Mercurial > repos > mvdbeek > deseq_with_replicates
changeset 0:da2dbe13adc2 draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq1_with_replicates commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
| author | mvdbeek |
|---|---|
| date | Sat, 05 Mar 2016 07:02:52 -0500 |
| parents | |
| children | |
| files | replicateDESeq.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, 2058 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/replicateDESeq.xml Sat Mar 05 07:02:52 2016 -0500 @@ -0,0 +1,49 @@ +<tool id="replicateDESeq" name="DESeq1 Profiling (replicates)" version="1.0.1"> + <description>with sample replicates</description> + <requirements> + <requirement type="package" version="3.1.2">R</requirement> + <requirement type="package" version="2.14">biocbasics</requirement> + </requirements> + <command>Rscript $replicateDESeq </command> + <inputs> + <param name="input" type="data" format="tabular" label="gene readcount list, more than 2 samples"/> + <param name="expPlan" type="text" label="experimental plan" help="Use a string of Cs and Ts. exemple: CCCTTT means 3 control samples versus 3 test samples"/> + </inputs> + <outputs> + <data name="output" format="tabular" label="DESeq differential calling" /> + </outputs> + <tests> + <test> + <param name="input" value="counts.tab" ftype="tabular"/> + <param name="expPlan" value="CCTTT"/> + <output name="output" file="dge.tab.re_match.modified" ftype="tabular" compare="re_match" lines_diff="5"/> + </test> + </tests> + <configfiles> + <configfile name="replicateDESeq"> + ## Setup R error handling to go to stderr + options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) + suppressMessages(require(DESeq)) + countsTable = read.delim("${input}", header=TRUE, check.names=FALSE) + rownames( countsTable )= countsTable[,1] + countsTable= countsTable[ , -1 ] + stringconds = "${expPlan}" + conds = unlist(strsplit(stringconds, split="")) + cds = newCountDataSet( countsTable, conds ) + cds = estimateSizeFactors( cds ) + cds = estimateDispersions( cds, method="per-condition", sharingMode="maximum") ## was fit-only before 9-12-2013 !! tried for RNAseq - Actually does not change anything ! + ## Attention: fitType="local" is added when parametricDispersionFit fails. remove after use ! + res = nbinomTest( cds, "C", "T" ) + # resNA = res[-which(is.na(res[,8])),] ## omitted the NA lignes, but this was causing a full delete of the table completely devoid of NA !! (not logical but true) + write.table ( res[order(res[,8]), ], file = "${output}", row.names=FALSE, col.names=TRUE, quote= FALSE, dec = ".", sep = "\t", eol = "\n") + </configfile> + </configfiles> + <help> + +**What it does** + +DESeq differential calling (order by padj, ascending), on more than two samples, with replicates. + + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/counts.tab Sat Mar 05 07:02:52 2016 -0500 @@ -0,0 +1,500 @@ +Geneid 2: Oocyte 1: accepted_hits 3: Oocyte 2: accepted_hits 4: Pronuclei 1: accepted_hits 5: pronuclei 2: accepted_hits 6: Pronuclei 3: accepted_hits +NM_001195025 0 0 0 0 0 +NM_028778 0 0 0 0 0 +NM_001290393 0 0 0 0 0 +NM_008922 3133 2276 2288 2659 820 +NM_175370 4 22 7 16 9 +NM_001290390 0 0 0 0 0 +NM_175642 977 1711 1013 459 430 +NM_001290392 0 0 0 0 0 +NM_027671 0 0 0 0 0 +NM_178884 0 0 0 2 3 +NM_199021 332 413 1436 836 1018 +NM_198680 0 0 0 0 0 +NM_011465 0 4 0 0 0 +NM_130890 0 0 0 0 0 +NM_001113393 0 0 0 0 0 +NM_001113392 0 0 0 0 0 +NM_001113391 19 3 88 15 31 +NM_031162 0 0 0 0 0 +NR_103716 0 0 0 0 0 +NM_001160371 0 0 0 0 0 +NM_177834 1 3 2 0 1 +NM_145381 606 445 367 306 259 +NM_177173 0 0 0 0 0 +NM_001160369 0 0 0 0 0 +NM_001160370 2 21 9 8 25 +NM_001289497 0 0 0 0 0 +NM_027974 0 0 6 7 8 +NM_133235 74 23 0 2 29 +NM_028096 77 87 2 0 17 +NM_201365 1 0 0 0 0 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dge.tab Sat Mar 05 07:02:52 2016 -0500 @@ -0,0 +1,500 @@ +id baseMean baseMeanA baseMeanB foldChange log2FoldChange pval padj +NM_030724 464.868786987954 42.7278970921829 746.296046918467 17.4662479950365 4.12649782447528 1.301203881287e-07 3.18794950915314e-05 +NM_001290814 187.149839999681 13.8361846647093 302.692276889662 21.8768601478492 4.45133378666581 2.20753427324853e-06 0.000270422948472945 +NM_009255 17377.4803462975 27214.4775715473 10819.482196131 0.397563472151408 -1.33074288569062 1.26299483519261e-05 0.00103144578207396 +NM_008801 794.929008530628 238.766220843347 1165.70420032215 4.88219898193623 2.28753109569312 2.27017297587472e-05 0.00139048094772327 +NM_029342 426.444164482568 102.585720376899 642.349793886348 6.26159071190768 2.64652920997787 2.93862583292896e-05 0.00143992665813519 +NM_023645 1272.93826196929 2043.5349277896 759.207151422419 0.371516601501702 -1.42850141475866 6.31001964014258e-05 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dge.tab.re_match.modified Sat Mar 05 07:02:52 2016 -0500 @@ -0,0 +1,500 @@ +id\ baseMean\ baseMeanA\ baseMeanB\ foldChange\ log2FoldChange\ pval\ padj +NM\_030724\ 464\.8687869879.*? 42\.72789709218.*? 746\.2960469184.*? 17\.46624799503.*? 4\.126497824475.*? 1\.301203881287e\-.*? 3\.18794950915314e\.*? +NM\_001290814\ 187\.1498399996.*? 13\.83618466470.*? 302\.6922768896.*? 21\.87686014784.*? 4\.451333786665.*? 2\.20753427324853e\-.*? 0\.000270422948472.*? +NM\_009255\ 17377\.48034629.*? 27214\.47757154.*? 10819\.4821961.*? 0\.3975634721514.*? \-1\.330742885690.*? 1\.26299483519261e\-.*? 0\.00103144578207.*? +NM\_008801\ 794\.9290085306.*? 238\.7662208433.*? 1165\.704200322.*? 4\.882198981936.*? 2\.287531095693.*? 2\.27017297587472e\-.*? 0\.00139048094772.*? +NM\_029342\ 426\.4441644825.*? 102\.5857203768.*? 642\.3497938863.*? 6\.261590711907.*? 2\.646529209977.*? 2\.93862583292896e\-.*? 0\.00143992665813.*? +NM\_023645\ 1272\.938261969.*? 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sat Mar 05 07:02:52 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>