diff coVennTree/coVennTree.xml @ 0:745aede829e9 draft default tip

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/coVennTree/coVennTree.xml	Fri Jan 30 09:55:45 2015 -0500
@@ -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>