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coVennTree/._.DS_Store coVennTree/coVennTree.pl coVennTree/coVennTree.xml coVennTree/static/._.DS_Store coVennTree/static/images/._example1.png coVennTree/static/images/._venn-graph-off.png coVennTree/static/images/._venn-graph-on.png coVennTree/static/images/example1.png coVennTree/static/images/venn-graph-off.png coVennTree/static/images/venn-graph-on.png coVennTree/tool_dependencies.xml |
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| diff -r 000000000000 -r 745aede829e9 coVennTree/coVennTree.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/coVennTree/coVennTree.pl Fri Jan 30 09:55:45 2015 -0500 |
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| b'@@ -0,0 +1,833 @@\n+#!/usr/bin/perl\n+use strict;\n+use File::Basename;\n+use List::MoreUtils qw( minmax );\n+\n+# --------------------------------------------------------------------------------------------------\n+# author:\tsteffen lott\n+# mail: \tsteffen.lott@uni-freiburg.de\n+# date: \t06-10-2014\n+# version: \t1.6\n+# \n+# description:\n+# \tThe tool converts an output from MEGAN in a special network which can visuallized with\n+#\tcytoscape. Gaper produces two files, the first one contains the network and the second one\n+#\tdescribes the attributes of the network. \n+# --------------------------------------------------------------------------------------------------\n+\n+# return version number\n+if (@ARGV == 0) {\n+\tprint "CoVennTree-Version 1.6\\n";\n+\tprint "COMMAND\\n";\n+\tprint "coventree argv0 argv1 argv2 argv3 argv4\\n";\n+\tprint "--------------\\n";\n+\tprint "argv0 = input file\\n";\n+\tprint "argv1 = color mode [1,4]\\n";\n+\tprint "argv2 = transformation function [1,7]\\n";\n+\tprint "argv3 = only leaf information => 0 ; all information => 1\\n";\n+\tprint "argv4 = output file name network\\n";\n+\tprint "argv5 = output file name attributes\\n";\n+\texit;\n+}\n+\n+\n+\n+\n+# container to represent the network\n+my @network = ();\n+\n+\n+\n+# 0 PARAMETER_______________\n+# read argument from command-line\n+# important: DSV -> taxon-path, count(s) -> assigned -> tab\n+my $megan_file = $ARGV[0];\n+\n+\n+# 1 PARAMETER_______________\n+my $colorMode; \n+# color mode for venn-diagrams 0,1,2,3,4\n+if(defined $ARGV[1]){\n+\t$colorMode = $ARGV[1];\n+}else{\n+\t$colorMode = 3;\n+}\n+\n+\n+# 2 PARAMETER_______________\n+# 2 different transformations functions\n+my $transFnc = "";\n+if(defined $ARGV[2]){ # small datasets\n+ \t$transFnc = $ARGV[2];\n+}else{\n+\t$transFnc = 1;\n+}\n+\n+\n+# 3 PARAMETER_______________\n+# the user can switch between "only leaf information" \n+# or the complete tree information. the last one takes also the not assigned reads\n+# and creates artificial nodes to keep this number\n+my $onlyLeafs;\n+if(defined $ARGV[3]){\n+\tif($ARGV[3] == 0){\n+\t\t$onlyLeafs = "on";\n+\t}elsif($ARGV[3] == 1){\n+\t\t$onlyLeafs = "off";\n+\t}\n+}else{ # all information will be used! not assigned and assigned\n+\t$onlyLeafs = "off";\n+}\n+\n+# 4 PARAMETER_______________\n+# output -> network\n+my $out_network = $ARGV[4];\n+\n+# 5 PARAMETER_______________\n+# output -> attributes\n+my $out_attributes = $ARGV[5];\n+\n+\n+\n+# check the input format of the file. only a file with exactly three datasets are excepted. the other one will fill up with zeros\n+\n+\n+# read-in MEGAN-file\n+# if #{data-sets} = 1 -> no heade line\n+# if #{data-sets} > 1 -> heade line " #Datasets\t\tset1\tset2\t..."\n+open(inFile , "<$megan_file") || die "File not found - \\"Path-File\\"!\\n";\n+my @pairIds = ();\n+my $header = "";\n+my @input_file = ();\n+my @numberOfSets = ();\n+\n+while(<inFile>){\n+\tchomp($_);\n+ \tif($_ =~ /^#/){\n+ \t\t$header = $_;\n+ \t\t@numberOfSets = split("\\t", $_);\n+ \t}else{\n+ \t\t#print @numberOfSets . "\\n";\n+ \t\t# check the number of datasets are included\n+ \t\tif(@numberOfSets == 0 || @numberOfSets == 1 || @numberOfSets > 4){\t\t\t# no set is in the file\n+ \t\t\tprint "Error: File doesn\'t contain any dataset or contain more than three!";\n+ \t\t\texit;\n+ \t\t}elsif(@numberOfSets == 2){\t\t# only one set is in the file -> add 2x zeros\n+ \t\t\t$_ .= "\\t" . 0 . "\\t" . 0;\n+ \t\t}elsif(@numberOfSets == 3){\t\t# only two sets are in the file -> add 1x zeros\n+ \t\t\t$_ .= "\\t" . 0;\n+ \t\t}\n+ \t\t\n+ \t\taddToNetwork($_);\n+ \t\tpush(@input_file, $_);\n+ \t}\n+}\n+close(inFile);\n+\n+\n+# --------------------------------------------------------------------------------------------------------------\n+# --------------------------------------------------------------------------------------------------------------\n+# (1) PREPROCESSING: detect all leaf nodes\n+my $modifiedInput = detectNonLeafs();\n+\n+# (2) MAIN COMPUTATION: compute deep by deep (path deep ex. root;Viruses; => deep 2)\n+my ($vennClusterOut, $specialNumberOut) = clusterVennBottomUp();\n+\n+# (3) VENN-END-PREPERATION'..b'n \\@modifiedFile;\n+}\n+\n+\n+# helper function for detectNonLeafs \n+sub getPathDeep{\n+\tmy $inPath = $_[0];\n+\tmy @deep = split(\';\', $inPath);\n+\tmy $size = $#deep;\n+\treturn $size;\n+}\n+\n+sub convertPath{\n+\tmy $inString = $_[0];\n+\t$inString =~ s/"//g;\n+\t$inString =~ s/\\s+/_/g;\n+\treturn $inString;\n+}\n+\n+sub getId{\n+\tmy $lineToParse = $_[0];\n+\tmy $idPos = $_[1];\n+\tmy $stringId = "";\n+\tmy @path = ();\n+\t\n+\t$lineToParse =~ s/"//g;\n+\t$lineToParse =~ s/\\s+/_/g;\n+\t@path = split(\';\',$lineToParse);\n+\tmy $num = @path;\n+\t\n+\tif(($num + $idPos) < 0){\n+\t\treturn -1;\n+\t}else{\n+\t\treturn $path[$idPos];\t\n+\t}\n+}\n+\n+sub computeLeafValues{\n+\tmy $meganValues = $_[0];\n+\tmy @rawValues = split(\'\\t\', $meganValues);\n+\tmy @nodeRelVal = ();\n+\t\n+\tmy $outValues = $rawValues[0] . " " . $rawValues[1] . " " . $rawValues[2]; \n+\n+\tif($rawValues[0] <= $rawValues[1]){\n+\t\t$outValues .= " " . $rawValues[0];\n+\t}else{\n+\t\t$outValues .= " " . $rawValues[1];\n+\t}\n+\tif($rawValues[0] <= $rawValues[2]){\n+\t\t$outValues .= " " . $rawValues[0];\n+\t}else{\n+\t\t$outValues .= " " . $rawValues[2];\n+\t}\n+\tif($rawValues[1] <= $rawValues[2]){\n+\t\t$outValues .= " " . $rawValues[1];\n+\t}else{\n+\t\t$outValues .= " " . $rawValues[2];\n+\t}\n+\t#my ($min, $max) = minmax @rawValues;\n+\tmy $min = 0;\n+\t$outValues .= " " . $min;\n+\t\n+\treturn $outValues;\n+}\n+# -----------------------------------------------------------------------------\n+\n+\n+# compute network (.sif)\n+sub addToNetwork{\n+\tmy $inLine = $_[0];\n+\tmy @splitInLine = split(\'\\t\',$inLine);\n+\t# remove \' " \' from line\n+\t$splitInLine[0] =~ s/"//g;\n+\t$splitInLine[0] =~ s/\\s+/_/g;\n+\tmy @elements = split(\';\' ,$splitInLine[0]); \n+\t\t\n+\tif(@elements > 1){\n+\t\tmy $outString = $elements[-2] . " pp " . $elements[-1];\n+\t\tpush(@network, $outString);\n+\t}\n+}\n+\n+\n+# store network in .sif file\n+sub storeNetwork{\n+\t# test\n+\tmy $tmpFileName = $out_network;\n+\t\n+\t#my $tmpFileName = "./network.sif";\n+\topen(FILE , ">$tmpFileName") || die "File can\'t be written - \\"sif - File\\"!\\n";\n+\t\tprint FILE join("\\n", @network) . "\\n";\n+\tclose(FILE);\n+}\n+\n+\n+# ---------------------------------------------------------------------------------------------\n+# two different lookup-tables are available!\n+# lookupPixel() => static ; lookupPixelSQRT() => dynamic\n+#\n+# lookup absolute node-size to pixel (frame-size for venn-diagram)\n+sub lookupPixel{\n+\tmy $query = $_[0];\n+\t\n+\tif($query < 10){\n+\t\treturn 30;\n+\t}elsif($query < 100){\n+\t\treturn 40;\n+\t}elsif($query < 1000){\n+\t\treturn 50;\n+\t}elsif($query < 10000){\n+\t\treturn 60;\n+\t}elsif($query < 100000){\n+\t\treturn 80;\n+\t}elsif($query < 1000000){\n+\t\treturn 100;\n+\t}elsif($query < 10000000){\n+\t\treturn 140;\n+\t}elsif($query < 20000000){\n+\t\treturn 180;\n+\t}elsif($query < 30000000){\n+\t\treturn 220;\n+\t}else{\n+\t\treturn 250;\t\n+\t}\n+}\n+\n+# lookup absolute node-size to pixel (frame-size for venn-diagram) <- this is currently used!\n+sub lookupPixelSQRT{\n+\t\n+\tif ($transFnc == 0) {\n+\t\treturn int(($_[0] ** (1/(1.6))) * 1.8 + 8); # 3,000 datapoints in sum\n+\t}elsif($transFnc == 1){\n+\t\treturn int(($_[0] ** (1/(2.1))) * 1.8 + 8); # 30,000 datapoints in sum\n+\t}elsif($transFnc == 2){\n+\t\treturn int(($_[0] ** (1/(2.6))) * 1.8 + 8); # 300,000 datapoints in sum\n+\t}elsif($transFnc == 3){\n+\t\treturn int(($_[0] ** (1/(3.1))) * 1.8 + 8); # 3,000,000 datapoints in sum\n+\t}elsif($transFnc == 4){\n+\t\treturn int(($_[0] ** (1/(3.7))) * 1.8 + 8); # 30,000,000 datapoints in sum\n+\t}elsif($transFnc == 5){\n+\t\treturn int(($_[0] ** (1/(4))) * 1.8 + 8); # 300,000,000 datapoints in sum\n+\t}elsif($transFnc == 6){\n+\t\treturn int(($_[0] ** (1/(4.7))) * 1.8 + 8); # 3,000,000,000 datapoints in sum\n+\t}\n+\t\n+\t#return int(($_[0] ** (1/(3.3))) * 1.8 + 30);\t# test version for small and large datasets?\n+\t#return int(($_[0] ** (1/(3.3))) * 1.8 + 5);\t# test version for small and large datasets?\n+\t#return int(($_[0] ** (1/(4))) * 1.8 + 8);\t # test version for small and large datasets?\n+\t#return int(($_[0] ** (1/6)) * 12);\t\t\t\t# old version this version is good for large datasets\n+}\n+\n+\n+\n+\n+\n+\n+\n+\n' |
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| diff -r 000000000000 -r 745aede829e9 coVennTree/coVennTree.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/coVennTree/coVennTree.xml Fri Jan 30 09:55:45 2015 -0500 |
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| @@ -0,0 +1,143 @@ +<tool id="coVennTree" name="CoVennTree (Comparative weighted Venn Tree) - Rooted Tree" version="1.6.0"> + <description>Comparative rooted tree analysis for files in dsv format</description> + <requirements> + <requirement type="package" version="1.6">coVennTree</requirement> + <requirement type="package" version="5.18.1">perl</requirement> + </requirements> + <command interpreter="perl"> + coVennTree.pl + $infile + $color_mode + $trans_func + $leafs_allInformation + $outfile_network + $outfile_attribute + </command> + + <inputs> + <param name="infile" type="data" format="tabular" label="Path File" help="Tabular file containing the paths and values"/> + + + <param name="color_mode" multiple="false" type="select" label="Select color mode for Venn diagrams"> + <option value="0">(1) Set1: blue Set2: red Set3: yellow</option> + <option value="1">(2) Set1: red Set2: green Set3: blue</option> + <option value="2">(3) Set1: green Set2: magenta Set3: blue</option> + <option value="3">(4) Set1: green Set2: purple Set3: red</option> + <option value="4">(5) Set1: dark gray Set2: mid-grey Set3: light gray</option> + </param> + + + <param name="trans_func" multiple="false" type="select" label="Select transformation function"> + <option value="0">(1) datasets max: 3,000 data points in sum</option> + <option value="1">(2) datasets max: 30,000 data points in sum</option> + <option value="2">(3) datasets max: 300,000 data points in sum</option> + <option value="3">(4) datasets max: 3,000,000 data points in sum</option> + <option value="4">(5) datasets max: 30,000,000 data points in sum</option> + <option value="5">(6) datasets max: 300,000,000 data points in sum</option> + <option value="6">(7) datasets max: 3,000,000,000 data points in sum</option> + </param> + + + <param name="leafs_allInformation" multiple="false" type="select" label="Select tree analyzes function"> + <option value="1">(1) leaf + inner nodes informations</option> + <option value="0">(2) only leaf information</option> + </param> + + </inputs> + + <outputs> + <data format="tabular" name="outfile_network" label="Network" /> + <data format="tabular" name="outfile_attribute" label="Attributes" /> + </outputs> + + <tests> + <test> + </test> + </tests> + + <help> +.. class:: infomark + +CoVennTree compares up to three rooted trees at the same time. + +CoVennTree (Comparative weighted Venn Tree) is a software to analyze and compare up to three datasets. Unlike other +methods, CoVennTree correlates data on the leaf level and transfers this information to the root node. CoVennTree works with numbers to compute weighted +Venn diagrams for each node in the graph (rooted tree). Therefore any kind of input data can be processed as long as the data structure will be taken into account. + + + +**Input** + +*Input example* + + +.. image:: $PATH_TO_IMAGES/example1.png + :height: 430 + :width: 600 + + +*dsv-format: The following table represents the graph.* + + +=========== ====== ====== ====== +#Datasets set1 set2 set3 +=========== ====== ====== ====== +"root;" 0 0 0 +"root;A;" 10000 0 0 +"root;A;C;" 600000 300000 500000 +"root;A;D;" 0 100000 200000 +"root;A;E;" 800000 0 100000 +"root;B;" 10000 20000 50000 +=========== ====== ====== ====== + + +------- + + +**Results** + +A specific color is assigned to each dataset in five optional color schemes (see parameter "Select color mode for weighted Venn diagrams"). +In this example set1 corresponds to color blue, set2 to red and set3 to yellow. +In order to cover a wide numerical range a non linear transformation function is used. + + +*Data format \*.sif* + +[parent_node] [connected_with] [child_node] + + +*Data format \*.venn* + +[id] [google_url] [id_vds] [Venn_abs_values] + + +*Output example "leaf information and not assigned information"* + +By selecting "leaf information + not assigned information" artificial nodes can be inserted. +Artificial nodes will be inserted if inner nodes have values larger than zero. + +.. image:: $PATH_TO_IMAGES/venn-graph-off.png + :height: 358 + :width: 425 + + +------- + + +*Output example "only leaf information"* + +By selecting "only leaf information" only leaf nodes are considered for the computation of weighted Venn diagrams. + +.. image:: $PATH_TO_IMAGES/venn-graph-on.png + :height: 358 + :width: 400 + + + + </help> + <citations> + <citation type="doi"> + + </citation>> + </citations> +</tool> |
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| diff -r 000000000000 -r 745aede829e9 coVennTree/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/coVennTree/tool_dependencies.xml Fri Jan 30 09:55:45 2015 -0500 |
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| @@ -0,0 +1,21 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="perl" version="5.18.1"> + <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="coVennTree" version="1.6"> + <install version="1.0"> + <actions> + <action type="setup_perl_environment"> + <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="perl" version="5.18.1" /> + </repository> + <!-- allow downloading and installing an Perl package from cpan.org--> + <package>http://search.cpan.org/CPAN/authors/id/A/AD/ADAMK/List-MoreUtils-0.33.tar.gz</package> + </action> + </actions> + </install> + <readme> + </readme> + </package> +</tool_dependency> |
