# HG changeset patch
# User fabio
# Date 1652997976 0
# Node ID 8c239bd7984a6ae9298a7a921fd811f81aa48baa

Uploading wrapper for honto

diff -r 000000000000 -r 8c239bd7984a honto.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/honto.xml	Thu May 19 22:06:16 2022 +0000
@@ -0,0 +1,235 @@
+<?xml version="1.0"?>
+<tool name="honto" id="honto" version="0.1.0">
+    <description>A novel method for assessing and measuring homophily in networks</description>
+    
+    <!-- Tool developers -->
+    <creator>
+        <person givenName="Paolo" familyName="Franciosa" 
+                url="http://www.statistica.uniroma1.it/users/pfrancio/" 
+                email="paolo.franciosa@uniroma1.it" />
+
+        <person givenName="Nicola" familyName="Apollonio" 
+                url="https://www.iac.rm.cnr.it/~apollonio/" 
+                email="nicola.apollonio@cnr.it" />
+
+        <person givenName="Daniele" familyName="Santoni" 
+                url="http://www.iasi.cnr.it/~dsantoni/" 
+                email="daniele.santoni@iasi.cnr.it" />
+
+        <person givenName="Fabio" familyName="Cumbo" 
+                url="https://fabio-cumbo.github.io/" 
+                email="fabio.cumbo@gmail.com" />
+    </creator>
+
+    <!-- Define dependencies -->
+    <requirements>
+        <requirement type="package" version="0.1.0">honto</requirement>
+    </requirements>
+
+    <command detect_errors="exit_code">
+<![CDATA[
+    ln -s ${edges} edges.txt;
+    ln -s ${nodes} nodes.txt;
+
+    honto 
+
+    --input_edges edges.txt
+    --input_nodes nodes.txt
+    --weight_threshold ${weight_threshold}
+    
+    #if $isolated == "yes":
+        --isolated
+    #end if
+
+    #if $log_transform.enable_lt == "yes":
+        --log_transform
+        #if $log_transform.scale_log.scale_type == "factor":
+            --scale_factor $log_transform.scale_log.scale_value
+        #elif $log_transform.scale_log.scale_type == "from_one":
+            --scale_from_one
+        #end if
+    #end if
+
+    --cmap $heatmap.cmap
+    --vmin $heatmap.vmin
+    --vmax $heatmap.vmax
+    --center $heatmap.center
+    #if $heatmap.cbar == "yes":
+        --cbar
+    #end if
+    
+    --nproc "\${GALAXY_SLOTS:-4}"
+    --overwrite
+    --verbose
+]]>
+    </command>
+
+    <inputs>
+        <!-- Select edges -->
+        <param name="edges" type="data" format="tsv" 
+               label="Select a network" 
+               help="Input network with the list of edges, one per line." />
+        
+        <!-- Select colors -->
+        <param name="nodes" type="data" format="tsv" 
+               label="Select a nodes definition file" 
+               help="This file contains a mapping between node names and colors." />
+        
+        <!-- Weight threshold -->
+        <param name="weight_threshold" type="integer" value="700" min="0" 
+               label="Weight threshold" 
+               help="Threshold for considering edges based in their weight." />
+        
+        <!-- Isolated -->
+        <param name="isolated" type="boolean" checked="false" truevalue="yes" falsevalue="no" 
+               label="Insert isolated nodes" />
+        
+        <!-- Log-transformation options -->
+        <conditional name="log_transform">
+            <!-- Enable log-transformation -->
+            <param name="enable_lt" type="boolean" checked="false" truevalue="yes" falsevalue="no" 
+                   label="Log-transform z-scores" />
+
+            <when value="yes">
+                <!-- Scale options -->
+                <conditional name="scale_log">
+                    <!-- Select a scale option -->
+                    <param name="scale_type" type="select" label="Choose one of the available scale options">
+                        <option value="default" selected="true">Scale automatically</option>
+                        <option value="factor">Factor</option>
+                        <option value="from_one">Truncate from one</option>
+                    </param>
+
+                    <!-- In case of "factor" -->
+                    <when value="factor">
+                        <param name="scale_value" type="float" value="0.0"
+                               label="Scale factor" 
+                               help="Rescale z-scores with this constant before log-transforming values." />
+                    </when>
+                </conditional>
+            </when>
+        </conditional>
+        
+        <!-- Heatmap customization options -->
+        <section name="heatmap" expanded="true" 
+                 title="Heatmap customization"
+                 help="Access advanced options to customize the produced heatmap by specifying the colormap, scale, and color bar">
+            <!-- Colormap -->
+            <param name="cmap" type="text" value="PiYG" 
+                   label="Heatmap colormap" />
+            
+            <!-- Vmin -->
+            <param name="vmin" type="float" value="2.2967"
+                   label="Select a vmin value" 
+                   help="Min value to anchor the colormap" />
+            
+            <!-- Vmax -->
+            <param name="vmax" type="float" value="4.3957"
+                   label="Select a vmax value" 
+                   help="Max value to anchor the colormap" />
+            
+            <!-- Center -->
+            <param name="center" type="float" value="2.9957"
+                   label="Select a center" 
+                   help="The value at which to center the colormap when plotting divergent data" />
+            
+            <!-- Cbar -->
+            <param name="cbar" type="boolean" checked="false" truevalue="yes" falsevalue="no" 
+                   label="Add a color bar" />
+        </section>
+    </inputs>
+
+    <outputs>
+        <!-- Output z-scores edges -->
+        <data format="tsv" name="zscores_edges" 
+              label="${tool.name} on ${on_string}: Edges z-scores" 
+              from_work_dir="edges_zscores_edges.txt" />
+        
+        <!-- Output z-scores singletons -->
+        <data format="tsv" name="zscores_singletons" 
+              label="${tool.name} on ${on_string}: Singletons z-scores" 
+              from_work_dir="edges_zscores_singletons.txt" />
+        
+        <!-- Output heatmap -->
+        <data format="pdf" name="out_heatmap" 
+              label="${tool.name} on ${on_string}: Heatmap" 
+              from_work_dir="edges.pdf" />
+    </outputs>
+
+    <help><![CDATA[
+**Homophily Network Tool**
+
+`honto` is a tool designed for assessing and measuring homophily in networks whose nodes have categorical attributes, 
+namely when the nodes of networks come partitioned into classes.
+
+Homophily evaluation is performed through the comparison between the relative edge density of the subgraphs, 
+induced by each class, and the corresponding expected relative edge density under a null model.
+
+The novelty of our approach consists in prescribing an endogenous null model, namely, the sample space of the null model 
+is built on the input network itself. This allows us to give exact explicit expressions for the z-scores of the 
+relative edge density of each class as well as other related statistics
+
+-----
+
+**Input**
+
+The first input is file representing an undirected network composed by a list of edges like the example below.
+No header lines are allowed.
+
++--------+--------+
+| TP0001 | TP1015 |
++--------+--------+
+| TP0001 | TP0949 |
++--------+--------+
+| TP0001 | TP0692 |
++--------+--------+
+| ...    | ...    |
++--------+--------+
+| TP0976 | TP0977 |
++--------+--------+
+| TP1032 | TP1033 |
++--------+--------+
+
+
+Please note that the above mentioned file could also have an additional column with numeric weight values.
+You may want to avoid considering some nodes by applying a threshold on this column.
+
+The second input is the nodes definition file. It contains a row for each node in the network with two columns
+with a mapping between the node name and a color or group id, like in the example below.
+No header lines are allowed in this case either.
+
++--------+-----+
+| TP0001 | L   |
++--------+-----+
+| TP1015 | K   |
++--------+-----+
+| TP0949 | U   |
++--------+-----+
+| TP0692 | L   |
++--------+-----+
+| ...    | ... |
++--------+-----+
+| TP1032 | X   |
++--------+-----+
+| TP1033 | X   |
++--------+-----+
+
+-----
+
+**Output**
+
+The tool produces three output files. Two of them contains the z-scores for both edges and singletons.
+The third output is a PDF with the final heatmap.
+
+-----
+
+.. class:: infomark
+
+**Notes**
+
+Please visit the official GitHub repository_ for other information about `honto`.
+
+.. _repository: https://github.com/fabio-cumbo/honto
+    ]]></help>
+
+</tool>
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