Mercurial > repos > yguitton > metams_rungc
changeset 1:142fbe102a9d draft
Uploaded version 2.0
| author | yguitton |
|---|---|
| date | Wed, 24 May 2017 07:25:50 -0400 |
| parents | 2066efbafd7c |
| children | 8e1b99a7d733 |
| files | README.rst Readme.txt lib_metams.r metams.r metams_runGC.xml planemo_test.sh static/images/gcms_workflow.png static/images/metaMS_BPCs.png test-data/BPCs_raw.pdf test-data/RI.csv test-data/TICs_raw.pdf test-data/W4M_GCMS_Dataset.zip test-data/dataMatrix.tsv test-data/peakspectra.msp test-data/peaktable.tsv test-data/sampleMetadata.tsv test-data/threeStdsDB.msp test-data/variableMetadata.tsv |
| diffstat | 14 files changed, 495 insertions(+), 132 deletions(-) [+] |
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--- a/README.rst Wed Jul 13 06:46:45 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,20 +0,0 @@ - -Changelog/News --------------- - -**Version 1.1 - 11/07/2016** - -- TEST: refactoring to pass planemo test using conda dependencies - - -**Version 1.0 - 01/06/2015** - -- NEW: new tool - - - - -Test Status ------------ - -Planemo test using conda: passed
--- a/Readme.txt Wed Jul 13 06:46:45 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,46 +0,0 @@ -####----------------------------------------------------------------------#### -#### GC-MS data processing version 0.99.5 #### -####----------------------------------------------------------------------#### - -I. Date: 2015-05-26 - -II. Author and maintainer: - - Yann GUITTON - LINA - équipe Combi (CNRS, Univ-Nantes, EMN, INRIA) - IRISA - équipe Dyliss (CNRS, Univ-Rennes 1, INRIA) - Phone: +33 2 51 12 53 90 - E-mail: yann.guitton@irisa.fr / yann.guitton@gmail.com - -III. Funding - - Developed within IDEALG project (http://www.idealg.ueb.eu/versionAnglaise/) - -IV. Usage restrictions - - Use of this tool is restricted to the service conditions of the MetaboHUB-IFB infrastructures. - For any question regarding the use of these services, please contact: yann.guitton@univ-nantes.fr - -V. Installation - - 4 files are required for installation: - - 1) 'README.txt' - Instructions for installation - - 2) 'idealg_metams_runGC.xml' - Configuration file; to be put into the './galaxy-dist/tools/' directory - + 2.png files for illustration - - 3) 'metams.R' - Wrapper code written in R aimed at launching the runGC function from the metaMS package given the arguments entered by the user through the Galaxy interface - - 4) 'metaMS R package ' - The 'metaMS' package requires dependencies and can be installed with - source("http://bioconductor.org/biocLite.R") - biocLite("metaMS") - - This code is for installation of the Galaxy module on the Workflow4metabolomics.org MetaboHUB-IFB platform only and must not be distributed without the author agreement - - -
--- a/metams.r Wed Jul 13 06:46:45 2016 -0400 +++ b/metams.r Wed May 24 07:25:50 2017 -0400 @@ -1,7 +1,7 @@ #!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file -# metams.r version="0.99.9" +# metams.r version="2.0" #created by Yann GUITTON - +#use RI options #Redirect all stdout to the log file log_file=file("metams.log", open = "wt") @@ -20,13 +20,23 @@ listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects -print("new version 8") +print("new version 2.0") print(listArguments) - + + if (listArguments[["ri"]]!="NULL"){ - RIarg=read.table(listArguments[["ri"]], h=T) + RIarg=read.table(listArguments[["ri"]]) + if (ncol(RIarg) < 2) RIarg=read.table(listArguments[["ri"]], h=T, sep=";") + if (ncol(RIarg) < 2) RIarg=read.table(listArguments[["ri"]], h=T, sep="\t") + if (ncol(RIarg) < 2) RIarg=read.table(listArguments[["ri"]], h=T, sep=",") + if (ncol(RIarg) < 2) { + error_message="Your RI file seems not well formatted. The column separators accepted are ; , and tabulation" + print(error_message) + stop(error_message) + } +#to do check real column names colnames(RIarg)<-c("rt","RI") # print(RIarg) } else { @@ -34,26 +44,32 @@ # cat("Ri= ",RIarg) } +if (listArguments[["rishift"]]!="none"){ + RIshift=listArguments[["rishift"]] + cat("Rishift used= ",RIshift, "\n") +} else { + RIshift = "none" + cat("Rishift NONE= ",RIshift, "\n") +} DBarg=listArguments[["db"]] # if (listArguments[["use_db"]]!="NULL"){ if (DBarg!="NULL"){ DBarg=listArguments[["db"]] - cat("Db= ",DBarg) + cat("Db= ",DBarg, "\n") } else { DBarg = NULL - cat("NO Db : ",DBarg) + cat("NO Db : ",DBarg, "\n") } - #for unknown EIC printing -if (listArguments[["unkn"]]!="NULL") { +if (listArguments[["unkn"]][1]!="NULL") { + unknarg<-listArguments[["unkn"]] +} else { unknarg<-"" -} else { - unknarg<-listArguments[["unkn"]] } print(paste("Unkn:",unknarg)) @@ -62,6 +78,7 @@ listArguments[["unkn"]]<-NULL listArguments[["db"]] <- NULL listArguments[["ri"]] <- NULL +listArguments[["rishift"]] <- NULL print(" step2") @@ -164,7 +181,18 @@ manual <- read.msp(DBarg) DBarg <- createSTDdbGC(stdInfo = NULL, settings = TSQXLS.GC, manualDB = manual) } - nSlaves=listArguments[["nSlaves"]] + + #use RI instead of rt for time comparison vs DB + if (RIshift!="none"){ + TSQXLS.GC@match2DB.timeComparison<-"RI" + TSQXLS.GC@match2DB.RIdiff<-as.numeric(RIshift) + TSQXLS.GC@betweenSamples.timeComparison<-"RI" + TSQXLS.GC@betweenSamples.RIdiff<-as.numeric(RIshift) + } + + nSlaves=listArguments[["nSlaves"]] + + if(!metams_zip_file=="") { resGC<-runGC(files=samples,settings=TSQXLS.GC, rtrange=rtrange, DB= DBarg, removeArtefacts = TRUE, findUnknowns = TRUE, returnXset = TRUE, RIstandards = RIarg, nSlaves = nSlaves) #default settings for GC from Wehrens et al } @@ -189,11 +217,11 @@ listArguments[["settings"]]=NULL #delete from the list of arguments fwhmparam=listArguments[["fwhm"]] rtdiffparam=listArguments[["rtdiff"]] - #RIdiffparam=listArguments[["RIdiff"]] #only if timeComparison = "RI" minfeatparam=listArguments[["minfeat"]] simthreshparam=listArguments[["simthreshold"]] minclassfractionparam=listArguments[["minclassfraction"]] minclasssizeparam=listArguments[["minclasssize"]] + if (listArguments[["rtrange"]]!="NULL") { rtrange=listArguments[["rtrange"]] cat("rtrange= ",rtrange) @@ -201,6 +229,8 @@ rtrange=NULL cat("rtrange= ",rtrange) } + + nSlaves=listArguments[["nSlaves"]] GALAXY.GC <- metaMSsettings("protocolName" = "GALAXY.GC", @@ -227,13 +257,16 @@ rtdiff = rtdiffparam, RIdiff = 5, minfeat = minfeatparam) - #to be used when DB option will be available - # metaSetting(GALAXY.GC, "matchIrrelevants") <- list( - # irrelevantClasses = c("Bleeding", "Plasticizers"), - # timeComparison = "rt", - # RIdiff = 2, - # rtdiff = rtdiffparam, - # simthresh = simthreshparam) + + #to used if contaminant filter + + # metaSetting(GALAXY.GC, "matchIrrelevants") <- list( + # irrelevantClasses = c("Bleeding", "Plasticizers"), + # timeComparison = "RI", + # RIdiff = RIdiffparam, + # rtdiff = rtdiffparam, + # simthresh = simthreshparam) + metaSetting(GALAXY.GC, "betweenSamples") <- list( min.class.fraction = minclassfractionparam, min.class.size = minclasssizeparam, @@ -242,7 +275,13 @@ RIdiff = 2, simthresh = simthreshparam) - + #ONLY use RI instead of rt for time comparison vs DB or samples + if (RIshift!="none"){ + GALAXY.GC@match2DB.timeComparison<-"RI" + GALAXY.GC@match2DB.RIdiff<-as.numeric(RIshift) + GALAXY.GC@betweenSamples.timeComparison<-"RI" + GALAXY.GC@betweenSamples.RIdiff<-as.numeric(RIshift) + } # files, xset, settings, rtrange = NULL, DB = NULL, # removeArtefacts = TRUE, findUnknowns = nexp > 1, # returnXset = FALSE, RIstandards = NULL, nSlaves = 0 @@ -302,6 +341,7 @@ print("Step QC plot") +#to do check if no peaks found #Quality controls plots but only working in R (don't know why) a<-plotUnknowns(resGC=resGC, unkn=unknarg) #use unknparam value
--- a/metams_runGC.xml Wed Jul 13 06:46:45 2016 -0400 +++ b/metams_runGC.xml Wed May 24 07:25:50 2017 -0400 @@ -1,4 +1,4 @@ - <tool id="metams_runGC" name="metaMS.runGC" version="1.1"> + <tool id="metams_runGC" name="metaMS.runGC" version="2.0"> <description>GC-MS data preprocessing using metaMS package</description> @@ -20,7 +20,7 @@ #elif $inputs.input == "xset": xset $inputs.xset #end if - + #if $settings.setting == "gcdefault": settings "default" #elif $settings.setting == "usersettings": @@ -40,11 +40,17 @@ #end if #if $settings.options_ri.option == "show": ri $settings.options_ri.ri_input - #end if + #end if #if $settings.options_ri.option == "hide": ri "NULL" #end if - #if $settings.options_db.option == "show": + #if $options_rifilter.option == "true": + rishift $options_rifilter.ri_shift + #end if + #if $options_rifilter.option == "false": + rishift "none" + #end if + #if $settings.options_db.option == "show": db $settings.options_db.db_input #end if #if $settings.options_db.option == "hide": @@ -52,7 +58,7 @@ #end if nSlaves \${GALAXY_SLOTS:-1} unkn "c($unkn)" - + </command> <inputs> @@ -103,10 +109,10 @@ </param> <when value="show"> <param name="ri_input" type="data" format="csv,tsv,gg" label=" RI file" help="A file with two column (rt and RI) with rt in minutes as needed for RI option in runGC" /> - </when> + </when> <when value="hide" /> - </conditional> - </when> + </conditional> + </when> <when value="usersettings"> <param name="fwhm" type="integer" value="5" label="FWHM" help="The FWHM of your peaks (matchedFilter method is used)" /> <conditional name="options_rtrange"> @@ -137,21 +143,33 @@ </when> <when value="hide" /> </conditional> - <conditional name="options_ri"> + <conditional name="options_ri"> <param name="option" type="select" label="Use RI option " > <option value="show">show</option> <option value="hide" selected="true">hide</option> </param> <when value="show"> <param name="ri_input" type="data" format="csv,tsv,gg" label=" RI file" help="A file with two column (rt and RI) with rt in minutes as needed for RI option in runGC" /> + </when> <when value="hide" /> + </conditional> - + </when> </conditional> <param name="unkn" type="text" value="1:5" label="EIC_Unknown" help="vector of peaks number to be plotted, for example 1:5 (mean 1 to 5) or 1,4,12 means 1 4 and 12). For all EIC use 0" /> - + <conditional name="options_rifilter"> + <param name="option" type="select" label="Use RI as filter" > + <option value="false" selected="true">FALSE</option> + <option value="true" >TRUE</option> + </param> + <when value="true"> + <param name="ri_shift" type="integer" value="5" label="RIshift" help="RI shift accepted" /> + + </when> + <when value="false" /> + </conditional> <!-- pour !is.null(DB) il faut un conditionnal avec un input type="text" pour charger la db au format msp et donc il faut définir un datatype (cf Misharl) --> </inputs> @@ -180,7 +198,6 @@ <param name="settings|options_rtrange|option" value="hide" /> <param name="settings|options_db|option" value="hide" /> <param name="settings|options_ri|option" value="hide" /> - <param name="methods|peakwidth" value="20,50" /> <output name="sampleMetadata" file="sampleMetadata.tsv" /> <output name="variableMetadata" file="variableMetadata.tsv" /> <output name="dataMatrix" file="dataMatrix.tsv" lines_diff="6" />
--- a/planemo_test.sh Wed Jul 13 06:46:45 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -planemo conda_install --conda_prefix=/tmp/mc . -planemo test --conda_dependency_resolution --conda_prefix /tmp/mc/ --install_galaxy
--- a/test-data/dataMatrix.tsv Wed Jul 13 06:46:45 2016 -0400 +++ b/test-data/dataMatrix.tsv Wed May 24 07:25:50 2017 -0400 @@ -1,12 +1,15 @@ -Name alg11 alg9 alg2 alg3 alg7 alg8 -Unknown 10 0 0 716439 2608558 10512594 7958675 -Unknown 11 0 0 350707 992454 0 1414530 -Unknown 8 0 48121464 0 0 69663216 47475608 -Unknown 9 0 6704169 0 0 6231146 5300219 -Unknown 3 73997431 64542302 3271105 8986693 23638072 18739515 -Unknown 2 75099028 47836465 5873408 16302374 56198912 40418507 -Unknown 4 49891456 36298101 0 0 57808911 34317665 -Unknown 7 19375952 13761534 0 0 6892322 14909830 -Unknown 6 25076752 18374954 0 0 9137481 19261173 -Unknown 5 28189000 19217984 0 0 11992763 20790174 -Unknown 1 171208192 180946294 19403078 51689436 196528995 111241302 +Name alg11 alg9 alg2 alg3 alg7 alg8 +Unknown 13 0 0 716439 2608558 10512590 7958675 +Unknown 14 0 0 350707 992454 0 1414530 +Unknown 9 0 48121464 0 0 69663216 47475608 +Unknown 10 0 6704169 0 0 6231146 5300219 +Unknown 3 72803808 65081589 3589932 8187611 23206222 18194987 +Unknown 2 75097568 48865604 6093497 15758826 54181335 41622436 +Unknown 8 18023032 10004727 1988810 3689811 0 0 +Unknown 12 0 0 2654953 9632150 12097267 7548017 +Unknown 4 49891456 36298101 0 0 57808911 34317665 +Unknown 7 19375952 13761534 0 0 6892322 14909830 +Unknown 6 25076752 18374954 10185579 14373674 9137481 19261173 +Unknown 11 0 0 4796783 8990726 0 8623775 +Unknown 5 28189000 19217984 11502111 23620477 11992763 20790174 +Unknown 1 171208192 180946294 19403078 51689436 196528995 111241302
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakspectra.msp Wed May 24 07:25:50 2017 -0400 @@ -0,0 +1,353 @@ +Name: Unknown 1 +DB.idx: -1 +rt: 19.5 +RI: 1657 +Class: Unknown +Num Peaks: 150 + 51 331136; 52 487032; 53 382068; 54 478333; 55 2583478; + 56 992765; 57 1777882; 58 5626000; 59 6964301; 60 1145051; + 61 2036806; 62 155584; 63 119910; 65 244797; 66 2961314; + 67 2120910; 68 726443; 69 696156; 70 2144465; 71 1355424; + 72 6645529; 73 98819264; 74 8454684; 75 11275124; 76 735302; + 77 496197; 80 364217; 81 216845; 82 381085; 83 536517; + 84 1917990; 85 1340575; 86 1974375; 87 570335; 88 226422; + 89 219472; 91 73819; 92 158904; 93 879456; 95 216841; + 96 276820; 97 307021; 98 874347; 99 1001781; 100 1752290; + 101 516126; 102 460645; 103 637106; 104 150101; 105 254080; + 106 75473; 107 656852; 109 92384; 110 433667; 111 267415; + 112 2175294; 113 756577; 114 1070691; 115 886853; 117 1293214; + 118 237363; 119 407189; 121 3484808; 122 461713; 124 132183; + 125 67941; 126 521370; 127 362714; 128 400572; 129 602485; + 131 2237082; 132 669029; 133 3928309; 134 537096; 135 312006; + 136 55974; 139 325019; 140 2944295; 141 1056576; 142 778921; + 143 229900; 144 210773; 146 566853; 147 24085640; 148 3919572; + 149 2384053; 150 315259; 151 197386; 153 511197; 154 2267097; + 156 171208192; 157 22453512; 158 7499734; 159 686597; 161 84383; + 167 64939; 168 302853; 169 105170; 170 258244; 171 71021; + 172 270649; 182 44425; 183 146013; 184 113902; 185 66156; + 186 230187; 190 308620; 192 37792; 196 25921; 198 85870; + 199 28476; 200 46655; 210 16303; 211 44081; 213 124907; + 214 1132050; 215 273402; 216 205199; 224 25884; 225 56107; + 227 97740; 228 983325; 230 14665124; 231 2839145; 242 45042; + 251 18275; 253 38297; 254 50631; 256 170157; 258 15215428; + 259 3227723; 260 1358519; 261 213955; 272 63951; 273 571738; + 274 128479; 275 56042; 307 44008; 309 9432; 320 22293; + 326 9240; 328 12816; 346 46823; 347 16823; 355 8059; + 357 8313; 366 14353; 374 4686; 393 3295; 438 2900; + +Name: Unknown 2 +DB.idx: -2 +rt: 15.31 +RI: 1453 +Class: Unknown +Num Peaks: 109 + 54 130985; 55 386304; 57 572006; 58 1626517; 59 11332940; + 60 1105852; 61 779043; 62 49838; 66 309409; 71 464676; + 72 2090765; 73 42740320; 74 3703100; 75 3623063; 76 274144; + 85 249850; 86 414586; 87 239455; 88 98221; 97 140325; + 99 1052895; 100 24192800; 101 2494568; 102 1015568; 103 546189; + 104 125585; 105 183390; 106 40513; 111 37644; 112 79349; + 113 463977; 114 6892017; 115 1341075; 116 1447155; 117 1475621; + 118 333477; 119 566729; 121 43164; 126 53442; 127 96521; + 128 223305; 129 541549; 130 2409628; 131 2458746; 132 713618; + 133 6865427; 134 1028935; 135 501012; 136 44352; 137 98973; + 141 33025; 142 228741; 143 102661; 146 477377; 147 13679376; + 148 2077954; 149 1185419; 150 119782; 158 1165756; 159 276042; + 161 159910; 171 108878; 172 1354853; 173 338360; 175 667469; + 176 157953; 178 27122; 183 99766; 185 204644; 186 577938; + 188 75097568; 189 13668140; 190 6203580; 191 1823164; 192 296459; + 193 101260; 194 19856; 200 323091; 201 92126; 202 875048; + 203 195692; 204 330140; 216 178605; 221 132418; 222 36299; + 223 18897; 232 176396; 246 854916; 247 204988; 251 20344; + 261 382321; 262 13058662; 263 3238526; 264 1545900; 265 284162; + 266 85796; 274 23404; 275 24860; 277 41487; 286 16538; + 289 99968; 290 2020076; 291 499514; 292 263523; 293 71717; + 294 20217; 305 21687; 330 6032; 437 4823; + +Name: Unknown 3 +DB.idx: -3 +rt: 13.95 +RI: 1391 +Class: Unknown +Num Peaks: 99 + 55 275674; 57 567253; 58 1478262; 59 6933425; 60 720049; + 61 481573; 66 311922; 71 414281; 72 1276925; 73 39534456; + 74 3388744; 75 3233900; 83 71403; 85 469296; 86 9324286; + 87 1084484; 88 442419; 95 114512; 97 55831; 99 353296; + 100 5044759; 101 1120621; 102 628876; 103 521107; 104 85943; + 105 186440; 106 29687; 108 53940; 111 26846; 113 252577; + 114 277777; 115 423714; 116 872565; 117 2052425; 118 402712; + 119 619934; 121 50662; 122 51533; 128 110744; 129 262357; + 130 2227990; 131 2005278; 132 780122; 133 6398239; 134 906366; + 135 500958; 136 52158; 137 31351; 143 111055; 144 701039; + 145 311500; 146 458753; 147 15067514; 148 2227934; 149 1194963; + 150 120392; 151 42267; 158 1140687; 159 378997; 160 462515; + 161 133845; 162 37605; 165 27185; 169 97176; 171 250277; + 172 1017193; 173 940267; 174 72803808; 175 13294342; 176 5449737; + 177 886532; 178 200676; 179 64615; 187 79575; 188 640832; + 189 197447; 190 158389; 192 35992; 202 386798; 203 106706; + 204 350926; 238 8165; 246 1136468; 247 586854; 248 14939852; + 249 3572854; 250 1822085; 251 314815; 252 77920; 253 29513; + 270 7919; 272 8665; 273 26930; 275 76070; 276 3515474; + 277 838789; 278 497049; 279 66975; 322 5998; + +Name: Unknown 4 +DB.idx: -4 +rt: 17.07 +RI: 1536 +Class: Unknown +Num Peaks: 113 + 53 193226; 54 92371; 55 696712; 57 634952; 58 1294722; + 59 2543004; 60 1023010; 61 2822931; 62 245449; 63 146108; + 68 202406; 69 284012; 70 3008194; 71 541376; 72 2457133; + 73 49891456; 74 6115050; 75 15041860; 76 1445795; 77 625427; + 83 105149; 85 179525; 87 411612; 88 305415; 89 350062; + 90 91783; 91 281691; 92 62178; 94 48505; 97 49365; + 98 289308; 99 463454; 100 2966973; 101 618090; 102 1211733; + 103 608440; 104 129414; 105 102984; 106 24953; 112 112308; + 113 151649; 114 279472; 116 12657332; 117 12152552; 118 1736110; + 119 615570; 123 90727; 125 30931; 126 140406; 127 189027; + 128 1088337; 129 958595; 130 15016632; 131 2242570; 132 959095; + 133 1187269; 134 205198; 135 184535; 136 32990; 143 197139; + 144 1964788; 145 381946; 146 1489727; 147 7059974; 148 1230966; + 149 899973; 150 123792; 151 47302; 159 1885199; 160 33960232; + 161 4172501; 162 1428985; 163 121361; 164 25965; 172 469187; + 187 224174; 190 221794; 191 105712; 192 72228; 200 38741; + 201 52618; 202 1300585; 203 310238; 204 208588; 216 123303; + 217 172550; 220 1337015; 221 242712; 222 138932; 232 185761; + 233 89849; 234 2843829; 235 576060; 236 260407; 237 35951; + 242 28888; 244 586408; 245 4311634; 246 856276; 247 398753; + 260 62703; 262 962171; 263 220596; 264 97394; 265 19980; + 277 87656; 279 16301; 305 18380; 347 6858; 357 10629; + 360 6579; 374 23186; 437 4134; + +Name: Unknown 5 +DB.idx: -5 +rt: 19.05 +RI: 1634 +Class: Unknown +Num Peaks: 122 + 53 154218; 54 159226; 55 492809; 56 369593; 57 313968; + 58 947133; 59 4863447; 60 527404; 61 339583; 62 46621; + 65 70713; 67 168084; 68 415958; 69 380561; 71 257044; + 72 753247; 73 14307406; 74 1341384; 80 50203; 81 107091; + 82 208326; 83 350569; 85 571922; 86 4803714; 87 559524; + 88 309053; 89 905223; 90 129822; 91 68513; 94 158330; + 95 135887; 96 1167000; 97 245382; 98 265921; 99 495911; + 100 2589118; 101 456738; 102 1358302; 104 83182; 106 21323; + 110 51122; 111 79160; 112 423287; 113 285048; 114 516947; + 115 281473; 116 657340; 117 745965; 118 219220; 119 99334; + 124 62092; 125 62427; 126 264480; 127 192382; 128 1014445; + 129 645595; 130 1717849; 131 644575; 132 274878; 138 37342; + 140 172195; 141 68063; 142 244026; 143 127656; 144 329432; + 145 89541; 146 296228; 152 134927; 153 81940; 158 643233; + 159 241157; 161 78768; 164 24696; 165 38779; 167 159973; + 168 4196277; 169 1566036; 170 465685; 171 222158; 172 947489; + 173 780163; 174 28189000; 175 4882837; 176 2239879; 177 262441; + 178 58836; 181 32572; 182 39407; 184 237428; 185 122887; + 186 1310350; 187 256905; 190 273831; 192 43909; 197 19540; + 199 69710; 200 258487; 201 549381; 202 212821; 203 63822; + 213 32123; 215 213748; 216 73608; 224 12990; 227 83973; + 229 31562; 239 26973; 241 118662; 242 58047; 253 26338; + 254 37767; 256 100391; 257 3373141; 258 821803; 259 323660; + 260 72241; 273 166402; 274 44227; 275 23946; 288 21702; + 331 14282; 443 5295; + +Name: Unknown 6 +DB.idx: -6 +rt: 17.88 +RI: 1575 +Class: Unknown +Num Peaks: 131 + 53 124474; 54 276979; 55 603288; 56 427708; 57 506170; + 58 1345773; 59 8274166; 60 849959; 61 421096; 65 112145; + 67 139171; 68 456999; 69 380651; 72 1071288; 73 25076752; + 74 2821478; 80 92310; 81 169346; 82 2699674; 83 370368; + 85 844170; 86 5958178; 87 1046354; 88 424030; 89 1719588; + 90 231787; 91 95302; 92 29464; 94 46476; 95 111259; + 96 104498; 97 157752; 98 551327; 99 545272; 100 3563505; + 101 709274; 102 2656620; 103 439861; 104 141232; 106 18978; + 107 35904; 109 23609; 110 78318; 111 97697; 112 535869; + 113 604807; 114 2887543; 115 601439; 116 1008889; 117 1047659; + 118 290366; 119 109877; 122 302330; 124 110311; 125 98551; + 126 540475; 127 248272; 128 611436; 129 457744; 130 2594427; + 131 927703; 132 443941; 137 26829; 138 213900; 139 143940; + 140 189209; 142 236512; 143 159138; 144 353290; 145 115256; + 146 496478; 151 66719; 153 415524; 154 10518680; 155 3648093; + 157 250726; 158 636763; 159 222577; 160 848557; 161 170240; + 162 257831; 163 54192; 166 31519; 168 61178; 169 406061; + 170 868333; 171 420609; 172 5908057; 173 1469566; 174 22169424; + 175 4116206; 176 1664871; 177 204203; 178 45204; 183 19189; + 184 77243; 185 67796; 186 545086; 187 410839; 190 554204; + 191 128331; 192 56567; 196 27343; 198 38119; 199 65223; + 200 177818; 201 807534; 202 223127; 210 34392; 212 34143; + 213 194308; 214 60656; 226 50904; 227 959138; 228 294910; + 229 141981; 238 23946; 240 39398; 242 156599; 243 9670236; + 244 2117521; 245 989181; 246 164575; 247 38057; 259 303520; + 260 72877; 272 16238; 274 15176; 330 9099; 357 7006; + 389 7923; + +Name: Unknown 7 +DB.idx: -7 +rt: 17.18 +RI: 1541 +Class: Unknown +Num Peaks: 50 + 54 110397; 59 3320113; 60 416252; 68 232675; 81 44353; + 82 279413; 83 105216; 85 272936; 86 2447133; 87 423088; + 88 248368; 89 1092833; 90 130221; 95 105135; 97 63205; + 98 204895; 100 1607438; 111 55722; 112 193175; 113 222787; + 114 365282; 122 102948; 124 41084; 126 127015; 127 91707; + 139 64170; 140 88860; 141 35493; 153 111431; 154 178971; + 155 3032453; 167 24738; 169 167888; 170 145792; 171 212961; + 172 721593; 173 557099; 174 19375952; 175 3419879; 176 1475088; + 177 210298; 178 41941; 185 71940; 186 86682; 200 65034; + 201 71922; 213 24098; 273 36838; 274 228112; 275 67908; + +Name: Unknown 8 +DB.idx: -8 +rt: 16.42 +RI: 1504 +Class: Unknown +Num Peaks: 71 + 54 96005; 55 405866; 56 1674349; 57 543850; 58 1252749; + 59 2045827; 60 343370; 61 642828; 62 53357; 66 426729; + 71 228653; 72 1180578; 73 18023032; 74 1800731; 75 3556445; + 76 246098; 86 351637; 87 201640; 88 162596; 95 120264; + 99 89407; 100 894566; 101 222762; 105 61332; 108 18656; + 113 72605; 114 792755; 117 768512; 118 109736; 119 127990; + 127 87005; 129 541428; 130 13180216; 131 2034223; 132 617467; + 133 628606; 134 100910; 135 51220; 144 216707; 146 237930; + 147 4871981; 148 765132; 149 446465; 150 71474; 158 345988; + 159 104038; 171 36409; 172 145556; 174 17576152; 175 2199021; + 176 766929; 177 78453; 201 120483; 203 119519; 204 2567063; + 205 573640; 206 261131; 232 220809; 233 64721; 272 11290; + 275 36359; 276 2468782; 277 517132; 278 234803; 279 53005; + 287 12957; 290 57358; 333 5348; 368 4218; 418 4287; + 438 7430; + +Name: Unknown 9 +DB.idx: -9 +rt: 13.25 +RI: 1360 +Class: Unknown +Num Peaks: 120 + 57 390054; 59 1639692; 60 250002; 61 582435; 62 45890; + 63 95002; 71 381999; 73 23557576; 74 1973826; 77 362958; + 85 166643; 87 224807; 90 98574; 91 148667; 97 35691; + 105 311016; 107 173337; 109 65936; 115 982633; 119 831035; + 120 216797; 121 629907; 122 87824; 123 253838; 124 60002; + 125 31629; 126 75065; 131 1007501; 132 471792; 133 4952319; + 134 811023; 135 1470056; 136 258418; 137 655240; 138 74410; + 139 82384; 145 117841; 151 505379; 152 71412; 153 117096; + 163 183204; 165 436676; 167 424754; 168 88361; 178 133563; + 179 368202; 181 1038322; 182 171518; 183 337997; 185 26994; + 189 726185; 191 2210788; 192 552202; 193 2870904; 194 525892; + 195 667739; 197 153670; 199 18708; 207 3298016; 208 655173; + 209 549089; 210 221053; 211 5254906; 212 780649; 213 454025; + 214 51284; 221 426955; 222 113503; 224 70619; 225 1419745; + 226 248991; 227 412550; 228 78233; 237 37136; 239 62017; + 241 26071; 252 18480; 253 266323; 255 174420; 256 39782; + 265 13170; 267 198725; 268 59515; 269 402886; 270 102930; + 271 62342; 272 9942; 279 17521; 282 106269; 283 2951052; + 284 684021; 285 486147; 286 82044; 287 23298; 289 28344; + 291 26122; 294 116585; 296 140885; 297 876085; 299 48121464; + 300 10462022; 301 6060726; 302 1044864; 303 221471; 304 31765; + 306 22437; 308 13922; 309 20969; 311 32836; 313 288045; + 314 6594540; 315 1540205; 316 921598; 317 174334; 318 57667; + 361 5714; 373 12172; 374 10019; 385 6332; 387 6522; + +Name: Unknown 10 +DB.idx: -10 +rt: 13.32 +RI: 1363 +Class: Unknown +Num Peaks: 27 + 88 94936; 89 338650; 101 500564; 103 2370715; 104 251305; + 113 91244; 117 3291236; 118 357036; 129 634783; 147 6704169; + 148 1095461; 149 708280; 150 100597; 175 445215; 177 377818; + 203 457034; 204 803831; 205 5185592; 206 1061940; 217 346315; + 218 1548849; 219 298102; 220 124613; 263 31206; 293 122443; + 323 4285; 381 6432; + +Name: Unknown 11 +DB.idx: -11 +rt: 18.74 +RI: 1618 +Class: Unknown +Num Peaks: 77 + 53 40812; 54 21260; 55 146430; 56 77603; 59 908307; + 60 106007; 61 53777; 67 29572; 68 37685; 69 64507; + 72 143191; 73 1762979; 74 194863; 80 35725; 81 27528; + 82 51068; 84 55681; 85 89896; 86 828644; 87 84646; + 88 49644; 89 205056; 90 20012; 91 19169; 94 13462; + 96 48668; 98 33260; 100 403811; 101 61630; 109 11536; + 111 28957; 112 79463; 113 54448; 114 61327; 115 54540; + 116 83696; 117 101112; 118 35941; 119 21167; 124 6835; + 126 42214; 127 44069; 129 66184; 130 200987; 131 80685; + 132 42641; 138 11726; 140 22741; 142 21205; 144 32215; + 146 24281; 152 24271; 153 20832; 158 61244; 161 16101; + 163 9971; 166 17850; 168 31693; 169 577126; 170 139563; + 171 66005; 173 127042; 174 4796783; 175 847814; 176 407684; + 177 62776; 178 12618; 183 32320; 184 19051; 186 54023; + 187 15389; 199 14205; 200 17445; 201 17567; 241 11800; + 288 10448; 290 5007; + +Name: Unknown 12 +DB.idx: -12 +rt: 16.97 +RI: 1531 +Class: Unknown +Num Peaks: 100 + 54 47878; 56 282539; 57 153571; 59 593941; 60 186652; + 61 240778; 62 29689; 67 51736; 68 118524; 70 138070; + 72 504478; 73 9093456; 74 1418244; 75 1616427; 76 145139; + 77 118021; 85 58780; 87 88493; 88 186504; 89 198370; + 90 73954; 91 34464; 98 86699; 100 242339; 101 136247; + 102 504345; 103 1774298; 104 242232; 105 109551; 111 26546; + 112 83080; 113 108938; 114 210996; 115 165449; 116 203302; + 117 219295; 118 86507; 119 78941; 124 13998; 126 50258; + 127 99432; 128 1099596; 129 1591586; 131 273502; 132 138850; + 133 494301; 134 92130; 135 63677; 141 32620; 142 200537; + 143 168256; 144 1650355; 145 326613; 146 188649; 147 1833438; + 148 324070; 149 338173; 150 62825; 151 25138; 161 33780; + 163 22733; 164 12143; 165 14428; 176 72804; 177 31961; + 189 817834; 190 186725; 191 95242; 192 15799; 200 24096; + 201 36112; 202 54941; 203 897664; 204 499809; 205 972365; + 206 202463; 213 13118; 215 43985; 216 45999; 217 335123; + 218 140404; 219 53933; 221 39622; 222 15163; 229 23829; + 231 35030; 233 445215; 234 9632150; 235 2048150; 236 912243; + 237 107163; 238 43814; 240 17452; 241 16833; 249 16027; + 291 10111; 306 9362; 310 9326; 323 6392; 408 4238; + +Name: Unknown 13 +DB.idx: -13 +rt: 10.49 +RI: 1243 +Class: Unknown +Num Peaks: 63 + 73 2608558; 74 259289; 119 45060; 133 119547; 146 126142; + 147 2071419; 148 320745; 149 203305; 150 41001; 163 21345; + 165 22740; 177 43829; 178 14755; 179 46037; 181 6454; + 189 53917; 191 202459; 193 83967; 195 13020; 203 31098; + 205 87391; 207 412488; 208 126065; 221 36364; 235 27212; + 237 19894; 247 40312; 249 329561; 250 112987; 251 103491; + 253 23929; 261 11575; 263 14377; 265 339935; 266 85092; + 267 77377; 269 8066; 277 22768; 279 46230; 281 2114038; + 282 568172; 283 408364; 284 90638; 285 39917; 286 10026; + 295 5943; 309 6064; 322 4007; 337 6595; 348 4820; + 353 27914; 355 13556; 361 6526; 366 8572; 368 19262; + 369 491049; 370 232649; 371 135119; 372 46012; 373 19844; + 374 2925; 392 1828; 434 1752; + +Name: Unknown 14 +DB.idx: -14 +rt: 11.43 +RI: 1281 +Class: Unknown +Num Peaks: 16 + 87 119129; 100 186341; 115 59259; 116 992454; 117 191691; + 118 63267; 122 20884; 190 122183; 191 47676; 192 22568; + 212 47401; 213 12863; 232 154371; 233 39862; 247 10897; + 356 9061; +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peaktable.tsv Wed May 24 07:25:50 2017 -0400 @@ -0,0 +1,15 @@ +"Name" "Class" "rt.sd" "rt" "RI" "alg11" "alg9" "alg2" "alg3" "alg7" "alg8" +"Unknown 13" "Unknown" 0.0049 10.488 1243 0 0 716439 2608558 10512590 7958675 +"Unknown 14" "Unknown" 0.005 11.428 1281 0 0 350707 992454 0 1414530 +"Unknown 9" "Unknown" 0.0038 13.246 1360 0 48121464 0 0 69663216 47475608 +"Unknown 10" "Unknown" 0.0032 13.317 1363 0 6704169 0 0 6231146 5300219 +"Unknown 3" "Unknown" 0.0021 13.954 1391 72803808 65081589 3589932 8187611 23206222 18194987 +"Unknown 2" "Unknown" 0.0036 15.313 1453 75097568 48865604 6093497 15758826 54181335 41622436 +"Unknown 8" "Unknown" 0.0033 16.415 1504 18023032 10004727 1988810 3689811 0 0 +"Unknown 12" "Unknown" 0.0047 16.968 1531 0 0 2654953 9632150 12097267 7548017 +"Unknown 4" "Unknown" 0.0042 17.073 1536 49891456 36298101 0 0 57808911 34317665 +"Unknown 7" "Unknown" 0.005 17.181 1541 19375952 13761534 0 0 6892322 14909830 +"Unknown 6" "Unknown" 0.0034 17.878 1575 25076752 18374954 10185579 14373674 9137481 19261173 +"Unknown 11" "Unknown" 0.0042 18.739 1618 0 0 4796783 8990726 0 8623775 +"Unknown 5" "Unknown" 0.0032 19.047 1634 28189000 19217984 11502111 23620477 11992763 20790174 +"Unknown 1" "Unknown" 0.0046 19.499 1657 171208192 180946294 19403078 51689436 196528995 111241302
--- a/test-data/sampleMetadata.tsv Wed Jul 13 06:46:45 2016 -0400 +++ b/test-data/sampleMetadata.tsv Wed May 24 07:25:50 2017 -0400 @@ -1,7 +1,7 @@ -sampleMetadata class -alg11 FWS_100perNaCl -alg9 FWS_100perNaCl -alg2 SWS -alg3 SWS -alg7 FWS_5percNaCL -alg8 FWS_5percNaCL +sampleMetadata class +alg11 FWS_100perNaCl +alg9 FWS_100perNaCl +alg2 SWS +alg3 SWS +alg7 FWS_5percNaCL +alg8 FWS_5percNaCL
--- a/test-data/variableMetadata.tsv Wed Jul 13 06:46:45 2016 -0400 +++ b/test-data/variableMetadata.tsv Wed May 24 07:25:50 2017 -0400 @@ -1,12 +1,15 @@ -Name Class rt.sd rt -Unknown 10 Unknown 0.0049 10.488 -Unknown 11 Unknown 0.005 11.428 -Unknown 8 Unknown 0.0038 13.246 -Unknown 9 Unknown 0.0032 13.317 -Unknown 3 Unknown 0.0033 13.965 -Unknown 2 Unknown 0.0026 15.323 -Unknown 4 Unknown 0.0042 17.073 -Unknown 7 Unknown 0.005 17.181 -Unknown 6 Unknown 0.0034 17.878 -Unknown 5 Unknown 0.0032 19.047 -Unknown 1 Unknown 0.0046 19.499 +Name Class rt.sd rt RI +Unknown 13 Unknown 0.0049 10.488 1243 +Unknown 14 Unknown 0.005 11.428 1281 +Unknown 9 Unknown 0.0038 13.246 1360 +Unknown 10 Unknown 0.0032 13.317 1363 +Unknown 3 Unknown 0.0021 13.954 1391 +Unknown 2 Unknown 0.0036 15.313 1453 +Unknown 8 Unknown 0.0033 16.415 1504 +Unknown 12 Unknown 0.0047 16.968 1531 +Unknown 4 Unknown 0.0042 17.073 1536 +Unknown 7 Unknown 0.005 17.181 1541 +Unknown 6 Unknown 0.0034 17.878 1575 +Unknown 11 Unknown 0.0042 18.739 1618 +Unknown 5 Unknown 0.0032 19.047 1634 +Unknown 1 Unknown 0.0046 19.499 1657