| Next changeset 1:03c13085aecc (2020-01-23) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043" |
|
added:
pathview.r pathview.xml static/images/dme00010_graphviz.png static/images/dme00010_native.png test-data/cpd_data.tabular test-data/dme00010.pdf test-data/dme00010.png test-data/dme00010_cpd.pdf test-data/dme00480.png test-data/dme00480_cpd.pdf test-data/gene_data.tabular test-data/pathways.tabular |
| b |
| diff -r 000000000000 -r bd99e8fbde97 pathview.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pathview.r Mon Aug 26 14:42:52 2019 -0400 |
| [ |
| @@ -0,0 +1,89 @@ +options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) + +# we need that to not crash galaxy with an UTF8 error on German LC settings. +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") + +suppressPackageStartupMessages({ + library("pathview") + library("optparse") +}) + +sessionInfo() + +option_list <- list( + make_option(c("--pathway_id"), type="character", default=NULL, help="Path to tabular file with gene data"), + make_option(c("--pathway_id_fp"), type="character", default=NULL, help="Path to tabular file with pathway ids"), + make_option(c("--pathway_id_header"), type="logical", default=FALSE, help="Header for tabular file with pathway ids"), + make_option(c("--species"), type="character", default="hsa", help="KEGG code, scientific name or the common name of the species"), + make_option(c("--gene_data"), type="character", default=NULL, help="Path to tabular file with gene data"), + make_option(c("--gd_header"), type="logical", default=FALSE, help="Header for the gene data file"), + make_option(c("--gene_idtype"), type="character", default="entrez", help="ID type used for the gene data"), + make_option(c("--cpd_data"), type="character", default=NULL, help="Path to tabular file with compound data"), + make_option(c("--cpd_header"), type="logical", default=FALSE, help="Header for the compound data file"), + make_option(c("--cpd_idtype"), type="character", default="kegg", help="ID type used for the compound data"), + make_option(c("--multi_state"), type="logical", default=TRUE, help="Are the gene and compound data paired?"), + make_option(c("--match_data"), type="logical", default=TRUE, help="Are the gene and compound data paired?"), + make_option(c("--kegg_native"), type="logical", default=TRUE, help="Render pathway graph as native KEGG grap? Alternative is the Graphviz layout"), + make_option(c("--same_layer"), type="logical", default=TRUE, help="Plot on same layer?"), + make_option(c("--map_null"), type="logical", default=TRUE, help="Map the NULL gene or compound data to pathway?"), + make_option(c("--split_group"), type="logical", default=FALSE, help="Split node groups into individual nodes?"), + make_option(c("--expand_node"), type="logical", default=FALSE, help="Expand multiple-gene nodes into single-gene nodes?"), + make_option(c("--sign_pos"), type="character", default="bottomright", help="Position of pathview signature") +) + +parser <- OptionParser(usage = "%prog [options] file", option_list=option_list) +args = parse_args(parser) +print(args) + +read_table = function(fp, header, rownames=1, colclasses=NA){ + table = read.table(fp, header=header, sep="\t", row.names=rownames, colClasses=colclasses) + # transform to vector if only one column + if(dim(table)[2] == 1){ + names = rownames(table) + table = table[,1] + names(table) = names + } + return(table) +} + +get_table = function(fp, header){ + table = NULL + if(!is.null(fp)){ + table = read_table(fp, header, rownames=1) + } + return(table) +} + +# load gene_data file +gene_data = get_table(args$gene_data, args$gd_header) + +# load compound data file +cpd_data = get_table(args$cpd_data, args$cpd_header) + +run_pathview = function(pathway_id){ + pathview( + pathway.id=pathway_id, + gene.data=gene_data, + gene.idtype=args$gene_idtype, + cpd.data=cpd_data, + cpd.idtype=args$cpd_idtype, + species=args$species, + multi.state=args$multi_state, + match.data=args$match_data, + kegg.native=args$kegg_native, + same.layer=args$same_layer, + split.group=args$split_group, + expand.node=args$expand_node, + sign.pos=args$sign_pos, + map.null=args$map_null) +} + +# get pathway ids +if(!is.null(args$pathway_id)){ + run_pathview(args$pathway_id) +} else { + pthws = read_table(args$pathway_id_fp, args$pathway_id_header, rownames=NULL, colclasses="character") + for(p in pthws){ + run_pathview(p) + } +} |
| b |
| diff -r 000000000000 -r bd99e8fbde97 pathview.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pathview.xml Mon Aug 26 14:42:52 2019 -0400 |
| [ |
| b'@@ -0,0 +1,405 @@\n+<tool id="pathview" name="Pathview" version="@VERSION@+@GALAXY_VERSION@">\n+ <description>for pathway based data integration and visualization</description>\n+ <macros>\n+ <token name="@VERSION@">1.24.0</token>\n+ <token name="@GALAXY_VERSION@">galaxy0</token>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="@VERSION@">bioconductor-pathview</requirement>\n+ <requirement type="package" version="3.8.2">bioconductor-org.ag.eg.db</requirement>\n+ <requirement type="package" version="3.8.2">bioconductor-org.at.tair.db</requirement>\n+ <requirement type="package" version="3.8.2">bioconductor-org.bt.eg.db</requirement>\n+ <requirement type="package" version="3.8.2">bioconductor-org.ce.eg.db</requirement>\n+ <requirement type="package" version="3.8.2">bioconductor-org.cf.eg.db</requirement>\n+ <requirement type="package" version="3.8.2">bioconductor-org.dm.eg.db</requirement>\n+ <requirement type="package" version="3.8.2">bioconductor-org.dr.eg.db</requirement>\n+ <requirement type="package" version="3.8.2">bioconductor-org.eck12.eg.db</requirement>\n+ <requirement type="package" version="3.8.2">bioconductor-org.ecsakai.eg.db</requirement>\n+ <requirement type="package" version="3.8.2">bioconductor-org.gg.eg.db</requirement>\n+ <requirement type="package" version="3.8.2">bioconductor-org.hs.eg.db</requirement>\n+ <requirement type="package" version="3.8.2">bioconductor-org.mm.eg.db</requirement>\n+ <requirement type="package" version="3.8.2">bioconductor-org.mmu.eg.db</requirement>\n+ <requirement type="package" version="3.8.2">bioconductor-org.pf.plasmo.db</requirement>\n+ <requirement type="package" version="3.8.2">bioconductor-org.pt.eg.db</requirement>\n+ <requirement type="package" version="3.8.2">bioconductor-org.rn.eg.db</requirement>\n+ <requirement type="package" version="3.8.2">bioconductor-org.sc.sgd.db</requirement>\n+ <requirement type="package" version="3.8.2">bioconductor-org.ss.eg.db</requirement>\n+ <requirement type="package" version="3.8.2">bioconductor-org.xl.eg.db</requirement>\n+ <requirement type="package" version="1.6.2">r-optparse</requirement>\n+ </requirements>\n+ <version_command><![CDATA[\n+echo $(R --version | grep version | grep -v GNU)", pathview version" $(R --vanilla --slave -e "library(pathview); cat(sessionInfo()\\$otherPkgs\\$pathview\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\\$otherPkgs\\$optparse\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", dplyr version" $(R --vanilla --slave -e "library(dplyr); cat(sessionInfo()\\$otherPkgs\\$dplyr\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", ggplot2 version" $(R --vanilla --slave -e "library(ggplot2); cat(sessionInfo()\\$otherPkgs\\$ggplot2\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")\n+ ]]></version_command>\n+ <command detect_errors="exit_code"><![CDATA[\n+Rscript \'$__tool_directory__/pathview.r\'\n+\n+#if str($pathway.nb) == \'one\'\n+ --pathway_id \'$pathway.one_id\'\n+#else\n+ --pathway_id_fp \'$pathway.tabular\'\n+ --pathway_id_header $pathway.header\n+#end if\n+\n+ --species \'$species\'\n+\n+#if str($gene_data.gd) == \'true\'\n+ --gene_data \'$gene_data.tabular\'\n+ --gd_header $gene_data.header\n+ --gene_idtype \'$gene_data.idtype\'\n+#end if\n+\n+#if str($cpd_data.cpd) == \'true\'\n+ --cpd_data \'$cpd_data.tabular\'\n+ --cpd_header $cpd_data.header\n+ --cpd_idtype \'$cpd_data.idtype\'\n+#end if\n+\n+ --multi_state $multi_state\n+ --match_data $match_data\n+\n+ --kegg_native $out.kegg_native.out\n+ --same_layer $out.kegg_native.same_layer\n+#if str($out.kegg_native.out) == \'TRUE\'\n+ --map_null $out.kegg_native.map_null\n+#else\n+ --split_group $out.kegg_native.split_group\n+ --expand_node $out.kegg_native.expand_node\n+ --sign_pos $out.kegg_native.sign_pos\n+#en'..b' <element name="dme00480" ftype="pdf" file="dme00480_cpd.pdf" compare="sim_size"/>\n+ </output_collection>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+.. class:: infomark\n+\n+**What it does**\n+\n+Pathview is a stand-alone software package for pathway based data integration and visualization. \n+\n+This package can be divided into four functional modules: the Downloader, Parser, Mapper andViewer. \n+Mostly importantly, pathview maps and renders user data on relevant pathway graphs. \n+\n+Notice that KEGG requires subscription for FTP access since May 2011. \n+However,Pathview downloads individual pathway graphs and data files through API or HTTP access, which is freely available (for academic and non-commerical uses).\n+Pathview uses KEGGgraph (Zhang and Wiemann, 2009) when parsing KEGG xml data files. \n+\n+\n+Options map closely to the excellent pathview manual_.\n+\n+-----\n+\n+**Inputs**\n+\n+Pathview provides strong support for data integration. It works with:\n+\n+- essentially all types of biological data mappable to pathways (gene expression, protein expression, genetic association, metabolite, genomic data, literature, etc)\n+- over 10 types of gene or protein IDs, and 20 types of compound or metabolite IDs\n+- pathways for about 4800 species as well as KEGG orthology\n+- various data attributes and formats, i.e. continuous/discrete data, matrices/vectors, single/multiple samples etc.\n+\n+Pathview can be directly used for metagenomic, microbiome or unknown species data when the data are mapped to KEGG ortholog pathways.\n+\n+*Pathway ids* \n+\n+Either just the name or a table with one column with the different pathway ids to represent.\n+\n+\n+*Gene data*\n+\n+The first input of Pathview is a gene data table. Here gene data is a broad concept including genes, transcripts, protein, enzymes and their expression, modifications and any measurable attributes. \n+\n+It should be a table with first column being the gene ids and other being information (p-value, fold change, levels, etc) from one or several samples.\n+The first line can include the sample names.\n+\n+Here gene id is a generic concepts, including multiple types of gene, transcript and protein uniquely mappable to KEGG gene IDs. KEGG ortholog IDs are also treated as gene IDs as to handle metagenomic data.\n+\n+Example:\n+\n+ =========== =================\n+ FBgn0039155\t-4.14844993705661\n+ FBgn0003360\t-2.99977727873544\n+ FBgn0026562\t-2.38016404989418\n+ FBgn0025111\t2.69993883050214\n+ FBgn0029167\t-2.10506155636758\n+ =========== =================\n+\n+*Compound data*\n+\n+We also frequently want to look at metabolic pathways too. Besides gene nodes, these pathways also have compound nodes. \n+Therefore, we may integrate or visualize both gene data and compound data with metabolic pathways.\n+\n+Here compound data is a broad concept including metabolites, drugs, their measurements and attributes. \n+\n+The format is similar to the gene data table, except named with IDs mappable to KEGG compound IDs.\n+Over 20 types of IDs included in CHEMBL database can be used here.\n+\n+-----\n+\n+**Outputs**\n+\n+Pathview generates both native KEGG view and Graphviz view for pathways. \n+\n+KEGG view keeps all the meta-data on pathways, spacial and temporal information, tissue/cell types, inputs, outputs and connections. This is important for human reading and interpretation of pathway biology.\n+\n+.. image:: $PATH_TO_IMAGES/dme00010_native.png\n+ :width: 60 %\n+\n+Graphviz view provides better control of node and edge attributes, better view of pathway topology, better understanding of the pathway analysis statistics.\n+\n+.. image:: $PATH_TO_IMAGES/dme00010_graphviz.png\n+ :width: 60 %\n+\n+.. _manual: https://bioconductor.org/packages/release/bioc/vignettes/pathview/inst/doc/pathview.pdf\n+.. _KEGG: http://www.genome.jp/kegg\n+\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btt285</citation>\n+ </citations>\n+</tool>\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r bd99e8fbde97 static/images/dme00010_graphviz.png |
| b |
| Binary file static/images/dme00010_graphviz.png has changed |
| b |
| diff -r 000000000000 -r bd99e8fbde97 static/images/dme00010_native.png |
| b |
| Binary file static/images/dme00010_native.png has changed |
| b |
| diff -r 000000000000 -r bd99e8fbde97 test-data/cpd_data.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cpd_data.tabular Mon Aug 26 14:42:52 2019 -0400 |
| b |
| b'@@ -0,0 +1,3000 @@\n+C00232\t-1.09759771890052\n+C01881\t0.128915365792426\n+C02424\t2.0785102666558\n+C07418\t0.932992454258254\n+C13756\t-0.00786047983581522\n+C07378\t-0.0902330032505592\n+C06633\t-1.00197436914991\n+C00251\t2.66218643563674\n+C01059\t-1.85078956265821\n+C02226\t-0.135552037249008\n+C03037\t-1.5832744194994\n+C10017\t0.951442661753311\n+C05590\t0.0389748404326761\n+C04221\t1.86546245325154\n+C03725\t0.677275239341894\n+C08817\t1.93743611595937\n+C12058\t-0.617105151942241\n+C11718\t-0.374217547892271\n+C00665\t0.57083478439713\n+C06921\t-1.03836032196294\n+C11306\t-0.607816182571304\n+C00691\t-1.16142384928919\n+C00540\t0.414534050566182\n+C04378\t-1.30043802614257\n+C01417\t-0.298384581704391\n+C16361\t-0.872472156799836\n+C07142\t0.503475862829171\n+C03881\t-0.933706156633543\n+C05299\t1.01206355253824\n+C02850\t-0.986409428176359\n+C11138\t-0.085126901443013\n+C04835\t-1.34965191541989\n+C02336\t-2.29011897264685\n+C11507\t0.755380597852141\n+C09665\t-0.221443906118851\n+C16838\t0.284760646968028\n+C01227\t1.03963324252118\n+C08284\t0.887648822299716\n+C03406\t-0.152778602382083\n+C05472\t0.681553170725032\n+C08153\t-0.71574122114\n+C01324\t-2.00777217542882\n+C14591\t0.271086252203443\n+C08585\t0.912556433549648\n+C16314\t0.962264542119107\n+C11849\t-0.030385684539541\n+C12893\t0.645030815852192\n+C04608\t-1.73904947794696\n+C11993\t-1.0820000731365\n+C00676\t-0.198331784615855\n+C07663\t-0.350924193373596\n+C07187\t-0.0635456054447326\n+C07569\t-0.56098879847242\n+C00014\t1.2061174166876\n+C05676\t1.0180940051607\n+C06422\t-0.470831130317495\n+C04540\t-2.18218212194695\n+C14326\t1.28150903961497\n+C11733\t-1.97369577763118\n+C06832\t1.54714206724657\n+C07185\t2.7194103695652\n+C14196\t-0.147224397178333\n+C04426\t-1.35220505623092\n+C15233\t-0.230804132212205\n+C06189\t0.172579371038513\n+C00770\t1.2442474934639\n+C01290\t0.339000592363082\n+C01164\t-1.27486066469278\n+C00431\t-0.706926933008814\n+C04652\t1.11596537132875\n+C00546\t2.21177356504198\n+C02367\t1.46489249474979\n+C11131\t-0.335192055129207\n+C07733\t1.09125370423392\n+C02766\t-2.73892216990146\n+C05950\t-0.267244580957982\n+C01673\t-0.21704486764732\n+C08319\t0.133144596775128\n+C11132\t0.84450908319495\n+C03505\t0.551589928351631\n+C02293\t0.315249849120073\n+C07647\t0.835607807766893\n+C15606\t0.838311339050156\n+C09631\t0.123735423571949\n+C03057\t0.920340665279873\n+C07005\t0.70344682284094\n+C12012\t-0.498122389686118\n+C00548\t-2.05936067149331\n+C09981\t-1.01526002125668\n+C13690\t-1.22089009770408\n+C03287\t1.72175964801585\n+C06174\t-0.462340245159745\n+C04315\t0.698299577598804\n+C14807\t0.766754268068229\n+C05528\t-0.540568258850326\n+C01661\t-1.151143960113\n+C16312\t0.656946490078059\n+C11525\t-0.525134299046918\n+C08123\t2.28110514919093\n+C01345\t0.961341761431342\n+C02269\t0.907353156986738\n+C01009\t-1.84363242299094\n+C04237\t0.316988871230123\n+C16737\t0.571453538110295\n+C03946\t0.387255308434192\n+C12369\t0.13564260994964\n+C02634\t0.941726619291221\n+C02430\t-2.34521949378514\n+C12626\t1.36684485695963\n+C06006\t0.863015966860248\n+C06150\t0.911479264948368\n+C03313\t-0.705849245882096\n+C06875\t-0.414461895262437\n+C02505\t2.27463903964806\n+C01529\t1.04132074478077\n+C01301\t-0.607311180473947\n+C01571\t0.391598412023664\n+C02347\t1.25252791912581\n+C06273\t-0.842004751391777\n+C07323\t0.91739661900282\n+C14147\t-0.0676055982384836\n+C06312\t-2.07191213618068\n+C09329\t0.336658230629862\n+C11208\t1.08671018826573\n+C08365\t0.139758526151904\n+C02557\t-0.342947779307441\n+C06899\t0.261674858862031\n+C12486\t0.418336806686223\n+C06112\t-0.381700743587026\n+C05852\t-0.785914425136886\n+C03312\t0.781295324580873\n+C05801\t-0.517667553308026\n+C01079\t-1.65002816856605\n+C02682\t1.6586279058961\n+C11933\t0.632367541695837\n+C00226\t0.787771051410271\n+C01904\t-1.98544358501365\n+C05272\t-2.0278679375694\n+C00379\t-0.316878705211743\n+C03232\t-1.16305011790004\n+C03444\t-2.55423408343177\n+C02147\t-1.08226513652653\n+C13734\t-0.256515335445509\n+C04586\t0.0500911137696876\n+C06411\t-0.361649062184464\n+C08050\t-0.668618525420942\n+C16633\t-1.00226085152763\n+C00489\t0.544294243328115\n+C12370\t-2.62793294015566\n+C08386\t0.4762724049383\n+C02477\t-0.313848123121175\n+C12978\t-0.36165783034483\n+C00182\t1.31466984608248\n'..b'\t0.493732428802335\n+C01197\t-0.262536348285006\n+C14776\t0.080092872249764\n+C07250\t-0.899491403446481\n+C06077\t-0.599870294529746\n+C04894\t-1.83240076546716\n+C02294\t0.168743021132976\n+C05610\t1.31938502959582\n+C15769\t0.744818822148536\n+C04581\t1.19794176002485\n+C08354\t1.68221596653236\n+C03052\t1.30613478484245\n+C00126\t0.846093496160024\n+C01837\t1.27310972860519\n+C16545\t0.0101147919525431\n+C06464\t-0.0387291039406534\n+C06823\t-0.418308556422805\n+C16850\t-1.52962588366352\n+C01283\t-2.13424060601105\n+C04425\t-1.20944483760901\n+C15771\t0.511180395435784\n+C03541\t0.845840774268429\n+C03001\t-0.920517095006837\n+C01152\t1.3040775339894\n+C03546\t-0.869767568225548\n+C07484\t0.965865129950341\n+C07877\t0.434907448962712\n+C02825\t0.55933091081022\n+C14040\t-0.314495605300858\n+C01191\t-0.0826263948812015\n+C00965\t0.00325162932046833\n+C04335\t0.513876515281579\n+C05339\t-2.15980339424932\n+C05067\t-0.912537343470008\n+C00292\t-1.63407146456009\n+C13556\t1.39817327097435\n+C01235\t-0.315513421013277\n+C02115\t1.73572789702512\n+C14524\t0.187018877905729\n+C01137\t-0.205006074548665\n+C07531\t0.731143554033343\n+C00474\t0.057251961363453\n+C08576\t2.39757418346288\n+C00969\t-1.15481810164277\n+C05204\t-1.32741050495612\n+C14362\t1.41077547562043\n+C01127\t-0.296457843595863\n+C03586\t-1.29194311926772\n+C05960\t-0.105596004658667\n+C00075\t1.35584331943028\n+C06337\t1.41125013977977\n+C01330\t-1.79026848570195\n+C10243\t0.63624664318343\n+C11508\t-0.71305657822221\n+C03783\t0.459323239922705\n+C14184\t-1.51449832884863\n+C06690\t0.370357643489359\n+C06881\t-0.0998755236407139\n+C09884\t1.26467538039016\n+C06658\t0.0402134094576424\n+C13258\t0.93015659783805\n+C13373\t-0.632220419245889\n+C08298\t1.22673621724786\n+C00257\t0.747791414922344\n+C15479\t-0.795135408974419\n+C00826\t-0.755821492479498\n+C10041\t0.682746020889373\n+C14812\t-0.308477397877819\n+C04366\t-0.192791869842524\n+C08810\t1.86730234443687\n+C02406\t0.134280106175788\n+C05797\t-0.450870899970905\n+C06032\t-2.12017629686027\n+C08068\t-2.25380836654178\n+C10889\t-1.17712060554045\n+C07290\t-0.594408146529528\n+C15589\t-0.587164306500368\n+C07633\t-0.812674781711682\n+C03568\t1.29807479617442\n+C01104\t0.682378960764108\n+C10991\t-0.280982360780613\n+C11111\t-1.51977214958202\n+C14334\t0.412564866568605\n+C07253\t0.306749611907597\n+C01161\t-0.273112712055366\n+C02344\t-0.400382813170287\n+C06399\t-2.79349321707968\n+C13881\t0.940427392226904\n+C11591\t-0.667598211923827\n+C00959\t-3.0922907485031\n+C00049\t0.775944838674524\n+C06391\t0.0839739600211849\n+C06465\t1.9231128221934\n+C01310\t0.00637000100696474\n+C01920\t1.23475787495279\n+C02080\t0.0173316948504173\n+C11388\t-0.0208663523020147\n+C05402\t1.37897416205289\n+C13455\t0.49156274279784\n+C09785\t1.11468238459804\n+C07457\t-1.02074765468056\n+C02351\t0.81373530835906\n+C03483\t-0.403834296544512\n+C04807\t-0.267214169010772\n+C00879\t0.105814072022219\n+C05454\t1.79176547137758\n+C11158\t0.0619662453446875\n+C00419\t-0.26689949164479\n+C00461\t1.64518142829588\n+C05913\t-0.288590814897913\n+C00836\t-0.555476459252263\n+C01499\t0.0269645391949056\n+C04752\t-1.27405809671927\n+C01444\t0.0993948850022874\n+C09617\t1.39639987699945\n+C00460\t0.693952589712729\n+C01802\t0.320421678685765\n+C06805\t0.64772956123791\n+C02490\t-2.09471790123815\n+C06917\t-0.169863414399045\n+C06099\t0.808985366031211\n+C03773\t0.612427502292522\n+C09810\t-0.42684870189383\n+C03543\t0.816149842259029\n+C02335\t-0.986221454126451\n+C09627\t-0.0444164732039946\n+C10828\t1.35691292698987\n+C03664\t-0.673555420288774\n+C02475\t0.827425354426537\n+C02061\t1.22784794287179\n+C04937\t0.0931254293017308\n+C10395\t-0.471583766115769\n+C07474\t-0.631220774473565\n+C09655\t-1.233507999155\n+C01011\t-0.103615201640138\n+C05831\t-0.527211189603222\n+C01970\t0.978081065677563\n+C02824\t0.703075534051757\n+C02744\t-0.375847688483704\n+C01402\t-0.399471365377513\n+C05994\t0.0663471474750085\n+C03925\t1.06787709825503\n+C03042\t-0.113558373225062\n+C00858\t1.02425010628011\n+C03091\t-0.383864220917446\n+C05119\t0.849995825799742\n+C03667\t-0.368312124152911\n+C14399\t1.62007008838326\n+C16637\t-0.951190414217461\n+C08282\t-1.30573169130498\n+C13524\t-0.174351416845985\n+C04404\t-0.42649518148328\n+C00751\t-0.445453661323308\n' |
| b |
| diff -r 000000000000 -r bd99e8fbde97 test-data/dme00010.pdf |
| b |
| Binary file test-data/dme00010.pdf has changed |
| b |
| diff -r 000000000000 -r bd99e8fbde97 test-data/dme00010.png |
| b |
| Binary file test-data/dme00010.png has changed |
| b |
| diff -r 000000000000 -r bd99e8fbde97 test-data/dme00010_cpd.pdf |
| b |
| Binary file test-data/dme00010_cpd.pdf has changed |
| b |
| diff -r 000000000000 -r bd99e8fbde97 test-data/dme00480.png |
| b |
| Binary file test-data/dme00480.png has changed |
| b |
| diff -r 000000000000 -r bd99e8fbde97 test-data/dme00480_cpd.pdf |
| b |
| Binary file test-data/dme00480_cpd.pdf has changed |
| b |
| diff -r 000000000000 -r bd99e8fbde97 test-data/gene_data.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_data.tabular Mon Aug 26 14:42:52 2019 -0400 |
| b |
| b'@@ -0,0 +1,17559 @@\n+FBgn0039155\t-4.14844993705661\n+FBgn0003360\t-2.99977727873544\n+FBgn0026562\t-2.38016404989418\n+FBgn0025111\t2.69993883050214\n+FBgn0029167\t-2.10506155636758\n+FBgn0039827\t-3.50301408325545\n+FBgn0035085\t-2.41407407908727\n+FBgn0034736\t-3.01817864351425\n+FBgn0264475\t-2.33448625218343\n+FBgn0000071\t2.36001723954814\n+FBgn0029896\t-2.20240483861831\n+FBgn0038832\t-2.34071110479025\n+FBgn0037754\t-2.0719936164101\n+FBgn0264753\t-2.59345911904556\n+FBgn0034897\t-1.79510650765491\n+FBgn0035189\t2.42860686965086\n+FBgn0011260\t1.96746091024373\n+FBgn0027279\t-1.16556778313582\n+FBgn0040099\t-1.65424331975076\n+FBgn0024288\t-2.86781820432562\n+FBgn0001226\t1.56713548792379\n+FBgn0085359\t-2.9091382332846\n+FBgn0040091\t-1.47305267344598\n+FBgn0262733\t1.85754995126772\n+FBgn0023479\t-1.44785739807618\n+FBgn0052407\t-1.86794067139063\n+FBgn0051092\t1.95080030279816\n+FBgn0039419\t-1.11967740680523\n+FBgn0261552\t-1.63112303837855\n+FBgn0034010\t-1.36781208403948\n+FBgn0261673\t2.40798626618518\n+FBgn0031150\t1.18524287689931\n+FBgn0033913\t-1.1260911294897\n+FBgn0264437\t2.14543847358038\n+FBgn0040827\t-1.72262561701716\n+FBgn0037290\t2.281484098595\n+FBgn0016715\t-1.91129816375253\n+FBgn0031912\t-1.09267486829965\n+FBgn0003748\t1.0412023680703\n+FBgn0001224\t1.349154395717\n+FBgn0051363\t0.924469229546748\n+FBgn0035147\t-1.11819742416834\n+FBgn0261362\t1.37429590315222\n+FBgn0024315\t-1.90966797199769\n+FBgn0261596\t-1.04695773378296\n+FBgn0032405\t1.94491333081251\n+FBgn0039109\t-1.24008932849044\n+FBgn0260011\t1.8965148802511\n+FBgn0037468\t0.89537749948062\n+FBgn0261584\t-1.76386401613538\n+FBgn0053307\t-1.30646106300559\n+FBgn0063649\t-1.14800827722833\n+FBgn0001137\t-1.27381945154534\n+FBgn0259715\t-1.5778164291723\n+FBgn0038149\t1.01091144748191\n+FBgn0050147\t-0.933148025532292\n+FBgn0031322\t-1.3275415547226\n+FBgn0001225\t1.22164287869086\n+FBgn0002868\t-1.71122707308258\n+FBgn0039464\t1.00615143225755\n+FBgn0265276\t1.58372312430796\n+FBgn0000406\t-1.70769202129996\n+FBgn0030041\t-1.97687245187781\n+FBgn0040271\t0.905305758945738\n+FBgn0033367\t1.26425708522546\n+FBgn0003137\t0.863597649412503\n+FBgn0036985\t-1.21294629483744\n+FBgn0039257\t-1.01387326590637\n+FBgn0039479\t1.31825102273628\n+FBgn0063498\t-1.2508957414737\n+FBgn0037153\t1.47261646432941\n+FBgn0051642\t1.60375790718999\n+FBgn0262057\t-0.933940441174044\n+FBgn0030237\t-0.903509311907447\n+FBgn0263232\t1.18650640959454\n+FBgn0032004\t-1.08846556495142\n+FBgn0001258\t0.858867295693903\n+FBgn0031327\t1.10350280678349\n+FBgn0051523\t-0.758049265171911\n+FBgn0034389\t-1.60944593661534\n+FBgn0037239\t-0.867164693503876\n+FBgn0033635\t1.07611561535751\n+FBgn0261800\t-0.728376617132168\n+FBgn0031449\t-0.833031095098507\n+FBgn0034885\t1.36090679256779\n+FBgn0051038\t-0.918452970102476\n+FBgn0031805\t-0.873232112713882\n+FBgn0024491\t0.964202482897134\n+FBgn0032598\t1.02358378388926\n+FBgn0000116\t1.0805007989723\n+FBgn0052521\t-0.81668034928734\n+FBgn0261284\t1.67303519611751\n+FBgn0023549\t-1.30846261532281\n+FBgn0051337\t-0.950459806691273\n+FBgn0051195\t0.771379172218764\n+FBgn0027580\t-0.8743299947404\n+FBgn0034438\t1.45443696212133\n+FBgn0031703\t-1.48939298900239\n+FBgn0052625\t1.3200529117641\n+FBgn0030805\t0.917822351095476\n+FBgn0038198\t1.63152954582761\n+FBgn0050463\t1.65857012208198\n+FBgn0000567\t-1.1195175657535\n+FBgn0036299\t0.83677995622731\n+FBgn0037646\t-1.69205017803083\n+FBgn0038528\t1.20404345235462\n+FBgn0261560\t-0.843805723615282\n+FBgn0036684\t-0.808602036007714\n+FBgn0004369\t-0.81175289247931\n+FBgn0033065\t1.73212244907444\n+FBgn0034638\t-0.866349973389654\n+FBgn0031359\t-0.823584745300544\n+FBgn0050069\t-0.839603031102558\n+FBgn0022160\t-0.884556869423913\n+FBgn0035968\t0.983583834807373\n+FBgn0036373\t-0.959351249269738\n+FBgn0024984\t1.21628653134435\n+FBgn0034718\t1.17897980652209\n+FBgn0013763\t-0.666030981735679\n+FBgn0040388\t-0.934147217593508\n+FBgn0043364\t-1.0257689875102\n+FBgn0028514\t-0.917255261538661\n+FBgn0037683\t-0.822384406202427\n+FBgn0040398\t-0.784525603090094\n+FBgn0033426\t-0.924427770042444\n+FBgn0053516\t-0.798216191860116\n+FBgn0004396\t1.00077246050143\n+FBgn0004893\t-0.820939121018225\n+FBgn0027515\t0.828169512117016\n+FBgn0003502\t0'..b'32\t-0.00527617139757588\n+FBgn0267609\tNA\n+FBgn0001313\t0.146569379876571\n+FBgn0058064\t-0.0132510749453709\n+FBgn0259853\tNA\n+FBgn0259838\t0.0116907700445181\n+FBgn0085673\t-0.013212713682036\n+FBgn0259850\t0.0116907700445181\n+FBgn0259851\tNA\n+FBgn0259852\tNA\n+FBgn0259861\tNA\n+FBgn0259857\tNA\n+FBgn0259858\tNA\n+FBgn0259859\tNA\n+FBgn0085523\tNA\n+FBgn0259863\t-0.0132510749453709\n+FBgn0259843\tNA\n+FBgn0259869\tNA\n+FBgn0267445\tNA\n+FBgn0267444\t0.0116524087811832\n+FBgn0259875\tNA\n+FBgn0259841\t-0.013212713682036\n+FBgn0259845\t0.0116907700445181\n+FBgn0259846\tNA\n+FBgn0259856\tNA\n+FBgn0259847\tNA\n+FBgn0259848\t0.0168790863725786\n+FBgn0267446\t-0.013212713682036\n+FBgn0085505\t0.0116907700445181\n+FBgn0046697\t0.0415629566141163\n+FBgn0058441\tNA\n+FBgn0267593\tNA\n+FBgn0267449\t0.0410940497301336\n+FBgn0267610\tNA\n+FBgn0259860\tNA\n+FBgn0259862\tNA\n+FBgn0259855\tNA\n+FBgn0265047\t0.171038551486606\n+FBgn0085831\t-0.0132510749453709\n+FBgn0085790\t-0.0241637759028751\n+FBgn0085791\tNA\n+FBgn0085788\tNA\n+FBgn0085644\tNA\n+FBgn0085520\t0.089778181402086\n+FBgn0267490\tNA\n+FBgn0267411\tNA\n+FBgn0267412\tNA\n+FBgn0267418\tNA\n+FBgn0267413\tNA\n+FBgn0267419\tNA\n+FBgn0267420\tNA\n+FBgn0267492\tNA\n+FBgn0267494\tNA\n+FBgn0267493\tNA\n+FBgn0267422\tNA\n+FBgn0267423\tNA\n+FBgn0267417\tNA\n+FBgn0267491\tNA\n+FBgn0267424\tNA\n+FBgn0262795\tNA\n+FBgn0267426\tNA\n+FBgn0267427\tNA\n+FBgn0046698\t0.0259048852758553\n+FBgn0046323\t0.0255014730403305\n+FBgn0267592\t0.0128022456752535\n+FBgn0267363\t0.0638650249330299\n+FBgn0052011\t0.0576847056232884\n+FBgn0052010\t-0.00374980952084868\n+FBgn0052009\t-0.0563903754108362\n+FBgn0266617\t0.110181739470077\n+FBgn0265633\t0.111087629072323\n+FBgn0263851\t0.0116907700445181\n+FBgn0052006\t-0.0883229511655807\n+FBgn0266725\t-0.0197644455667126\n+FBgn0267734\t0.0741122156818308\n+FBgn0264793\t-0.0107656898021209\n+FBgn0039900\t0.0151062405847882\n+FBgn0266618\tNA\n+FBgn0263385\t-0.0798848245086766\n+FBgn0264794\t0.0575738813004444\n+FBgn0266619\t0.1858337006464\n+FBgn0266726\t-0.0985039138908206\n+FBgn0262302\t-0.0176047448530155\n+FBgn0264820\t-0.0135058940445566\n+FBgn0266727\t-0.0997409181499728\n+FBgn0039939\t0.0171071999189566\n+FBgn0039937\t-0.19858691991772\n+FBgn0053797\tNA\n+FBgn0266616\t-0.0275753020346908\n+FBgn0263344\tNA\n+FBgn0266728\t-0.013212713682036\n+FBgn0083990\t0.0216889984381714\n+FBgn0264823\t0.00100140154930125\n+FBgn0039930\t0.113783920160028\n+FBgn0024913\t0.0797294610910849\n+FBgn0013696\tNA\n+FBgn0013703\tNA\n+FBgn0013700\tNA\n+FBgn0013680\tNA\n+FBgn0013709\tNA\n+FBgn0013690\tNA\n+FBgn0013710\tNA\n+FBgn0013674\tNA\n+FBgn0013699\tNA\n+FBgn0013675\tNA\n+FBgn0013697\tNA\n+FBgn0013691\tNA\n+FBgn0013673\tNA\n+FBgn0013672\tNA\n+FBgn0013676\tNA\n+FBgn0013694\tNA\n+FBgn0013681\tNA\n+FBgn0013689\tNA\n+FBgn0013704\tNA\n+FBgn0013701\tNA\n+FBgn0013705\tNA\n+FBgn0013692\tNA\n+FBgn0013693\tNA\n+FBgn0013684\tNA\n+FBgn0013695\tNA\n+FBgn0262952\tNA\n+FBgn0013683\tNA\n+FBgn0013707\tNA\n+FBgn0013702\tNA\n+FBgn0013685\tNA\n+FBgn0013678\tNA\n+FBgn0013706\tNA\n+FBgn0013679\tNA\n+FBgn0013698\tNA\n+FBgn0013686\tNA\n+FBgn0013708\tNA\n+FBgn0013688\tNA\n+FBgn0261386\tNA\n+FBgn0040038\tNA\n+FBgn0267508\tNA\n+FBgn0267509\tNA\n+FBgn0267510\tNA\n+FBgn0085753\tNA\n+FBgn0267511\tNA\n+FBgn0267505\tNA\n+FBgn0085802\tNA\n+FBgn0267512\tNA\n+FBgn0267496\tNA\n+FBgn0267497\tNA\n+FBgn0267506\tNA\n+FBgn0267498\tNA\n+FBgn0267499\tNA\n+FBgn0267500\tNA\n+FBgn0267507\tNA\n+FBgn0267501\tNA\n+FBgn0267502\tNA\n+FBgn0267503\tNA\n+FBgn0267504\tNA\n+FBgn0085692\tNA\n+FBgn0085828\tNA\n+FBgn0085816\tNA\n+FBgn0085817\tNA\n+FBgn0267594\tNA\n+FBgn0259837\tNA\n+FBgn0085777\tNA\n+FBgn0259839\tNA\n+FBgn0259840\tNA\n+FBgn0267596\tNA\n+FBgn0259842\tNA\n+FBgn0259817\tNA\n+FBgn0085805\tNA\n+FBgn0259849\tNA\n+FBgn0085807\tNA\n+FBgn0085755\tNA\n+FBgn0085808\tNA\n+FBgn0085744\tNA\n+FBgn0085760\tNA\n+FBgn0085494\tNA\n+FBgn0085540\tNA\n+FBgn0085746\tNA\n+FBgn0085751\tNA\n+FBgn0085773\tNA\n+FBgn0267595\tNA\n+FBgn0259864\tNA\n+FBgn0085752\tNA\n+FBgn0085795\tNA\n+FBgn0085827\tNA\n+FBgn0085822\tNA\n+FBgn0085803\tNA\n+FBgn0085506\tNA\n+FBgn0085768\tNA\n+FBgn0085757\tNA\n+FBgn0085758\tNA\n+FBgn0085764\tNA\n+FBgn0259870\tNA\n+FBgn0085761\tNA\n+FBgn0085748\tNA\n+FBgn0085756\tNA\n+FBgn0085799\tNA\n+FBgn0085759\tNA\n+FBgn0085826\tNA\n+FBgn0085737\tNA\n+FBgn0085511\tNA\n+FBgn0085766\tNA\n+FBgn0085772\tNA\n+FBgn0085825\tNA\n' |
| b |
| diff -r 000000000000 -r bd99e8fbde97 test-data/pathways.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pathways.tabular Mon Aug 26 14:42:52 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +00010 +00480 |
