# HG changeset patch
# User iuc
# Date 1566844972 14400
# Node ID bd99e8fbde97c08eb9325285d97ac48a769985c7

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"

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)
+  }
+}
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
@@ -0,0 +1,405 @@
+<tool id="pathview" name="Pathview" version="@VERSION@+@GALAXY_VERSION@">
+    <description>for pathway based data integration and visualization</description>
+    <macros>
+        <token name="@VERSION@">1.24.0</token>
+        <token name="@GALAXY_VERSION@">galaxy0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@VERSION@">bioconductor-pathview</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.ag.eg.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.at.tair.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.bt.eg.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.ce.eg.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.cf.eg.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.dm.eg.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.dr.eg.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.eck12.eg.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.ecsakai.eg.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.gg.eg.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.hs.eg.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.mm.eg.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.mmu.eg.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.pf.plasmo.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.pt.eg.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.rn.eg.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.sc.sgd.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.ss.eg.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.xl.eg.db</requirement>
+        <requirement type="package" version="1.6.2">r-optparse</requirement>
+    </requirements>
+    <version_command><![CDATA[
+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" $(R --vanilla --slave -e "library(ggplot2); cat(sessionInfo()\$otherPkgs\$ggplot2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
+    ]]></version_command>
+    <command detect_errors="exit_code"><![CDATA[
+Rscript '$__tool_directory__/pathview.r'
+
+#if str($pathway.nb) == 'one'
+    --pathway_id '$pathway.one_id'
+#else
+    --pathway_id_fp '$pathway.tabular'
+    --pathway_id_header $pathway.header
+#end if
+
+    --species '$species'
+
+#if str($gene_data.gd) == 'true'
+    --gene_data '$gene_data.tabular'
+    --gd_header $gene_data.header
+    --gene_idtype '$gene_data.idtype'
+#end if
+
+#if str($cpd_data.cpd) == 'true'
+    --cpd_data '$cpd_data.tabular'
+    --cpd_header $cpd_data.header
+    --cpd_idtype '$cpd_data.idtype'
+#end if
+
+    --multi_state $multi_state
+    --match_data $match_data
+
+    --kegg_native $out.kegg_native.out
+    --same_layer $out.kegg_native.same_layer
+#if str($out.kegg_native.out) == 'TRUE'
+    --map_null $out.kegg_native.map_null
+#else
+    --split_group $out.kegg_native.split_group
+    --expand_node $out.kegg_native.expand_node
+    --sign_pos $out.kegg_native.sign_pos
+#end if
+
+&& 
+ls .
+    ]]></command>
+    <inputs>
+        <conditional name="pathway">
+            <param name="nb" type="select" label="Number of pathways to plot">
+                <option value="one" selected="true">One</option>
+                <option value="multiple">Multiple</option>
+            </param>
+            <when value="one">
+                <param name="one_id" type="text" label="KEGG pathway" help="KEGG pathway ID with 5 digits and without the 3 letter KEGG species code.">
+                    <validator type="regex" message="It should be the 5 digits of the KEGG pathway ID.">^(?:\d\d\d\d\d)?$</validator>
+                </param>
+            </when>
+            <when value="multiple">
+                <param name="tabular" type="data" format="tabular" optional="true" label="KEGG pathways" help="A table with one-column with KEGG pathways to plot"/>
+                <param name="header" type="boolean" checked="true" label="Does the file have header (a first line with column names)?"/>
+            </when>
+        </conditional>
+        <param name="species" type="select" label="Species to use">
+            <option value="aga">Anopheles</option>
+            <option value="ath">Arabidopsis</option>
+            <option value="bta">Bovine</option>
+            <option value="cel">Worm</option>
+            <option value="cfa">Canine</option>
+            <option value="dme">Fly</option>
+            <option value="dre">Zebrafish</option>
+            <option value="eco">E coli strain K12</option>
+            <option value="ecs">E coli strain Sakai</option>
+            <option value="gga">Chicken</option>
+            <option value="hsa" selected="true">Human</option>
+            <option value="mmu">Mouse</option>
+            <option value="mcc">Rhesus</option>
+            <option value="pfa">Malaria</option>
+            <option value="ptr">Chimp</option>
+            <option value="rno">Rat</option>
+            <option value="sce">Yeast</option>
+            <option value="ssc">Pig</option>
+            <option value="xla">Xenopus</option>
+        </param>
+        <conditional name="gene_data">
+            <param name="gd" type="select" label="Provide a gene data file?" help="Gene data is a broad concept including genes, transcripts, protein, enzymes and their expression, modifications and any measurable attributes.">
+                <option value="true">Yes</option>
+                <option value="false">No</option>
+            </param>
+            <when value="true">
+                <param name="tabular" type="data" format="tabular" label="Gene data" help="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."/>
+                <param name="header" type="boolean" checked="true" label="Does the file have header (a first line with sample names)?"/>
+                <param name="idtype" type="select" label="Format for gene data">
+                    <option value="entrez" selected="true">Entrez Gene ID</option>
+                    <option value="symbol">Gene Symbol</option>
+                    <option value="genename">Gene Name</option>
+                    <option value="ensembl">Ensembl Gene ID</option>
+                    <option value="ensemblprot">Ensembl Protein ID</option>
+                    <option value="ensembltrans">Ensembl Trans ID</option>
+                    <option value="unigene">UniGene</option>
+                    <option value="uniprot">UniProt</option>
+                    <option value="refseq">RefSeq</option>
+                    <option value="enzyme">Enzyme</option>
+                    <option value="tair">TAIR</option>
+                    <option value="prosite">Prosite</option>
+                    <option value="orf">ORF</option>
+                </param>
+            </when>
+            <when value="false"/>
+        </conditional>
+        <conditional name="cpd_data">
+            <param name="cpd" type="select" label="Provide a compound data file?" help="compound data is a broad concept including metabolites, drugs, their  measurements and attributes.">
+                <option value="true">Yes</option>
+                <option value="false" selected="true">No</option>
+            </param>
+            <when value="true">
+                <param name="tabular" type="data" format="tabular" label="Compound data" help="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."/>
+                <param name="header" type="boolean" checked="true" label="Does the file have header (a first line with sample names)?"/>
+                <param name="idtype" type="select" label="Format for compound data">
+                    <option value="kegg" selected="true">KEGG (include compound, glycan and drug accessions)</option>
+                </param>
+            </when>
+            <when value="false"/>
+        </conditional>
+        <param name="multi_state" type="boolean" checked="true" label="Should multiple states of gene or compond data be intergrated and plotted in the same graph?" help="Gene or compound nodes will be sliced into multiple pieces corresponding to the number of states in the data" />
+        <param name="match_data" type="boolean" checked="true" label="Are the gene and compound data paired?" help="When let sample sizes of gene and compound be m and n, when m>n, extra columns of NA's (mapped to no color) will be added to make the sample size the same" />
+        <section name="out" title="Output Options" expanded="true">
+            <conditional name="kegg_native">
+                <param name="out" type="select" label="Output for pathway">
+                    <option value="TRUE" selected="true">KEGG native</option>
+                    <option value="FALSE">Graphviz</option>
+                </param>
+                <when value="TRUE">
+                    <param name="same_layer" type="boolean" checked="true" label="Plot on same layer?" help="If yes, node colors will be plotted in the same layer as the pathway graph." />
+                    <param name="map_null" type="boolean" checked="true" label="Map the NULL gene or compound data to pathway?" help="When NULL data are mapped, the gene or compound nodes in the pathway will berendered as actually mapped nodes, except with NA-valued color. When NULL data are not mapped, the nodes are rendered as unmapped nodes." />
+                </when>
+                <when value="FALSE">
+                    <param name="same_layer" type="boolean" checked="true" label="Plot on same layer?" help="If yes, edge/node type legend will be plotted in the same page." />
+                    <param name="split_group" type="boolean" checked="false" label="Split node groups into individual nodes?" help="Each split member nodes inherits all edges from the node group. This option also effects most metabolic pathways even without group nodes defined orginally. For these pathways, genes involved in the same reaction are grouped automatically when converting reactions to edges unless split.group is true." />
+                    <param name="expand_node" type="boolean" checked="false" label="Expand multiple-gene nodes into single-gene nodes?" help="Each expanded single-gene nodes inherits all edges from the original multiple-gene node. This option is not effective for most metabolic pathways where it conflits with converting reactions to edges." />
+                    <param name="sign_pos" type="select" label="Position of pathview signature">
+                        <option value="bottomright" selected="true">Bottom right</option>
+                        <option value="bottomleft">Bottom left</option>
+                        <option value="topleft">Top left</option>
+                        <option value="topright">Top right</option>
+                    </param>
+                </when>
+            </conditional>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="one_kegg_native" format="png" from_work_dir="*.pathview.png" label="${tool.name} on ${on_string}: KEGG Pathway (${species}${pathway.one_id})">
+            <filter>pathway['nb'] == 'one'</filter>
+            <filter>out['kegg_native']['out'] == 'TRUE'</filter>
+        </data>
+        <data name="one_graphviz" format="pdf" from_work_dir="*.pathview.pdf" label="${tool.name} on ${on_string}: KEGG Pathway (${species}${pathway.one_id}), Graphviz format">
+            <filter>pathway['nb'] == 'one'</filter>
+            <filter>out['kegg_native']['out'] == 'FALSE'</filter>
+        </data>
+        <collection name="multiple_kegg_native" type="list" label="${tool.name} on ${on_string}: KEGG Pathways">
+            <filter>pathway['nb'] == 'multiple'</filter>
+            <filter>out['kegg_native']['out'] == 'TRUE'</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.pathview\.png" directory="." ext="png"/>
+        </collection>
+        <collection name="multiple_graphviz" type="list" label="${tool.name} on ${on_string}: KEGG Pathways, Graphviz format">
+            <filter>pathway['nb'] == 'multiple'</filter>
+            <filter>out['kegg_native']['out'] == 'FALSE'</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.pathview\.pdf" directory="." ext="pdf"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <conditional name="pathway">
+                <param name="nb" value="one" />
+                <param name="one_id" value="00010"/>
+            </conditional>
+            <param name="species" value="dme"/>
+            <conditional name="gene_data">
+                <param name="gd" value="true"/>
+                <param name="tabular" value="gene_data.tabular"/>
+                <param name="header" value="false"/>
+                <param name="idtype" value="ensembl"/>
+            </conditional>
+            <conditional name="cpd_data">
+                <param name="cpd" value="false"/>
+            </conditional>
+            <param name="multi_state" value="true" />
+            <param name="match_data" value="true"/>
+            <section name="out">
+                <conditional name="kegg_native">
+                    <param name="out" value="TRUE" />
+                    <param name="same_layer" value="true"/>
+                    <param name="map_null" value="true"/>
+                </conditional>
+            </section>
+            <output name="one_kegg_native" ftype="png" file="dme00010.png" compare="sim_size" delta="30000"/>
+        </test>
+        <test>
+            <conditional name="pathway">
+                <param name="nb" value="one" />
+                <param name="one_id" value="00010"/>
+            </conditional>
+            <param name="species" value="dme"/>
+            <conditional name="gene_data">
+                <param name="gd" value="true"/>
+                <param name="tabular" value="gene_data.tabular"/>
+                <param name="header" value="false"/>
+                <param name="idtype" value="ensembl"/>
+            </conditional>
+            <conditional name="cpd_data">
+                <param name="cpd" value="false"/>
+            </conditional>
+            <param name="multi_state" value="true" />
+            <param name="match_data" value="true"/>
+            <section name="out">
+                <conditional name="kegg_native">
+                    <param name="out" value="FALSE" />
+                    <param name="same_layer" value="true"/>
+                    <param name="split_group" value="false" />
+                    <param name="expand_node" value="false"/>
+                    <param name="sign_pos" value="bottomright"/>
+                </conditional>
+            </section>
+            <output name="one_graphviz" ftype="pdf" file="dme00010.pdf" compare="sim_size"/>
+        </test>
+        <test>
+            <conditional name="pathway">
+                <param name="nb" value="multiple" />
+                <param name="tabular" value="pathways.tabular"/>
+                <param name="header" value="false"/>
+            </conditional>
+            <param name="species" value="dme"/>
+            <conditional name="gene_data">
+                <param name="gd" value="true"/>
+                <param name="tabular" value="gene_data.tabular"/>
+                <param name="header" value="false"/>
+                <param name="idtype" value="ensembl"/>
+            </conditional>
+            <conditional name="cpd_data">
+                <param name="cpd" value="false"/>
+            </conditional>
+            <param name="multi_state" value="true" />
+            <param name="match_data" value="true"/>
+            <section name="out">
+                <conditional name="kegg_native">
+                    <param name="out" value="TRUE" />
+                    <param name="same_layer" value="true"/>
+                    <param name="map_null" value="true"/>
+                </conditional>
+            </section>
+            <output_collection name="multiple_kegg_native" count="2">
+                <element name="dme00010" ftype="png" file="dme00010.png" compare="sim_size" delta="30000"/>
+                <element name="dme00480" ftype="png" file="dme00480.png" compare="sim_size" delta="40000"/>
+            </output_collection>
+        </test>
+        <test>
+            <conditional name="pathway">
+                <param name="nb" value="multiple" />
+                <param name="tabular" value="pathways.tabular"/>
+                <param name="header" value="false"/>
+            </conditional>
+            <param name="species" value="dme"/>
+            <conditional name="gene_data">
+                <param name="gd" value="true"/>
+                <param name="tabular" value="gene_data.tabular"/>
+                <param name="header" value="false"/>
+                <param name="idtype" value="ensembl"/>
+            </conditional>
+            <conditional name="cpd_data">
+                <param name="cpd" value="false"/>
+                <param name="tabular" value="cpd_data.tabular"/>
+                <param name="header" value="false"/>
+                <param name="idtype" value="kegg"/>
+            </conditional>
+            <param name="multi_state" value="true" />
+            <param name="match_data" value="true"/>
+            <section name="out">
+                <conditional name="kegg_native">
+                    <param name="out" value="FALSE" />
+                    <param name="same_layer" value="false"/>
+                    <param name="split_group" value="false" />
+                    <param name="expand_node" value="false"/>
+                    <param name="sign_pos" value="bottomright"/>
+                </conditional>
+            </section>
+            <output_collection name="multiple_graphviz" count="2">
+                <element name="dme00010" ftype="pdf" file="dme00010_cpd.pdf" compare="sim_size"/>
+                <element name="dme00480" ftype="pdf" file="dme00480_cpd.pdf" compare="sim_size"/>
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What it does**
+
+Pathview is a stand-alone software package for pathway based data integration and visualization. 
+
+This package can be divided into four functional modules: the Downloader, Parser, Mapper andViewer.  
+Mostly importantly, pathview maps and renders user data on relevant pathway graphs. 
+
+Notice that KEGG requires subscription for FTP access since May 2011. 
+However,Pathview downloads individual pathway graphs and data files through API or HTTP access, which is freely available (for academic and non-commerical uses).
+Pathview uses KEGGgraph (Zhang and Wiemann, 2009) when parsing KEGG xml data files. 
+
+
+Options map closely to the excellent pathview manual_.
+
+-----
+
+**Inputs**
+
+Pathview provides strong support for data integration. It works with:
+
+- essentially all types of biological data mappable to pathways (gene expression, protein expression, genetic association, metabolite, genomic data, literature, etc)
+- over 10 types of gene or protein IDs, and 20 types of compound or metabolite IDs
+- pathways for about 4800 species as well as KEGG orthology
+- various data attributes and formats, i.e.  continuous/discrete data, matrices/vectors, single/multiple samples etc.
+
+Pathview can be directly used for metagenomic, microbiome or unknown species data when the data are mapped to KEGG ortholog pathways.
+
+*Pathway ids* 
+
+Either just the name or a table with one column with the different pathway ids to represent.
+
+
+*Gene data*
+
+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.  
+
+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.
+The first line can include the sample names.
+
+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.
+
+Example:
+
+    =========== =================
+    FBgn0039155	-4.14844993705661
+    FBgn0003360	-2.99977727873544
+    FBgn0026562	-2.38016404989418
+    FBgn0025111	2.69993883050214
+    FBgn0029167	-2.10506155636758
+    =========== =================
+
+*Compound data*
+
+We also frequently want to look at metabolic pathways too. Besides gene nodes, these pathways also have compound nodes. 
+Therefore, we may integrate or visualize both gene data and compound data with metabolic pathways.
+
+Here compound data is a broad concept including metabolites, drugs, their  measurements and attributes.  
+
+The format is similar to the gene data table, except named with IDs mappable to KEGG compound IDs.
+Over 20 types of IDs included in CHEMBL database can be used here.
+
+-----
+
+**Outputs**
+
+Pathview generates both native KEGG view and Graphviz view for pathways. 
+
+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.
+
+.. image:: $PATH_TO_IMAGES/dme00010_native.png
+   :width: 60 %
+
+Graphviz view provides better control of node and edge attributes, better view of pathway topology, better understanding of the pathway analysis statistics.
+
+.. image:: $PATH_TO_IMAGES/dme00010_graphviz.png
+   :width: 60 %
+
+.. _manual: https://bioconductor.org/packages/release/bioc/vignettes/pathview/inst/doc/pathview.pdf
+.. _KEGG: http://www.genome.jp/kegg
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btt285</citation>
+    </citations>
+</tool>
\ No newline at end of file
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diff -r 000000000000 -r bd99e8fbde97 static/images/dme00010_native.png
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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
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_data.tabular	Mon Aug 26 14:42:52 2019 -0400
@@ -0,0 +1,17559 @@
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+FBgn0038914	-0.02465850654921
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+FBgn0038919	0.00977083897200336
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+FBgn0038927	NA
+FBgn0266538	NA
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+FBgn0038938	-0.0374159462426192
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+FBgn0038941	-0.0239020821772528
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+FBgn0038945	-0.0192473431473063
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+FBgn0038958	0.0681411700521357
+FBgn0051165	NA
+FBgn0051162	NA
+FBgn0051167	NA
+FBgn0051166	NA
+FBgn0038959	0.0259048852758553
+FBgn0038960	-0.0110641509355519
+FBgn0038967	-0.190490423825771
+FBgn0263554	NA
+FBgn0038978	0.0175436511702277
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+FBgn0039008	0.0936315286326921
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+FBgn0267208	NA
+FBgn0039015	-0.000740779082636834
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+FBgn0262538	-0.207945722926072
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+FBgn0263664	0.0116907700445181
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+FBgn0265157	0.0116907700445181
+FBgn0039041	0.0116907700445181
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+FBgn0039045	NA
+FBgn0039048	0.18098462513967
+FBgn0039050	0.0370255374945172
+FBgn0039049	0.0170599720226749
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+FBgn0265381	-0.0925334349074965
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+FBgn0262010	NA
+FBgn0051515	NA
+FBgn0263217	NA
+FBgn0265382	-0.0104715474396846
+FBgn0039077	0.00103976281263618
+FBgn0259193	0.00100140154930125
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+FBgn0085318	NA
+FBgn0039081	0.00264552225403609
+FBgn0039083	-0.0239020821772528
+FBgn0039084	0.10700171317814
+FBgn0039085	0.00620838793792284
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+FBgn0051143	0.0116524087811832
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+FBgn0039104	-0.0347991677813404
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+FBgn0047351	-0.0115548488015654
+FBgn0051148	0.0166280616277821
+FBgn0051413	0.0166940180059705
+FBgn0051414	0.0258312740263523
+FBgn0264844	NA
+FBgn0039106	0.0953149432890024
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+FBgn0267760	-0.133002045134226
+FBgn0262974	0.0347770582413837
+FBgn0004187	-0.00165497598594472
+FBgn0004186	NA
+FBgn0004185	NA
+FBgn0039124	0.305971728439728
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+FBgn0264741	NA
+FBgn0264740	0.00103976281263618
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+FBgn0267761	0.0682013578560441
+FBgn0264906	NA
+FBgn0039147	-0.0553045538598915
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+FBgn0039151	0.103392171798511
+FBgn0039154	-0.166033213142093
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+FBgn0002863	NA
+FBgn0264901	-0.0773911390618347
+FBgn0261452	NA
+FBgn0051130	-0.0360044129953397
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+FBgn0267222	-0.061236396159064
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+FBgn0053339	0.212784978514067
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+FBgn0086610	NA
+FBgn0039197	0.0046453075757512
+FBgn0039198	0.00100140154930127
+FBgn0039199	0.0272256363281572
+FBgn0039200	NA
+FBgn0000036	0.0301300793249436
+FBgn0267612	NA
+FBgn0263409	NA
+FBgn0267209	0.0414203162619417
+FBgn0051128	-0.0239020821772528
+FBgn0000039	0.0824837173088787
+FBgn0262389	NA
+FBgn0264791	NA
+FBgn0039202	0.00997262703764162
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+FBgn0011845	0.0166940180059705
+FBgn0004188	-0.0239404434405877
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+FBgn0267763	-0.151601258774789
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+FBgn0262858	0.0319971368003285
+FBgn0262431	NA
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+FBgn0003719	0.0588669239016608
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+FBgn0039224	-0.0360044129953397
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+FBgn0266743	-0.0238637209139179
+FBgn0053658	-0.013212713682036
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+FBgn0004897	0.0465732801304427
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+FBgn0054027	0.0731465635042654
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+FBgn0260229	NA
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+FBgn0039283	0.0311384252298648
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+FBgn0039298	0.00103976281263618
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+FBgn0266741	-0.0343147497277118
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+FBgn0039312	-0.0282445790869461
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+FBgn0039341	NA
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+FBgn0039346	-0.127166150296052
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+FBgn0267577	NA
+FBgn0262388	NA
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+FBgn0039371	NA
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+FBgn0263622	NA
+FBgn0263623	-0.013212713682036
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+FBgn0250831	0.0116907700445181
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+FBgn0263453	0.00660707788742401
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+FBgn0082923	0.0234974310374596
+FBgn0039565	NA
+FBgn0259990	NA
+FBgn0051253	NA
+FBgn0051054	0.010624404787608
+FBgn0267108	NA
+FBgn0051131	NA
+FBgn0039568	-0.0260546553889348
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+FBgn0267749	NA
+FBgn0266401	0.0116524087811832
+FBgn0002865	-0.0371826061592737
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+FBgn0039576	0.00103976281263618
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+FBgn0267773	0.0450191576222557
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+FBgn0039582	0.109623920201262
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+FBgn0263579	-0.013212713682036
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+FBgn0039625	NA
+FBgn0039628	-0.0384155063708854
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+FBgn0039645	-0.0520276782380036
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+FBgn0262448	NA
+FBgn0262404	NA
+FBgn0039656	-0.209506150438705
+FBgn0051427	-0.139576535978552
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+FBgn0267107	0.187214576775736
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+FBgn0040623	NA
+FBgn0039666	0.0626294668825027
+FBgn0039669	0.0165556269155051
+FBgn0263588	-0.0132510749453709
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+FBgn0039683	-0.109602510082851
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+FBgn0039685	0.118710411806916
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+FBgn0039723	-0.0617545205695294
+FBgn0051202	0.0183414304150306
+FBgn0260759	NA
+FBgn0260760	NA
+FBgn0004622	0.101977745072263
+FBgn0039728	-0.24672868034839
+FBgn0085327	0.0200884654517208
+FBgn0039739	0.0116907700445181
+FBgn0267780	0.0190926555348738
+FBgn0264837	NA
+FBgn0041102	0.0344041030623057
+FBgn0001281	-0.0308060990452605
+FBgn0003510	-0.013212713682036
+FBgn0003511	NA
+FBgn0264838	-0.0569977864957178
+FBgn0039744	0.103475484724818
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+FBgn0267781	-0.126572203549967
+FBgn0266442	-0.0163581534031206
+FBgn0266443	0.0941883438575417
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+FBgn0263402	0.115313687061957
+FBgn0039758	-0.0126320894472401
+FBgn0051383	NA
+FBgn0051023	NA
+FBgn0085328	-0.0444219253731768
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+FBgn0267783	0.288564753971982
+FBgn0267130	0.0414203162619417
+FBgn0027544	NA
+FBgn0261704	NA
+FBgn0039768	-0.0513201449661608
+FBgn0039769	0.00952509822164646
+FBgn0039770	-0.0124465689520283
+FBgn0039771	-0.0227136623572088
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+FBgn0051371	-0.064511008916901
+FBgn0051014	-0.007733219917331
+FBgn0039782	-0.00257380867137143
+FBgn0263527	NA
+FBgn0054041	0.0591284298604563
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+FBgn0051524	0.0417037837151231
+FBgn0039784	0.16468579767345
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+FBgn0051017	0.0271596180674347
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+FBgn0266259	NA
+FBgn0264985	0.0259048852758553
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+FBgn0051013	0.0368147450517201
+FBgn0051015	-0.0275753020346908
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+FBgn0039796	0.0352042867026678
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+FBgn0267654	-0.0104715474396846
+FBgn0267784	NA
+FBgn0051010	-0.0343147497277118
+FBgn0262883	7.25765988310375e-06
+FBgn0262444	0.0116524087811832
+FBgn0003720	0.0170989679487544
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+FBgn0267786	-0.013212713682036
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+FBgn0039816	0.080203231628958
+FBgn0039817	0.0437479894478369
+FBgn0039818	0.213619476271765
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+FBgn0263412	0.0197371086043364
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+FBgn0004389	0.0598415560445086
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+FBgn0039832	0.15077621349394
+FBgn0039838	-0.0317890942807231
+FBgn0040628	0.0659145857505564
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+FBgn0035103	0.27489371983196
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+FBgn0083992	-0.00806630212479075
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+FBgn0266927	0.0219591499824967
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+FBgn0267664	0.062549111911956
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+FBgn0052482	-0.0551812833709636
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+FBgn0086062	-0.0059488126142821
+FBgn0086063	-0.013212713682036
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+FBgn0004429	-0.00799050515028647
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+FBgn0052318	0.00100140154930126
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+FBgn0003295	-0.0903311994521602
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+FBgn0052328	NA
+FBgn0052329	NA
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+FBgn0052324	NA
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+FBgn0011854	NA
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+FBgn0250911	NA
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+FBgn0052288	NA
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+FBgn0266436	-0.0270372935632874
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+FBgn0086068	-0.0435761742858795
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+FBgn0035431	0.160406949346886
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+FBgn0265721	-0.00165027872122254
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+FBgn0054047	-0.0084183607797989
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+FBgn0267306	-0.013212713682036
+FBgn0011986	NA
+FBgn0052420	NA
+FBgn0052421	NA
+FBgn0265708	-0.013212713682036
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+FBgn0267307	-0.0084183607797989
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+FBgn0085371	-0.0815713957048884
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+FBgn0065097	NA
+FBgn0003486	0.0128800515721138
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+FBgn0052404	-0.0680082009011717
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+FBgn0086900	NA
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+FBgn0085267	NA
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+FBgn0003378	0.0764987306865879
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+FBgn0262437	NA
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+FBgn0267545	-0.013212713682036
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+FBgn0036221	0.0144199024639676
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+FBgn0264488	-0.0665980867084628
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+FBgn0267550	NA
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+FBgn0036606	0.00100140154930127
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+FBgn0036607	0.0046453075757512
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+FBgn0040795	0.0209615164725702
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+FBgn0036612	0.0267594037349494
+FBgn0267553	NA
+FBgn0053257	0.128092708175545
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+FBgn0036617	0.0275429169209358
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+FBgn0267697	-0.0378450803539929
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+FBgn0036715	0.0425670212417659
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+FBgn0266675	NA
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+FBgn0265759	0.0116907700445181
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+FBgn0052189	NA
+FBgn0266685	-0.00413459690897029
+FBgn0054002	0.0542797970009038
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+FBgn0260721	NA
+FBgn0036767	-0.0132510749453709
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+FBgn0267794	0.057841703303948
+FBgn0266942	-0.0482928994220537
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+FBgn0267598	-0.0238637209139179
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+FBgn0262998	-0.013212713682036
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+FBgn0015946	NA
+FBgn0267637	NA
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+FBgn0036786	0.0674846902976554
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+FBgn0265881	NA
+FBgn0265882	-0.013212713682036
+FBgn0036787	0.00100140154930125
+FBgn0028415	NA
+FBgn0028416	NA
+FBgn0265883	NA
+FBgn0265884	NA
+FBgn0036789	-0.0104715474396846
+FBgn0052198	NA
+FBgn0036790	0.040163306387823
+FBgn0266984	NA
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+FBgn0266938	NA
+FBgn0266939	-0.013212713682036
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+FBgn0265268	0.0241590774796037
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+FBgn0085283	0.0257114584676606
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+FBgn0264717	0.0178794074626748
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+FBgn0267601	-0.226969635192074
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+FBgn0036822	0.421487741327471
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+FBgn0267296	0.248138917349512
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+FBgn0037162	0.0046453075757512
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+FBgn0263034	0.0116907700445181
+FBgn0266978	NA
+FBgn0262182	NA
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+FBgn0264980	0.0116524087811832
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+FBgn0011888	NA
+FBgn0011887	NA
+FBgn0011880	NA
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+FBgn0011955	NA
+FBgn0040502	-0.0157087656977755
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+FBgn0053664	NA
+FBgn0053669	NA
+FBgn0053668	NA
+FBgn0053667	NA
+FBgn0053666	NA
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+FBgn0065071	-0.0362799938261874
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+FBgn0011950	NA
+FBgn0011951	NA
+FBgn0011980	NA
+FBgn0011982	NA
+FBgn0053247	NA
+FBgn0053246	NA
+FBgn0053245	NA
+FBgn0053244	NA
+FBgn0053243	NA
+FBgn0053242	NA
+FBgn0053241	NA
+FBgn0053240	NA
+FBgn0053239	NA
+FBgn0053238	NA
+FBgn0053237	NA
+FBgn0053236	NA
+FBgn0011974	NA
+FBgn0011977	NA
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+FBgn0031289	0.00548665747964909
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+FBgn0266887	0.049961041057507
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+FBgn0031367	NA
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+FBgn0031423	0.0377818545513836
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+FBgn0031432	0.0910136260581415
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+FBgn0263330	0.0144199024639676
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+FBgn0263583	0.0116524087811832
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+FBgn0013696	NA
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+FBgn0267499	NA
+FBgn0267500	NA
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+FBgn0267502	NA
+FBgn0267503	NA
+FBgn0267504	NA
+FBgn0085692	NA
+FBgn0085828	NA
+FBgn0085816	NA
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+FBgn0259837	NA
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+FBgn0267596	NA
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+FBgn0259817	NA
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+FBgn0085808	NA
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+FBgn0085760	NA
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+FBgn0085746	NA
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+FBgn0085773	NA
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+FBgn0085752	NA
+FBgn0085795	NA
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+FBgn0085822	NA
+FBgn0085803	NA
+FBgn0085506	NA
+FBgn0085768	NA
+FBgn0085757	NA
+FBgn0085758	NA
+FBgn0085764	NA
+FBgn0259870	NA
+FBgn0085761	NA
+FBgn0085748	NA
+FBgn0085756	NA
+FBgn0085799	NA
+FBgn0085759	NA
+FBgn0085826	NA
+FBgn0085737	NA
+FBgn0085511	NA
+FBgn0085766	NA
+FBgn0085772	NA
+FBgn0085825	NA
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
@@ -0,0 +1,2 @@
+00010
+00480