Mercurial > repos > mvdbeek > deseq2
changeset 0:a903407e3ca0 draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
| author | mvdbeek |
|---|---|
| date | Sat, 05 Mar 2016 07:05:06 -0500 |
| parents | |
| children | |
| files | deseq2.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, 2065 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/deseq2.xml Sat Mar 05 07:05:06 2016 -0500 @@ -0,0 +1,56 @@ +<tool id="DESeq2" name="DESeq2 Profiling" version="1.0.2" hidden="true"> + <description>of readcount lists</description> + <requirements> + <requirement type="package" version="3.1.2">R</requirement> + <requirement type="package" version="2.14">biocbasics</requirement> + </requirements> + <command>Rscript $DESeq2 </command> + <inputs> + <param name="input" type="data" format="tabular" label="miR hit lists, more thant 2 samples"/> + <param name="expPlan" type="text" label="experimental plan" help="Use a string of Cs and Ts. exemple: CCCTTT means 3 control samples versus 3 test samples"/> + </inputs> + <outputs> + <data name="output" format="tabular" label="DESeq2 differential calling" /> + </outputs> + <tests> + <test> + <param name="input" value="counts.tab" ftype="tabular"/> + <param name="expPlan" value="CCTTT"/> + <output name="output" file="dge.tab.re_match.modified" ftype="tabular" compare="re_match" lines_diff="50"/> + </test> + </tests> +<configfiles> + <configfile name="DESeq2"> + ## Setup R error handling to go to stderr + options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) + suppressMessages(require(DESeq2)) + ## suppressMessages(require(ReportingTools)) + countData = read.delim("${input}", header=TRUE, check.names=FALSE) + rownames( countData )= countData[,1] + countData= countData[ , -1 ] + stringconds = "${expPlan}" + conds = unlist(strsplit(stringconds, split="")) + colData=data.frame(row.names=colnames(countData), condition=conds) + dds = DESeqDataSetFromMatrix(countData = countData, colData = colData, design = ~ condition) + colData(dds)\$condition = factor(colData(dds)\$condition, levels=c("C","T")) + dds = DESeq(dds, quiet=TRUE) + res = results(dds) + res = res[order(res\$padj),] + baseMeanA = rowMeans(counts(dds, normalized=TRUE)[rownames(res),colData(dds)\$condition== "C"]) + baseMeanB = rowMeans(counts(dds, normalized=TRUE)[rownames(res),colData(dds)\$condition== "T"]) + res2 = data.frame (gene=rownames(res), baseMeanA=baseMeanA, baseMeanB=baseMeanB, res) + ## resNA = res[-which(is.na(res[,8])),] ## omit the NA lignes + write.table ( res2, file = "${output}", row.names=FALSE, col.names=TRUE, quote= FALSE, dec = ".", sep = "\t", eol = "\n") + ## write.csv(as.data.frame(res), file="${output}") + </configfile> + </configfiles> + <help> + +**What it does** + +DESeq2 differential calling (order by padj, ascending). +Still in development and testing for replicates/no replicates + + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/counts.tab Sat Mar 05 07:05:06 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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NA +NM_001276412 0 0 0 NA NA NA NA NA +NM_001276411 0 0 0 NA NA NA NA NA +NM_001276410 0 0 0 NA NA NA NA NA +NM_001276409 0 0 0 NA NA NA NA NA +NM_010233 0 0 0 NA NA NA NA NA +NM_001276413 0 0 0 NA NA NA NA NA +NM_008342 0 0.561494717258207 0.336896830354924 0.286552408470409 0.510690894121541 0.561107338644286 0.574724365627878 NA +NM_176980 3.15915923811485 6.03461506007489 4.88443273129087 0.207445396740765 0.699195143577849 0.296691701374307 0.766701893269917 NA +NM_001170641 0 0 0 NA NA NA NA NA +NM_027884 0 0 0 NA NA NA NA NA +NR_045311 12.6366369524594 6.74031938995988 9.09884641495969 -0.288663762643429 0.763714138569315 -0.377973574227904 0.705450225003955 NA +NM_001034060 0 0 0 NA NA NA NA NA +NM_001289895 0 0 0 NA NA NA NA NA +NM_009518 0 0 0 NA NA NA NA NA +NM_001039495 0 0 0 NA NA NA NA NA +NM_001159884 0 0 0 NA NA NA NA NA +NM_001159885 0 1.84971979530508 1.10983187718305 0.341530939138289 0.545528223441631 0.626055489821657 0.531278545545514 NA +NM_001159883 0 0.383498646871284 0.23009918812277 0.253165513151483 0.486165361864932 0.520739511717451 0.602548245637964 NA +NM_178055 0 0 0 NA NA NA NA NA +NM_020266 0 0 0 NA NA NA NA NA +NR_037976 0 0 0 NA NA NA NA NA +NM_008781 9.02616925175671 0.73988791812203 4.0544004515759 -0.585513841147185 0.63537910546698 -0.921518879215982 0.356779589173685 NA +NM_026713 0 0 0 NA NA NA NA NA +NM_001159520 0 0 0 NA NA NA NA NA +NM_001285927 0 0 0 NA NA NA NA NA +NM_029777 0 0 0 NA NA NA NA NA +NM_007735 0 0 0 NA NA NA NA NA +NM_172430 0 13.9766726216056 8.38600357296334 1.08532277460524 0.765742470992951 1.41734697462697 0.156381507508417 NA +NM_001081746 10.2653077356166 12.1701962795385 11.4082408619697 0.122684192771473 0.825130466380477 0.148684599309053 0.881802514119701 NA +NM_001144993 0 0 0 NA NA NA NA NA +NM_001144992 0 0 0 NA NA NA NA NA +NM_001172157 0 0 0 NA NA NA NA NA +NM_001081082 0 0 0 NA NA NA NA NA +NM_153530 0 0 0 NA NA NA NA NA +NM_201644 0 0 0 NA NA NA NA NA +NM_001110192 0 0 0 NA NA NA NA NA +NM_001205391 0 0 0 NA NA NA NA NA +NM_019867 0 0.561494717258207 0.336896830354924 0.286552408470409 0.510690894121541 0.561107338644286 0.574724365627878 NA +NM_001205392 0 0 0 NA NA NA NA NA +NM_201410 0 0 0 NA NA NA NA NA +NM_029846 0 0 0 NA NA NA NA NA +NM_001110212 0 0 0 NA NA NA NA NA +NM_001111314 0 10.2921757171822 6.17530543030933 0.862182867065928 0.729016942588022 1.18266506126067 0.236941916299098 NA +NM_146112 0 0 0 NA NA NA NA NA +NM_010566 0 0 0 NA NA NA NA NA +NR_122078 0 0 0 NA NA NA NA NA +NM_201642 0 0 0 NA NA NA NA NA +NM_201641 0 0 0 NA NA NA NA NA +NM_001110193 0 0 0 NA NA NA NA NA +NM_145079 0 0 0 NA NA NA NA NA +NM_029269 0 0 0 NA NA NA NA NA +NM_139152 0 0 0 NA NA NA NA NA +NM_178119 0.942207696785575 3.45816490398115 2.45178202110292 0.23912879124041 0.590086443595563 0.405243661900333 0.685298413793502 NA +NM_001037136 0 0 0 NA NA NA NA NA +NM_001111312 0 0.369943959061015 0.221966375436609 0.251236829594032 0.484659763413011 0.518377733329465 0.604194747223895 NA +NM_001243009 0 0 0 NA NA NA NA NA +NM_001243008 0 0 0 NA NA NA NA NA +NM_023046 0 0 0 NA NA NA NA NA +NM_001039126 0 0 0 NA NA NA NA NA +NM_007855 0 0 0 NA NA NA NA NA +NM_001271884 0 0 0 NA NA NA NA NA +NM_207031 0 1.04774465237167 0.628646791423002 0.31923308341291 0.532154371221071 0.59988811645088 0.548580802705268 NA +NM_172463 37.6605416637659 8.27272545553742 20.0278519388288 -1.36450538728293 0.80057392783942 -1.70440897440346 0.0883047084715896 NA +NM_008798 6.76962693881753 22.490873287303 16.2023747479088 0.612702946002264 0.802129735826712 0.763845196900454 0.444959499193142 NA +NR_040467 0 0 0 NA NA NA NA NA +NM_028942 0 0 0 NA NA NA NA NA +NR_120500 13.0879454150472 25.7366540925439 20.6771706215453 0.397553100481943 0.814316545181192 0.488204621205976 0.625404911601836 NA +NM_027584 0 0 0 NA NA NA NA NA +NM_001164233 0 0 0 NA NA NA NA NA +NM_013626 4.16075309231528 5.46445760829258 4.94297580190166 0.11114846061368 0.742510223014856 0.14969283542303 0.881006960992266 NA +NM_173187 0 0 0 NA NA NA NA NA +NM_009399 0 1.47977583624406 0.887865501746437 0.333753920102786 0.540973444950313 0.61695065297233 0.537267275055595 NA +NM_178779 0 0 0 NA NA NA NA NA +NM_029349 0 0 0 NA NA NA NA NA +NM_001160368 0 0 0 NA NA NA NA NA +NM_009741 14.4814615744206 14.9625266561117 14.7701006234353 0.0250257143887851 0.824676761721047 0.0303460889774049 0.975791039793048 NA +NM_198028 0 0 0 NA NA NA NA NA +NM_001160307 0 0 0 NA NA NA NA NA +NR_102307 0 0 0 NA NA NA NA NA +NR_102306 0 0 0 NA NA NA NA NA +NM_172853 0 8.7031681175022 5.22190087050132 0.563197806076453 0.647878985885826 0.869294757733821 NA NA +NM_001077425 0 14.6886569031533 8.81319414189195 1.13270305596256 0.771815467334734 1.46758273693848 0.14221760004542 NA +NM_029709 0 0 0 NA NA NA NA NA +NM_001293300 0 0.280747358629103 0.168448415177462 0.236266271681685 0.47261510198017 0.499912657661113 0.617136579212974 NA +NM_001293301 0 0 0 NA NA NA NA NA +NM_022327 0 0 0 NA NA NA NA NA 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277.065108631351 -0.0344125191892855 0.516914896097389 -0.0665728913000837 NA NA +NM_026976 0 0 0 NA NA NA NA NA +NM_007799 0 0 0 NA NA NA NA NA +NM_172510 8.00876542267739 20.284760304162 15.3743623515682 0.611900915963187 0.823917669299397 0.742672403765179 0.457680041250665 NA +NM_175294 0 0 0 NA NA NA NA NA +NM_001145804 0 0 0 NA NA NA NA NA +NM_001160318 0 0 0 NA NA NA NA NA +NM_001160317 0 0 0 NA NA NA NA NA +NM_001160316 0 0 0 NA NA NA NA NA +NM_182716 0 1.53399458748513 0.920396752491081 0.334952026879345 0.541682645308212 0.618354731835207 0.536341530882536 NA +NM_144530 0 0 0 NA NA NA NA NA +NM_001276767 0 0 0 NA NA NA NA NA +NM_001145300 0 0 0 NA NA NA NA NA +NM_053106 0 0 0 NA NA NA NA NA +NM_001291015 0 0 0 NA NA NA NA NA +NM_177642 0 0.766997293742567 0.46019837624554 0.301930674074754 0.521081592818901 0.579430703820099 0.562298591673325 NA +NM_030676 0 0 0 NA NA NA NA NA +NM_001159769 0 0.383498646871284 0.23009918812277 0.253165513151483 0.486165361864932 0.520739511717451 0.602548245637964 NA +NM_011210 0 0 0 NA NA NA NA NA +NM_001111316 0 0 0 NA NA NA NA NA +NM_001268286 0 0 0 NA NA NA NA NA +NM_181347 0 0 0 NA NA NA NA NA +NM_001166501 0.451308462587835 1.13694125280358 0.862688136717284 0.14483340196651 0.542474828609351 0.2669864007106 0.789479631817819 NA +NR_040455 0 0 0 NA NA NA NA NA +NM_001081027 0 0 0 NA NA NA NA NA +NR_040604 0 0 0 NA NA NA NA NA +NM_020025 1.88441539357115 0 0.75376615742846 -0.478082733990246 0.537452218826069 -0.88953532471128 0.373715447294592 NA +NR_110891 0 0 0 NA NA NA NA NA +NM_001290269 0 0 0 NA NA NA NA NA +NM_153171 0 0 0 NA NA NA NA NA +NM_001145807 0 0 0 NA NA NA NA NA +NM_153539 0 0 0 NA NA NA NA NA +NM_008869 35.653368544439 0 14.2613474177756 -1.91885952308802 0.790573257173068 -2.42717484518699 0.0152169203007714 NA +NM_001110146 0 0 0 NA NA NA NA NA +NM_024458 0 0 0 NA NA NA NA NA +NM_001159730 0 0 0 NA NA NA NA NA +NR_040603 0 0 0 NA NA NA NA NA +NM_021400 0.922412310980623 4.55483922383083 3.10186845869075 0.398948760080105 0.67305191911394 0.592745891885002 0.553351223818174 NA +NM_001024720 0 0 0 NA NA NA NA NA +NM_022018 12.2289046724075 12.0519046511016 12.122704659624 -0.00571325189775561 0.80461082939856 -0.00710064007220263 0.994334556522362 NA +NM_010877 2.70785077552701 6.73793660709848 5.12590227446989 0.236159941499862 0.655339498277251 0.360362746516388 0.71857588174249 NA +NR_108050 0 0 0 NA NA NA NA NA +NR_046171 0 0 0 NA NA NA NA NA +NM_177838 0 0 0 NA NA NA NA NA +NM_001277730 0 0 0 NA NA NA NA NA +NM_001134741 3.66985385811754 7.77979843828435 6.13582060621763 0.384559430761919 0.797430774550789 0.482248043384769 0.629629751412181 NA +NM_026683 0 0 0 NA NA NA NA NA +NM_023141 4.06177616329052 13.4806387799198 9.71309373326807 0.511865528371584 0.773248932023639 0.661967326656372 0.50799216160275 NA +NR_027640 0.471103848392788 0 0.188441539357115 -0.343626431501831 0.478911579314015 -0.717515396044581 0.473056140037951 NA +NM_001159968 0 0 0 NA NA NA NA NA +NM_001159965 0 0 0 NA NA NA NA NA +NM_001159967 0 0 0 NA NA NA NA NA +NM_001159966 0 0 0 NA NA NA NA NA +NM_023884 0 0 0 NA NA NA NA NA +NR_038031 0 0 0 NA NA NA NA NA +NR_038030 0 0 0 NA NA NA NA NA +NM_001162896 0 0 0 NA NA NA NA NA +NM_001038619 0 0 0 NA NA NA NA NA +NM_172646 0 0 0 NA NA NA NA NA +NM_001293313 0 0 0 NA NA NA NA NA +NM_138314 0 0 0 NA NA NA NA NA +NM_001081126 0.942207696785575 0.766997293742567 0.83708145495977 -0.0390258061465042 0.54270349190546 -0.0719099963950527 0.942673534674585 NA +NM_001164306 6.31831847622969 6.05345883164822 6.15940268948081 -0.0158292992457534 0.727327354869798 -0.0217636517309144 0.982636489031444 NA +NM_001160049 0 0 0 NA NA NA NA NA +NM_001033344 0 0 0 NA NA NA NA NA +NM_198932 0 0 0 NA NA NA NA NA +NM_011137 0 0 0 NA NA NA NA NA +NM_030724 42.7278970921829 746.296046918467 464.868786987954 3.76305551214874 0.461005878034587 8.16270614203842 NA NA +NM_033652 7.33970771623508 41.9683654481833 28.116902355404 1.66404402883696 0.768767950863607 2.16455957479449 0.0304214296407256 NA +NM_175461 0 0 0 NA NA NA NA NA +NM_001160261 0 0 0 NA NA NA NA NA +NM_001160262 0 0 0 NA NA NA NA NA +NM_183355 0 0 0 NA NA NA NA NA +NM_008783 0 0 0 NA NA NA NA NA +NM_001291509 0 0 0 NA NA NA NA NA +NM_001291508 0 0 0 NA NA NA NA NA +NM_027528 0.942207696785575 0 0.37688307871423 -0.420087470788302 0.514998495489618 -0.815706209760705 0.414668186551214 NA +NM_013489 0 0 0 NA NA NA NA NA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dge.tab.re_match Sat Mar 05 07:05:06 2016 -0500 @@ -0,0 +1,500 @@ +gene\ baseMeanA\ baseMeanB\ baseMean\ log2FoldChange\ lfcSE\ stat\ pvalue\ padj +NM\_001290814\ 13\.8361846647093\ 302\.692276889662\ 187\.149839999681\ 4\.02298530293272\ 0\.475300264296235\ 8\.46409229098463\ 2\.58155340319795e\-17\ 3\.84651457076494e\-15 +NM\_175296\ 42\.3873901225727\ 938\.523758683365\ 580\.069211259048\ 3\.98548352659215\ 0\.502124973720984\ 7\.93723422489391\ 2\.06739417563206e\-15\ 1\.54020866084588e\-13 +NM\_010472\ 166\.814206844757\ 1470\.37801982385\ 948\.952494632214\ 2\.93850691094032\ 0\.401906370179809\ 7\.31142158713647\ 2\.643307621836e\-13\ 1\.31284278551188e\-11 +NM\_029342\ 102\.585720376899\ 642\.349793886348\ 426\.444164482568\ 2\.47979721531494\ 0\.398185092542637\ 6\.22775001314096\ 4\.73181277129915e\-10\ 1\.76260025730893e\-08 +NM\_001033408\ 10\.067353877567\ 192\.663868743505\ 119\.62526279713\ 3\.55941286675189\ 0\.592903302264483\ 6\.0033615146979\ 1\.93273620816604e\-09\ 5\.75955390033481e\-08 +NM\_008801\ 238\.766220843347\ 1165\.70420032215\ 794\.929008530628\ 2\.16023652550394\ 0\.376164519001384\ 5\.74279714428886\ 9\.31252640346199e\-09\ 2\.31261072352639e\-07 +NM\_199021\ 342\.796872715182\ 1102\.82797928137\ 798\.815536654893\ 1\.6260740249254\ 0\.304536884403641\ 5\.33949780207956\ 9\.32043996944546e\-08\ 1\.98392222206768e\-06 +NM\_009255\ 27214\.4775715473\ 10819\.482196131\ 17377\.4803462975\ \-1\.29469303336041\ 0\.268165046272498\ \-4\.82797087598358\ 1\.3793125924685e\-06\ 2\.56896970347259e\-05 +NM\_023645\ 2043\.5349277896\ 759\.207151422419\ 1272\.93826196929\ \-1\.38274254401162\ 0\.289726371358106\ \-4\.77258089255026\ 1\.81880019099805e\-06\ 2\.89691190975949e\-05 +NM\_172849\ 25\.633576260334\ 208\.094346965569\ 135\.110038683475\ 2\.6194543990624\ 0\.552643837861215\ 4\.73985995971644\ 2\.1386597991513e\-06\ 2\.89691190975949e\-05 +NM\_177445\ 251\.161459424046\ 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0\.797430774550789\ 0\.482248043384769\ 0\.629629751412181\ NA +NM\_026683\ 0\ 0\ 0\ NA\ NA\ NA\ NA\ NA +NM\_023141\ 4\.06177616329052\ 13\.4806387799198\ 9\.71309373326807\ 0\.511865528371584\ 0\.773248932023639\ 0\.661967326656372\ 0\.50799216160275\ NA +NR\_027640\ 0\.471103848392788\ 0\ 0\.188441539357115\ \-0\.343626431501831\ 0\.478911579314015\ \-0\.717515396044581\ 0\.473056140037951\ NA +NM\_001159968\ 0\ 0\ 0\ NA\ NA\ NA\ NA\ NA +NM\_001159965\ 0\ 0\ 0\ NA\ NA\ NA\ NA\ NA +NM\_001159967\ 0\ 0\ 0\ NA\ NA\ NA\ NA\ NA +NM\_001159966\ 0\ 0\ 0\ NA\ NA\ NA\ NA\ NA +NM\_023884\ 0\ 0\ 0\ NA\ NA\ NA\ NA\ NA +NR\_038031\ 0\ 0\ 0\ NA\ NA\ NA\ NA\ NA +NR\_038030\ 0\ 0\ 0\ NA\ NA\ NA\ NA\ NA +NM\_001162896\ 0\ 0\ 0\ NA\ NA\ NA\ NA\ NA +NM\_001038619\ 0\ 0\ 0\ NA\ NA\ NA\ NA\ NA +NM\_172646\ 0\ 0\ 0\ NA\ NA\ NA\ NA\ NA +NM\_001293313\ 0\ 0\ 0\ NA\ NA\ NA\ NA\ NA +NM\_138314\ 0\ 0\ 0\ NA\ NA\ NA\ NA\ NA +NM\_001081126\ 0\.942207696785575\ 0\.766997293742567\ 0\.83708145495977\ \-0\.0390258061465042\ 0\.54270349190546\ \-0\.0719099963950527\ 0\.942673534674585\ NA +NM\_001164306\ 6\.31831847622969\ 6\.05345883164822\ 6\.15940268948081\ \-0\.0158292992457534\ 0\.727327354869798\ \-0\.0217636517309144\ 0\.982636489031444\ NA +NM\_001160049\ 0\ 0\ 0\ NA\ NA\ NA\ NA\ NA +NM\_001033344\ 0\ 0\ 0\ NA\ NA\ NA\ NA\ NA +NM\_198932\ 0\ 0\ 0\ NA\ NA\ NA\ NA\ NA +NM\_011137\ 0\ 0\ 0\ NA\ NA\ NA\ NA\ NA +NM\_030724\ 42\.7278970921829\ 746\.296046918467\ 464\.868786987954\ 3\.76305551214874\ 0\.461005878034587\ 8\.16270614203842\ NA\ NA +NM\_033652\ 7\.33970771623508\ 41\.9683654481833\ 28\.116902355404\ 1\.66404402883696\ 0\.768767950863607\ 2\.16455957479449\ 0\.0304214296407256\ NA +NM\_175461\ 0\ 0\ 0\ NA\ NA\ NA\ NA\ NA +NM\_001160261\ 0\ 0\ 0\ NA\ NA\ NA\ NA\ NA +NM\_001160262\ 0\ 0\ 0\ NA\ NA\ NA\ NA\ NA +NM\_183355\ 0\ 0\ 0\ NA\ NA\ NA\ NA\ NA +NM\_008783\ 0\ 0\ 0\ NA\ NA\ NA\ NA\ NA +NM\_001291509\ 0\ 0\ 0\ NA\ NA\ NA\ NA\ NA +NM\_001291508\ 0\ 0\ 0\ NA\ NA\ NA\ NA\ NA +NM\_027528\ 0\.942207696785575\ 0\ 0\.37688307871423\ \-0\.420087470788302\ 0\.514998495489618\ \-0\.815706209760705\ 0\.414668186551214\ NA +NM\_013489\ 0\ 0\ 0\ NA\ NA\ NA\ NA\ NA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dge.tab.re_match.modified Sat Mar 05 07:05:06 2016 -0500 @@ -0,0 +1,500 @@ +gene\ baseMeanA\ baseMeanB\ baseMean\ log2FoldChange\ lfcSE\ stat\ pvalue\ padj +NM\_001290814\ 13\.836184664.*? 302\.69227688.*? 187\.14983999.*? 4\.0229853029.*? 0\.47530026429.*? 8\.4640922909.*? 2\.5815534.*? 3\.8465145.*? +NM\_175296\ 42\.387390122.*? 938\.52375868.*? 580\.06921125.*? 3\.9854835265.*? 0\.50212497372.*? 7\.9372342248.*? 2\.0673941.*? 1\.5402086.*? +NM\_010472\ 166\.81420684.*? 1470\.3780198.*? 948\.95249463.*? 2\.9385069109.*? 0\.40190637017.*? 7\.3114215871.*? 2\.64330.*? 1\.3128427.*? +NM\_029342\ 102\.58572037.*? 642\.34979388.*? 426\.44416448.*? 2\.4797972153.*? 0\.39818509254.*? 6\.2277500131.*? 4\.7318127.*? 1\.7626002.*? +NM\_001033408\ 10\.06735387.*? 192\.66386874.*? 119\.6252627.*? 3\.5594128667.*? 0\.59290330226.*? 6\.003361514.*? 1\.9327362.*? 5\.7595539.*? +NM\_008801\ 238\.76622084.*? 1165\.7042003.*? 794\.92900853.*? 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sat Mar 05 07:05:06 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>