Mercurial > repos > mvdbeek > simple_deseq
changeset 0:d00e0214e517 draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_no_replicate commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
| author | mvdbeek |
|---|---|
| date | Sat, 05 Mar 2016 07:00:59 -0500 |
| parents | |
| children | |
| files | simpleDESeq.xml test-data/counts.tab test-data/dge.tab test-data/dge.tab.re_match test-data/dge.tab.re_match.modified tool_dependencies.xml |
| diffstat | 6 files changed, 1212 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/simpleDESeq.xml Sat Mar 05 07:00:59 2016 -0500 @@ -0,0 +1,43 @@ +<tool id="simpleDESeq" name="DESeq Profiling" version="1.0.2" hidden="true"> + <description>2 samples / no replicates</description> + <requirements> + <requirement type="package" version="3.1.2">R</requirement> + <requirement type="package" version="2.14">biocbasics</requirement> + </requirements> + <command interpreter="Rscript">$simpleDESeq </command> + <inputs> + <param name="input" type="data" format="tabular" label="readcount lists, 2 samples"/> + </inputs> + <outputs> + <data name="output" format="tabular" label="DESeq differential calling" /> + </outputs> + <tests> + <test> + <param name="input" value="counts.tab" ftype="tabular"/> + <output name="output" file="dge.tab.re_match.modified" ftype="tabular" compare="re_match" lines_diff="5"/> + </test> + </tests> + <configfiles> + <configfile name="simpleDESeq"> + ## Setup R error handling to go to stderr + options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) + suppressMessages(require(DESeq)) + countsTable = read.delim("${input}", header=TRUE, check.names=FALSE) + rownames( countsTable )= countsTable[,1] + countsTable= countsTable[ , -1 ] + conds = c("C","T") + cds = newCountDataSet( countsTable, conds ) + cds = estimateSizeFactors( cds ) + cds = estimateDispersions( cds, method="blind", sharingMode="fit-only" ) #fitType="local" when dispersion fucks the test. Otherwise DESeq performs a parametric fit using a gamma-family GLM + res = nbinomTest( cds, "C", "T" ) + resNA = res[-which(is.na(res[,8])),] ## omit the NA lignes + write.table ( resNA[order(resNA[,8]), ], file = "${output}", row.names=FALSE, col.names=TRUE, quote= FALSE, dec = ".", sep = "\t", eol = "\n") + </configfile> + </configfiles> + <help> + +**What it does** + +DESeq (version 1) differential calling (order by padj, ascending), on two samples, no replicate + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/counts.tab Sat Mar 05 07:00:59 2016 -0500 @@ -0,0 +1,500 @@ +Geneid 2: Oocyte 1: accepted_hits 4: Pronuclei 1: accepted_hits +NM_001195025 0 0 +NM_028778 0 0 +NM_001290393 0 0 +NM_008922 3133 2288 +NM_175370 4 7 +NM_001290390 0 0 +NM_175642 977 1013 +NM_001290392 0 0 +NM_027671 0 0 +NM_178884 0 0 +NM_199021 332 1436 +NM_198680 0 0 +NM_011465 0 0 +NM_130890 0 0 +NM_001113393 0 0 +NM_001113392 0 0 +NM_001113391 19 88 +NM_031162 0 0 +NR_103716 0 0 +NM_001160371 0 0 +NM_177834 1 2 +NM_145381 606 367 +NM_177173 0 0 +NM_001160369 0 0 +NM_001160370 2 9 +NM_001289497 0 0 +NM_027974 0 6 +NM_133235 74 0 +NM_028096 77 2 +NM_201365 1 0 +NM_001126046 0 0 +NM_001081198 31 144 +NM_001160386 890 1226 +NM_009418 456 774 +NM_001114663 369 353 +NM_001252070 346 463 +NR_045151 0 0 +NM_001081050 93 35 +NM_007642 0 0 +NM_025728 0 0 +NM_029160 0 0 +NM_175210 290 346 +NM_010154 31 23 +NM_175291 0 0 +NM_010472 265 1666 +NM_023314 0 20 +NM_027456 0 0 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dge.tab Sat Mar 05 07:00:59 2016 -0500 @@ -0,0 +1,220 @@ +id baseMean baseMeanA baseMeanB foldChange log2FoldChange pval padj +NM_175296 550.257081641789 23.0570665650267 1077.45709671855 46.7300163132137 5.54627763572775 2.94263028018847e-05 0.00644436031361274 +NM_008922 2761.88390328638 3439.89474039184 2083.87306618093 0.605795590694022 -0.723097017425946 0.347606050966418 1 +NM_175370 5.38365399113096 4.39182220286222 6.37548577939971 1.45167210440457 0.537715622224322 0.990005634217648 1 +NM_175642 997.663221848256 1072.7025730491 922.623870647415 0.86009290350158 -0.217435593000529 0.813633092837835 1 +NM_199021 836.203305648638 364.521242837565 1307.88536845971 3.58795377267635 1.84316130264284 0.0626078198560322 1 +NM_001113391 50.5050597737388 20.8611554635956 80.148964083882 3.8420194041384 1.94186480536043 0.588949394940853 1 +NM_177834 1.45976145812916 1.09795555071556 1.82156736554277 1.65905383360522 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10.9294041932566 0 21.8588083865133 Inf Inf 0.664222165731265 1 +NM_007842 52.2957303476831 47.2120886807689 57.3793720145974 1.21535338973406 0.281375868964537 0.939940510089822 1 +NM_009782 54.4916414491142 51.6039108836311 57.3793720145974 1.11191905869286 0.153051771988997 0.969366092533617 1 +NM_011273 1496.44177089116 1047.44959538264 1945.43394639968 1.85730554957062 0.893211175848761 0.292421771185619 1 +NM_021433 2129.69882925607 2199.20496808326 2060.19269042888 0.936789758266352 -0.0942027916561689 0.905903396463426 1 +NM_001145781 239.82537418297 206.415643534525 273.235104831416 1.32371316511055 0.404590538984962 0.788991307165971 1 +NM_028250 40.367777672332 8.78364440572445 71.9519109389395 8.19157830342577 3.03414144834382 0.482708376221887 1 +NM_001039184 322.900577876936 251.431821113862 394.36933464001 1.5684941265307 0.649380126796499 0.624863582601285 1 +NM_001134741 4.37928437438749 3.29386665214667 5.46470209662832 1.65905383360522 0.730360700166718 0.987881556521901 1 +NR_027640 0.548977775357778 1.09795555071556 0 0 -Inf 0.998927694411559 1 +NM_177644 303.169170314832 265.705243273165 340.633097356499 1.28199614414949 0.358391922779761 0.79329056722861 1 +NM_001085376 62.520777248413 97.7180440136845 27.3235104831416 0.279615814652565 -1.83848213519116 0.555165964028929 1 +NM_011931 13857.3655158581 12072.0212801175 15642.7097515986 1.29578215516915 0.373823195017213 0.58763054091543 1 +NM_009786 42.0339655207058 60.3875552893556 23.6803757520561 0.392139997033961 -1.35055929521685 0.736887140104642 1 +NM_001038621 865.113746993009 580.818486328529 1149.40900765749 1.97894701135141 0.984732983035242 0.305440365844675 1 +NM_001039482 175.78886302788 122.971021680142 228.606704375618 1.85902907247728 0.894549332059886 0.607263898835369 1 +NM_080844 2073.97086836343 2603.25261074658 1544.68912598027 0.593368895359438 -0.75299879275209 0.347025601808978 1 +NM_008030 65.8513618268071 40.6243553764756 91.0783682771387 2.24196464000705 1.16476352431249 0.697613912150911 1 +NM_011347 2142.52010221024 2349.62487853129 1935.4153258892 0.823712475796984 -0.279787255209365 0.724556567127995 1 +NM_010629 59.450800390458 29.64479986932 89.2568009115959 3.01087547580207 1.59018304211846 0.620485460994598 1 +NM_001081126 1.09795555071556 2.19591110143111 0 0 -Inf 0.985480439249778 1 +NM_028759 156.806142937552 146.028088245169 167.584197629935 1.14761618565173 0.198640220722542 0.916823445715141 1 +NM_145512 255.714832876747 264.607287722449 246.822378031046 0.932787528852727 -0.100379594709372 0.947462877116986 1 +NM_001164306 5.46470209662832 0 10.9294041932566 Inf Inf 0.844659017704419 1 +NM_030724 303.079614397155 66.9752885936489 539.183940200661 8.05049073355976 3.00907672823278 0.0385537793679552 1 +NM_033652 37.9036465974594 6.58773330429334 69.2195598906254 10.5073409461664 3.39332571288915 0.458890814677737 1 +NM_023284 10195.2332879558 9097.6596932291 11292.8068826824 1.24128701924156 0.311836744283208 0.654375068484487 1 +NM_133806 1116.62079507772 1116.62079507772 1116.62079507772 1 -6.40685300762984e-16 1 1 +NM_001081304 2984.54409472827 3866.99944962019 2102.08873983636 0.543596855190353 -0.879390985019008 0.250093159071343 1 +NM_001198955 1742.28037716653 1773.19821440562 1711.36253992744 0.965127601654554 -0.0512083979945135 0.950717130189934 1 +NM_001109985 101.460585813391 159.203554853756 43.7176167730266 0.274602013838105 -1.86458588912706 0.427034456668414 1 +NM_027528 1.09795555071556 2.19591110143111 0 0 -Inf 0.985480439249778 1 +NM_011070 1373.31089189797 1568.97848197253 1177.6433018234 0.75057963850649 -0.413922941118844 0.629505128976364 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dge.tab.re_match Sat Mar 05 07:00:59 2016 -0500 @@ -0,0 +1,220 @@ +id\ baseMean\ baseMeanA\ baseMeanB\ foldChange\ log2FoldChange\ pval\ padj +NM\_175296\ 550\.257081641789\ 23\.0570665650267\ 1077\.45709671855\ 46\.7300163132137\ 5\.54627763572775\ 2\.94263028018847e\-05\ 0\.00644436031361274 +NM\_008922\ 2761\.88390328638\ 3439\.89474039184\ 2083\.87306618093\ 0\.605795590694022\ \-0\.723097017425946\ 0\.347606050966418\ 1 +NM\_175370\ 5\.38365399113096\ 4\.39182220286222\ 6\.37548577939971\ 1\.45167210440457\ 0\.537715622224322\ 0\.990005634217648\ 1 +NM\_175642\ 997\.663221848256\ 1072\.7025730491\ 922\.623870647415\ 0\.86009290350158\ \-0\.217435593000529\ 0\.813633092837835\ 1 +NM\_199021\ 836\.203305648638\ 364\.521242837565\ 1307\.88536845971\ 3\.58795377267635\ 1\.84316130264284\ 0\.0626078198560322\ 1 +NM\_001113391\ 50\.5050597737388\ 20\.8611554635956\ 80\.148964083882\ 3\.8420194041384\ 1\.94186480536043\ 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1935\.4153258892\ 0\.823712475796984\ \-0\.279787255209365\ 0\.724556567127995\ 1 +NM\_010629\ 59\.450800390458\ 29\.64479986932\ 89\.2568009115959\ 3\.01087547580207\ 1\.59018304211846\ 0\.620485460994598\ 1 +NM\_001081126\ 1\.09795555071556\ 2\.19591110143111\ 0\ 0\ \-Inf\ 0\.985480439249778\ 1 +NM\_028759\ 156\.806142937552\ 146\.028088245169\ 167\.584197629935\ 1\.14761618565173\ 0\.198640220722542\ 0\.916823445715141\ 1 +NM\_145512\ 255\.714832876747\ 264\.607287722449\ 246\.822378031046\ 0\.932787528852727\ \-0\.100379594709372\ 0\.947462877116986\ 1 +NM\_001164306\ 5\.46470209662832\ 0\ 10\.9294041932566\ Inf\ Inf\ 0\.844659017704419\ 1 +NM\_030724\ 303\.079614397155\ 66\.9752885936489\ 539\.183940200661\ 8\.05049073355976\ 3\.00907672823278\ 0\.0385537793679552\ 1 +NM\_033652\ 37\.9036465974594\ 6\.58773330429334\ 69\.2195598906254\ 10\.5073409461664\ 3\.39332571288915\ 0\.458890814677737\ 1 +NM\_023284\ 10195\.2332879558\ 9097\.6596932291\ 11292\.8068826824\ 1\.24128701924156\ 0\.311836744283208\ 0\.654375068484487\ 1 +NM\_133806\ 1116\.62079507772\ 1116\.62079507772\ 1116\.62079507772\ 1\ \-6\.40685300762984e\-16\ 1\ 1 +NM\_001081304\ 2984\.54409472827\ 3866\.99944962019\ 2102\.08873983636\ 0\.543596855190353\ \-0\.879390985019008\ 0\.250093159071343\ 1 +NM\_001198955\ 1742\.28037716653\ 1773\.19821440562\ 1711\.36253992744\ 0\.965127601654554\ \-0\.0512083979945135\ 0\.950717130189934\ 1 +NM\_001109985\ 101\.460585813391\ 159\.203554853756\ 43\.7176167730266\ 0\.274602013838105\ \-1\.86458588912706\ 0\.427034456668414\ 1 +NM\_027528\ 1\.09795555071556\ 2\.19591110143111\ 0\ 0\ \-Inf\ 0\.985480439249778\ 1 +NM\_011070\ 1373\.31089189797\ 1568\.97848197253\ 1177\.6433018234\ 0\.75057963850649\ \-0\.413922941118844\ 0\.629505128976364\ 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dge.tab.re_match.modified Sat Mar 05 07:00:59 2016 -0500 @@ -0,0 +1,220 @@ +id\ baseMean\ baseMeanA\ baseMeanB\ foldChange\ log2FoldChange\ pval\ padj +NM\_175296\ 550\.2570816417.*? 23\.05706656502.*? 1077\.457096718.*? 46\.73001631321.*? 5\.546277635727.*? 2\.94263028018847e\-.*? 0\.00644436031361.*? +NM\_008922\ 2761\.883903286.*? 3439\.894740391.*? 2083\.873066180.*? 0\.6057955906940.*? \-0\.7230970174259.*? 0\.3476060509664.*? .*? +NM\_175370\ 5\.383653991130.*? 4\.391822202862.*? 6\.375485779399.*? 1\.451672104404.*? 0\.5377156222243.*? 0\.9900056342176.*? .*? +NM\_175642\ 997\.6632218482.*? 1072\.70257304.*? 922\.6238706474.*? 0\.860092903501.*? \-0\.2174355930005.*? 0\.8136330928378.*? .*? +NM\_199021\ 836\.2033056486.*? 364\.5212428375.*? 1307\.885368459.*? 3\.587953772676.*? 1\.843161302642.*? 0\.06260781985603.*? .*? +NM\_001113391\ 50\.50505977373.*? 20\.86115546359.*? 80\.1489640838.*? 3\.84201940413.*? 1\.941864805360.*? 0\.5889493949408.*? .*? +NM\_177834\ 1\.459761458129.*? 1\.097955550715.*? 1\.821567365542.*? 1\.659053833605.*? 0\.7303607001667.*? .*? .*? +NM\_145381\ 499\.8093376553.*? 665\.3610637336.*? 334\.2576115770.*? 0\.502370261495.*? \-0\.993177030463.*? 0\.3803026440680.*? .*? +NM\_001160370\ 5\.19648212318.*? 2\.195911101431.*? 8\.197053144942.*? 3\.732871125611.*? 1\.900285701609.*? 0\.9441257644198.*? .*? +NM\_027974\ 2\.732351048314.*? .*? 5\.464702096628.*? 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sat Mar 05 07:00:59 2016 -0500 @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="R" version="3.1.2"> + <repository changeset_revision="1ca39eb16186" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="biocbasics" version="2.14"> + <repository changeset_revision="d243626801e2" name="package_biocbasics_2_14" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>