ENSG00000145354\t0.360340226327433\n+ENSG00000158467\t0.810768292961056\n+ENSG00000164934\t0.596506037729255\n+ENSG00000134986\t1.41212629180466e-07\n+ENSG00000121988\t0.913419273715737\n+ENSG00000178996\t0.10888972327876\n' |
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| 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 |
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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 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 |
| b |
| 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' |
| b |
| 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 |
| b |
| @@ -0,0 +1,11 @@ +<tables> + <!-- Location of Picard dict file and other files --> + <table name="go_genomes" comment_char="#"> + <columns>value, name</columns> + <file path="${__HERE__}/test-data/genomes.loc" /> + </table> + <table name="go_gene_ids" comment_char="#"> + <columns>value, name</columns> + <file path="${__HERE__}/test-data/gene_ids.loc" /> + </table> +</tables> \ No newline at end of file |
| b |
| diff -r 8ce951313688 -r 1b03f6232900 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Thu Feb 25 08:49:20 2016 -0500 +++ b/tool_data_table_conf.xml.sample Fri Feb 26 08:49:59 2016 -0500 |
| b |
| @@ -1,7 +1,11 @@ <tables> - <!-- Locations of all fasta files under genome directory --> - <table name="all_fasta" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/all_fasta.loc" /> + <!-- Location of Picard dict file and other files --> + <table name="go_genomes" comment_char="#"> + <columns>value, name</columns> + <file path="${__HERE__}/test-data/genomes.loc" /> + </table> + <table name="go_gene_ids" comment_char="#"> + <columns>value, name</columns> + <file path="${__HERE__}/test-data/gene_ids.loc" /> </table> </tables> |
| b |
| 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 |
| b |
| @@ -0,0 +1,11 @@ +<tables> + <!-- Location of Picard dict file and other files --> + <table name="go_genomes" comment_char="#"> + <columns>value, name</columns> + <file path="tool-data/genomes.loc" /> + </table> + <table name="go_gene_ids" comment_char="#"> + <columns>value, name</columns> + <file path="tool-data/gene_ids.loc" /> + </table> +</tables> |