| Previous changeset 3:6f52c0dc56d4 (2019-05-10) |
|
Commit message:
"planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit 3af73b895c2dac2b8d87d1dec15204e5d30c709a-dirty" |
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modified:
chipeakanno_annopeaks.xml test-data/annoTab.tabular |
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added:
test-data/Differentially_Methylated_Positions.bed |
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removed:
test-data/Differentially_Methylated_Regions.interval |
| b |
| diff -r 6f52c0dc56d4 -r 104882a2de00 chipeakanno_annopeaks.xml --- a/chipeakanno_annopeaks.xml Fri May 10 06:45:34 2019 -0400 +++ b/chipeakanno_annopeaks.xml Sun Feb 23 07:58:07 2020 -0500 |
| [ |
| @@ -1,9 +1,10 @@ <tool id="chipeakanno_annopeaks" name="ChIPpeakAnno annoPeaks" version="0.1.0"> <description>annotate peaks by annoGR object in the given range</description> <requirements> - <requirement type="package" version="3.16.0-0">bioconductor-chippeakanno</requirement> - <requirement type="package" version="2.99.0-3">bioconductor-ensdb.hsapiens.v75</requirement> - <requirement type="package" version="1.42.1-1">bioconductor-rtracklayer</requirement> + <requirement type="package" version="3.20.0">bioconductor-chippeakanno</requirement> + <requirement type="package" version="2.99.0">bioconductor-ensdb.hsapiens.v75</requirement> + <requirement type="package" version="1.46.0">bioconductor-rtracklayer</requirement> + <requirement type="package" version="1.2.2">bioconductor-genomeinfodbdata</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ Rscript '$chipeakanno_annopeaks_script' @@ -13,16 +14,17 @@ require("ChIPpeakAnno", quietly = TRUE) require("EnsDb.Hsapiens.v75", quietly = TRUE) require("rtracklayer", quietly = TRUE) +require("GenomeInfoDbData", quietly = TRUE) options(warn = -1) -data <- read.table('$dmp') +data <- read.table('$dmp',header=FALSE) peaks <- GRanges(seqnames = data[, 1], ranges = IRanges - (start = data[, 2], end = data[, 3]),score=data[, as.numeric('$score')]) + (start = as.numeric(data[, 2]), end = as.numeric(data[, 3]), score = data[, as.numeric('$score')])) -db <- toGRanges(EnsDb.Hsapiens.v75) +db <- toGRanges(EnsDb.Hsapiens.v75, feature="gene") seqlevelsStyle(peaks) <- seqlevelsStyle(db) start <- as.numeric('$start') @@ -35,7 +37,7 @@ </configfile> </configfiles> <inputs> - <param type="data" name="dmp" format="interval" label="Differentially Methylated Positions"/> + <param type="data" name="dmp" format="bed" label="Differentially Methylated Positions"/> <param name="type" type="select" label="bindingType" help="Specifying the criteria to associate peaks with annotation e.g. startSite start position of the feature strand"> <option value="startSite">startSite</option> <option value="endSite">endSite</option> @@ -52,7 +54,7 @@ </outputs> <tests> <test> - <param name="dmp" value="Differentially_Methylated_Regions.interval"/> + <param name="dmp" value="Differentially_Methylated_Positions.bed"/> <param name="type" value="startSite"/> <param name="start" value="-5000"/> <param name="end" value="5000"/> |
| b |
| diff -r 6f52c0dc56d4 -r 104882a2de00 test-data/Differentially_Methylated_Positions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Differentially_Methylated_Positions.bed Sun Feb 23 07:58:07 2020 -0500 |
| b |
| b'@@ -0,0 +1,464888 @@\n+chr\tstart\tend\tnames\tpval\tqval\n+chr16\t53468112\t53468112\tcg00000029\t0.273485175006601\t0.239609190206712\n+chr3\t37459206\t37459206\tcg00000108\t0.623243998636913\t0.39258989981719\n+chr3\t171916037\t171916037\tcg00000109\t0.232539543925332\t0.216244969633372\n+chr1\t91194675\t91194675\tcg00000165\t0.248020671814953\t0.225232373436069\n+chr8\t42263295\t42263295\tcg00000236\t0.230215862279736\t0.214851543324713\n+chr14\t69341139\t69341139\tcg00000289\t0.268327315390556\t0.236767279985355\n+chr16\t28890100\t28890100\tcg00000292\t0.0058372332805385\t0.0220344081686113\n+chr8\t41167803\t41167803\tcg00000321\t0.462489859333497\t0.330321758498426\n+chr1\t230560793\t230560793\tcg00000363\t0.0385403800900197\t0.0665130564433204\n+chr15\t23034447\t23034447\tcg00000622\t0.18160031067637\t0.184482262176172\n+chr9\t139997925\t139997925\tcg00000658\t0.631469535337436\t0.395501230069459\n+chr19\t54695678\t54695678\tcg00000714\t0.900754608784968\t0.47905542242334\n+chr6\t25282780\t25282780\tcg00000721\t0.0455820567003055\t0.0741735576910669\n+chr3\t128902377\t128902377\tcg00000734\t0.960672634519289\t0.494732871296244\n+chr12\t124086477\t124086477\tcg00000769\t0.899624518031061\t0.478732527820523\n+chr4\t154609858\t154609858\tcg00000884\t0.906826256415091\t0.480736216615489\n+chr15\t59785307\t59785307\tcg00000905\t0.709841485040243\t0.422009978640979\n+chr11\t2720463\t2720463\tcg00000924\t0.933364876748635\t0.487711474670278\n+chr8\t49890609\t49890609\tcg00000948\t0.978493984862554\t0.499333411033056\n+chr1\t5937253\t5937253\tcg00000957\t0.0592699234314915\t0.0881400020336562\n+chr8\t87081553\t87081553\tcg00001099\t0.269277956580276\t0.237308413102509\n+chr3\t15106711\t15106711\tcg00001245\t0.728616646274826\t0.428116835020146\n+chr14\t60389786\t60389786\tcg00001249\t0.160188380275175\t0.169981775579059\n+chr16\t3463964\t3463964\tcg00001261\t0.0602365606021472\t0.0890826668240909\n+chr20\t48959005\t48959005\tcg00001269\t0.0185995917225724\t0.0419275290139671\n+chr1\t166958440\t166958440\tcg00001349\t0.00210678338535948\t0.0145319619679991\n+chr1\t214170377\t214170377\tcg00001364\t0.281669878488749\t0.244056526948174\n+chr1\t43831042\t43831042\tcg00001446\t0.00813133824320487\t0.0261085946594264\n+chr19\t54746946\t54746946\tcg00001510\t0.871735099155927\t0.470986350866867\n+chr1\t51034866\t51034866\tcg00001534\t0.941336640837796\t0.489841381999452\n+chr10\t80828703\t80828703\tcg00001582\t0.495135464109364\t0.343901384447645\n+chr1\t200011787\t200011787\tcg00001583\t0.000186463642048131\t0.00907721359047842\n+chr2\t11484705\t11484705\tcg00001594\t0.847778025682725\t0.464401674520496\n+chr16\t89761661\t89761661\tcg00001687\t0.70875697089707\t0.421649727009037\n+chr2\t105460264\t105460264\tcg00001747\t0.300585127007446\t0.254220166025132\n+chr2\t103414042\t103414042\tcg00001791\t0.00741837801699207\t0.0248538270071218\n+chr12\t11905390\t11905390\tcg00001793\t0.778442060769949\t0.443806097170459\n+chr14\t101154025\t101154025\tcg00001809\t0.0100420599352783\t0.0292462908122588\n+chr16\t47008491\t47008491\tcg00001854\t0.490463407920156\t0.341969954541432\n+chr10\t69990589\t69990589\tcg00001874\t0.0259219428577307\t0.0515649861220453\n+chr18\t60055085\t60055085\tcg00001930\t0.643274774132072\t0.399594721762803\n+chr1\t20960011\t20960011\tcg00002028\t0.322334023696921\t0.265507774104347\n+chr19\t39798482\t39798482\tcg00002033\t0.00538940317056318\t0.0212042423412914\n+chr21\t30390417\t30390417\tcg00002080\t0.00218210824223853\t0.014697261364833\n+chr17\t79670411\t79670411\tcg00002116\t0.29221122878682\t0.249772316213451\n+chr2\t238249537\t238249537\tcg00002145\t0.00274012547425348\t0.0159175767587452\n+chr8\t19555033\t19555033\tcg00002190\t0.358060059556713\t0.283070409602944\n+chr8\t144120399\t144120399\tcg00002224\t0.707474789933135\t0.421226361675999\n+chr18\t67873061\t67873061\tcg00002236\t0.0882303094313435\t0.114641108069523\n+chr16\t30366435\t30366435\tcg00002406\t0.929549023034964\t0.486698299957923\n+chr3\t57743543\t57743543\tcg00002426\t0.151242152548759\t0.163736565345604\n+chr10\t28961565\t28961565\tcg00002449\t0.744754807347051\t0.433313520653788\n+chr8\t120428418\t120428418\tcg00002464\t0.524129700744645\t0.355542290873176\n+chr2\t218988877\t218988877\tcg00002473\t0.0863486733476217\t0.112974531628471\n+chr4\t2264510\t2264510\tcg000'..b'+chr19\t21666099\t21666099\tcg27663389\t0.110740163126761\t0.133250041564222\n+chr15\t80444408\t80444408\tcg27663476\t0.00888627086723007\t0.0273738880202672\n+chr14\t102360737\t102360737\tcg27663587\t0.269411540397791\t0.237379183218323\n+chr17\t15523510\t15523510\tcg27663733\t0.0294158194660536\t0.0558947504810295\n+chr16\t71929910\t71929910\tcg27663791\t0.839424788037992\t0.462081226590046\n+chr12\t49504641\t49504641\tcg27663799\t0.549789377111119\t0.365563581892934\n+chr11\t60162624\t60162624\tcg27663936\t0.0174377170555988\t0.040304458138289\n+chr12\t103696381\t103696381\tcg27663938\t0.189554529176272\t0.189650769488219\n+chr16\t57405979\t57405979\tcg27664018\t0.0149229028642423\t0.036730604332484\n+chr15\t89157815\t89157815\tcg27664085\t0.000234062398958426\t0.00924549719362486\n+chr7\t98904273\t98904273\tcg27664120\t0.0470597623952925\t0.0757710493568061\n+chr13\t115080392\t115080392\tcg27664182\t0.23700213535066\t0.218887198565267\n+chr2\t132570865\t132570865\tcg27664268\t0.43346071651402\t0.317762946312163\n+chr12\t133296225\t133296225\tcg27664343\t0.664604738897768\t0.406846734687486\n+chr15\t59171929\t59171929\tcg27664390\t0.567913659448734\t0.372331638414046\n+chr16\t5116675\t5116675\tcg27664407\t0.0070969624075262\t0.0243102314415128\n+chr19\t54214532\t54214532\tcg27664418\t0.650636804887619\t0.40211160562709\n+chr12\t113515835\t113515835\tcg27664496\t0.959602633247624\t0.494477917524275\n+chr10\t98479703\t98479703\tcg27664530\t0.0198194884731675\t0.0435846436444787\n+chr15\t44487605\t44487605\tcg27664600\t0.598687800786434\t0.383714468654274\n+chr16\t53634479\t53634479\tcg27664614\t0.116312542367993\t0.137660125527242\n+chr5\t167126706\t167126706\tcg27664687\t0.00385424931403696\t0.018239553962232\n+chr2\t152830665\t152830665\tcg27664689\t0.0861118483961435\t0.11277403024455\n+chr7\t128693986\t128693986\tcg27664783\t0.107156404495293\t0.130394302764243\n+chr2\t119532487\t119532487\tcg27664844\t0.245359678581411\t0.223719352871042\n+chr5\t179234150\t179234150\tcg27664881\t0.954209123170011\t0.49308602934066\n+chr5\t35622295\t35622295\tcg27664901\t0.340243634758163\t0.274453236070168\n+chr7\t47698707\t47698707\tcg27665018\t1.17702740080276e-05\t0.00776590710285016\n+chr12\t12618834\t12618834\tcg27665123\t0.687882504306869\t0.414700927237671\n+chr19\t50102212\t50102212\tcg27665130\t0.490112003559203\t0.341801340913372\n+chr15\t51369926\t51369926\tcg27665146\t0.0638692248157794\t0.0925982070023493\n+chr15\t38857079\t38857079\tcg27665171\t0.721973386058949\t0.426040593799695\n+chr16\t70720150\t70720150\tcg27665181\t0.114242896143708\t0.136002471150743\n+chr6\t168168454\t168168454\tcg27665188\t0.0047688909946671\t0.0200424680189996\n+chr15\t80866134\t80866134\tcg27665327\t0.0224503121460271\t0.0471063614018397\n+chr2\t120770691\t120770691\tcg27665377\t0.00620807097517499\t0.0227031785365282\n+chr2\t3262407\t3262407\tcg27665397\t0.79053015248496\t0.447560073805347\n+chr2\t71204401\t71204401\tcg27665449\t0.0133258327974226\t0.0343575064490366\n+chrX\t51075531\t51075531\tcg27665489\t0.0942626915466662\t0.119757964256038\n+chr16\t70624354\t70624354\tcg27665571\t0.0198604454610085\t0.043643008809442\n+chr5\t1065466\t1065466\tcg27665580\t0.0862440348986026\t0.112884464261826\n+chr22\t30112404\t30112404\tcg27665648\t0.00168241034106321\t0.0135448679503258\n+chr7\t100797596\t100797596\tcg27665659\t0.584346078991673\t0.378506691242143\n+chr16\t562977\t562977\tcg27665715\t0.565808683755868\t0.371560825409313\n+chr6\t30740117\t30740117\tcg27665754\t0.195179452569979\t0.193212324935199\n+chr5\t140764485\t140764485\tcg27665767\t0.0295829291099367\t0.0560871447063137\n+chr4\t2757761\t2757761\tcg27665769\t0.177882849041852\t0.182039911106554\n+chr2\t232055230\t232055230\tcg27665808\t0.00434225884607847\t0.019201058500285\n+chr16\t460516\t460516\tcg27665823\t0.148620718970358\t0.161955931003592\n+chr4\t20698773\t20698773\tcg27665829\t0.394276592448795\t0.300134258028209\n+chr11\t68970673\t68970673\tcg27665860\t0.955577402360683\t0.49344753316125\n+chr19\t12098906\t12098906\tcg27665925\t0.260247596853584\t0.232230250278869\n+chr15\t66116728\t66116728\tcg27665985\t0.00479246995199277\t0.020080550136482\n+chr17\t80279077\t80279077\tcg27666046\t0.375864790319015\t0.291535231589006\n+chr5\t126988030\t126988030\tcg27666123\t0.0945960279891915\t0.120041937916321\n' |
| b |
| diff -r 6f52c0dc56d4 -r 104882a2de00 test-data/Differentially_Methylated_Regions.interval --- a/test-data/Differentially_Methylated_Regions.interval Fri May 10 06:45:34 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,347006 +0,0 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|
| b |
| diff -r 6f52c0dc56d4 -r 104882a2de00 test-data/annoTab.tabular --- a/test-data/annoTab.tabular Fri May 10 06:45:34 2019 -0400 +++ b/test-data/annoTab.tabular Sun Feb 23 07:58:07 2020 -0500 |
| b |
| b'@@ -1,236428 +1,129256 @@\n 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|