--- a/hicPlotTADs.xml	Wed Mar 07 03:46:02 2018 -0500
+++ b/hicPlotTADs.xml	Fri Apr 27 03:38:47 2018 -0400
@@ -1,5 +1,5 @@
 <tool id="hicexplorer_hicplottads" name="@BINARY@" version="@WRAPPER_VERSION@.0">
-    <description>Plots the diagonal, and some values close to the diagonal of a HiC matrix</description>
+    <description>plot Hi-C contact matrices heatmaps alongside other data tracks</description>
     <macros>
         <token name="@BINARY@">hicPlotTADs</token>
         <import>macros.xml</import>
@@ -30,7 +30,7 @@
 #end if
 #end if
 #for $counter, $track in enumerate($tracks):
-#if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option":  
+#if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option":
 [hic_section_$counter]
 file = $track.track_file_style_conditional.matrix_h5_cooler
 file_type = hic_matrix
@@ -44,7 +44,7 @@
 #if $track.track_file_style_conditional.min_value:
 min_value = $track.track_file_style_conditional.min_value
 #end if
-#if $track.track_file_style_conditional.max_value: 
+#if $track.track_file_style_conditional.max_value:
 max_value = $track.track_file_style_conditional.max_value
 #end if
 transform = $track.track_file_style_conditional.transform
@@ -65,7 +65,7 @@
 scale factor = $track.track_file_style_conditional.scale_factor
 #end if
 
-#end if 
+#end if
 #if $track.track_file_style_conditional.track_file_style_selector == "tad_score_track_option":
 
 [tad_score_$counter]
@@ -91,7 +91,7 @@
 file_type = bedgraph
 #end if
 type = lines
-#end if 
+#end if
 #if $track.track_file_style_conditional.track_file_style_selector == "chrom_states_option":
 
 [chrom states_$counter]
@@ -116,34 +116,34 @@
 title = $track.track_file_style_conditional.title
 #if $track.track_file_style_conditional.color:
 color = $track.track_file_style_conditional.color
-#end if 
+#end if
 
 #if $track.track_file_style_conditional.width_bed:
 width = $track.track_file_style_conditional.width_bed
-#end if 
+#end if
 
 #if $track.track_file_style_conditional.labels:
 labels = $track.track_file_style_conditional.labels
-#end if 
+#end if
 
 #if $track.track_file_style_conditional.type:
 type = $track.track_file_style_conditional.type
-#end if 
+#end if
 
 file_type = bed
 #if $track.track_file_style_conditional.fontsize:
 fontsize = $track.track_file_style_conditional.fontsize
-#end if 
+#end if
 
 #if $track.track_file_style_conditional.gene_rows:
 gene rows = $track.track_file_style_conditional.gene_rows
-#end if 
+#end if
 
 #if $track.track_file_style_conditional.global_max_row:
 global max row = $track.track_file_style_conditional.global_max_row
-#end if 
+#end if
 
-#end if 
+#end if
 
 
 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_track_option":
@@ -168,7 +168,7 @@
 file_type = bedgraph
 #end if
 type = lines
-#end if 
+#end if
 
 #if $track.track_file_style_conditional.track_file_style_selector == "bigwig_track_option":
 
@@ -195,14 +195,14 @@
 type = fill
 #elif $track.track_file_style_conditional.type_conditional == 'line_option':
 type = line:$track.track_file_style_conditional.type_conditional.width_line
-#elif $track.track_file_style_conditional.type_conditional == 'point_option': 
+#elif $track.track_file_style_conditional.type_conditional == 'point_option':
 type = points:$track.track_file_style_conditional.type_conditional.width_point
 #end if
 #if $track.track_file_style_conditional.data_range:
 show data range = $track.track_file_style_conditional.data_range
 #end if
 file_type = bigwig
-#end if 
+#end if
 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_matrix_track_option":
 
 [bedgraph_matrix_$counter]
@@ -223,21 +223,21 @@
 #end if
 file_type = bedgraph_matrix
 plot horizontal lines=False
-#end if 
+#end if
 #if $track.track_file_style_conditional.track_file_style_selector == "vlines_track_option":
 
 [vlines_$counter]
 file = $track.track_file_style_conditional.track_input_bed
 type = vlines
 file_type = bed
-#end if 
+#end if
 #if $track.track_file_style_conditional.track_file_style_selector == "spacer_option":
 
 [spacer]
 #if $track.track_file_style_conditional.spacer_width:
 width = $track.track_file_style_conditional.spacer_width
 #end if
-#end if 
+#end if
 #end for</configfile>
     </configfiles>
     <inputs>
@@ -249,7 +249,7 @@
                 <param name="track_file_style_selector" type="select" label="Choose style of the track">
                     <option value="hic_matrix_option">TAD visualization</option>
                     <option value="chrom_states_option">Chromatine states</option>
-                    <option value="tad_score_track_option">TAD score</option>                    
+                    <option value="tad_score_track_option">TAD score</option>
                     <option value="gene_track_option">Gene track / Bed track</option>
                     <option value="bigwig_track_option">Bigwig track</option>
                     <option value="bedgraph_track_option">Bedgraph track </option>
@@ -260,7 +260,7 @@
                 <when value="hic_matrix_option">
                     <expand macro="plot_title" />
                     <expand macro="matrix_h5_cooler_macro" />
-                    
+
                     <expand macro="colormap" />
                     <param name="depth" type="integer" value="8000000" optional="True" label="Depth" />
                     <param name="min_value" type="float" value="" optional="True" label="Minimum value"/>
@@ -269,10 +269,10 @@
                         <option value="log1p" selected="True" >log1p</option>
                         <option value="log">log</option>
                         <option value="-log">-log</option>
-                        
+
                     </param>
                     <param name="width_matrix" type="float" value="1.5" optional="True" label="Width"/>
-                    
+
                     <param name="type" type="select" optional="True" label="Plotting type">
                         <option value="arcplot">arcplot</option>
                         <option value="interaction">interaction</option>
@@ -292,14 +292,14 @@
                             label="Set 'type' to 'lines'" help="if type is set as lines, then the TAD score lines are drawn instead
                             of the matrix set to lines if a heatmap representing the matrix is not wanted"/>
                     <param name="width_tad" type="float" value="0.2" optional="True" label="Width"/>
-                    <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" />                   
+                    <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" />
                 </when>
                 <when value="chrom_states_option">
                     <expand macro="plot_title" />
-                
+
                     <expand macro="track_input_bed_macro" />
                     <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
-                    
+
                     <param name="border_color" type="color" value="#000000" label="Border color" optional="True" />
                     <param name="width_chrom" type="float" value="1.5" optional="True" label="Width"/>
                      <param name="labels" type="boolean" truevalue="on" falsevalue="off" checked="true"
@@ -307,7 +307,7 @@
                 </when>
                 <when value="gene_track_option">
                     <expand macro="plot_title" />
-                
+
                     <expand macro="track_input_bed_macro" />
                     <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
                     <param name="width_bed" type="float" value="1.5" optional="True" label="Width"/>
@@ -321,25 +321,25 @@
                             label="Global max rows" />
                     <param name="gene_rows" type="integer" value="" optional="True" label="Gene rows" />
                     <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
-                    
+
                 </when>
                 <when value="bedgraph_track_option">
                     <expand macro="plot_title" />
                     <expand macro="track_input_bedgraph_macro" />
                     <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
-                    
+
                     <param name="width_bedgraph" type="float" value="0.2" optional="True" label="Width"/>
-                    <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" />                   
+                    <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" />
                 </when>
                 <when value="bigwig_track_option">
                     <expand macro="plot_title" />
-                
+
                     <expand macro="track_input_bigwig_macro" />
                     <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
-                    
+
                     <param name="min_value" type="float" value="" optional="True" label="Minimum value"/>
                     <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>
-                    
+
                     <param name="width_bigwig" type="float" value="1.5" optional="True" label="Width"/>
                     <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" />
                     <param name="nans_to_zeros" type="boolean" truevalue="True" falsevalue="False" checked="false"
@@ -360,11 +360,11 @@
                     </conditional>
                     <param name="data_range" type="boolean" truevalue="yes" falsevalue="no" optional="True" checked="false" />
                 </when>
-                
-               
+
+
                 <when value="bedgraph_matrix_track_option">
                     <expand macro="plot_title" />
-                
+
                     <expand macro="track_input_bedgraph_matrix_macro" />
                     <param name="min_value" type="float" value="" optional="True" label="Minimum value"/>
                     <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>
@@ -382,10 +382,10 @@
                     <expand macro="spacer_macro" />
                 </when>
             </conditional>
-           
+
         </repeat>
 
-        
+
         <conditional name="x_axis">
             <param name="x_axis_select" type="select" label="Configure x-axis">
                 <option value="no" selected="True">No</option>
@@ -406,7 +406,7 @@
         </param>
     </inputs>
     <outputs>
-        <data format="png" name="outFileName" from_work_dir="plot">
+        <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on [${on_string}]: Plot">
             <change_format>
                 <when input="image_file_format" value="png" format="png" />
                 <when input="image_file_format" value="svg" format="svg" />
@@ -418,7 +418,7 @@
             <param name="region" value="chrX:3000000-3500000"/>
             <conditional name="x_axis">
                 <param name="x_axis_select" value="yes" />
-            </conditional>   
+            </conditional>
             <repeat name="tracks">
                 <conditional name="track_file_style_conditional">
                     <param name="track_file_style_selector" value="hic_matrix_option" />
@@ -430,9 +430,9 @@
                     <param name="transform" value="log1p" />
                     <param name="boundaries_file" value="domains.bed" />
                     <param name="x_labels" value="True" />
-                </conditional>   
+                </conditional>
             </repeat>
-            <repeat name="tracks">             
+            <repeat name="tracks">
                 <conditional name="track_file_style_conditional">
                     <param name="track_file_style_selector" value="spacer_option" />
                     <param name="spacer_width" value="0.05" />
@@ -445,7 +445,7 @@
                     <param name="title" value="TAD state" />
                     <param name="width_chrom" value="0.5" />
                     <param name="labels" value="off" />
-                </conditional>   
+                </conditional>
             </repeat>
             <repeat name="tracks">
                 <conditional name="track_file_style_conditional">
@@ -455,7 +455,7 @@
                     <param name="width_tad" value="10" />
                 </conditional>
             </repeat>
-            <repeat name="tracks">             
+            <repeat name="tracks">
                 <conditional name="track_file_style_conditional">
                     <param name="track_file_style_selector" value="spacer_option" />
                     <param name="spacer_width" value="1" />
@@ -468,7 +468,7 @@
                     <param name="title" value="bedgraph" />
                     <param name="width_bedgraph" value="4" />
                     <param name="color" value="blue" />
-                </conditional>   
+                </conditional>
             </repeat>
             <repeat name="tracks">
                 <conditional name="track_file_style_conditional">
@@ -480,9 +480,9 @@
                     <conditional name="type_conditional">
                         <param name="type_selector" value="fill_option" />
                     </conditional>
-                </conditional>   
+                </conditional>
             </repeat>
-            
+
             <repeat name="tracks">
                 <conditional name="track_file_style_conditional">
                     <param name="track_file_style_selector" value="bigwig_track_option" />
@@ -494,7 +494,7 @@
                         <param name="type_selector" value="line_option" />
                         <param name="width_line" value="1" />
                     </conditional>
-                </conditional>   
+                </conditional>
             </repeat>
 
             <repeat name="tracks">
@@ -507,11 +507,11 @@
                     <conditional name="type_conditional">
                         <param name="type_selector" value="line_option" />
                         <param name="width_line" value="0.1" />
-                        
+
                     </conditional>
-                </conditional>   
+                </conditional>
             </repeat>
-            
+
             <repeat name="tracks">
                 <conditional name="track_file_style_conditional">
                     <param name="track_file_style_selector" value="bigwig_track_option" />
@@ -522,12 +522,12 @@
                     <conditional name="type_conditional">
                         <param name="type_selector" value="point_option" />
                         <param name="width_point" value="0.5" />
-                        
+
                     </conditional>
-                </conditional>   
+                </conditional>
             </repeat>
 
-            <repeat name="tracks">             
+            <repeat name="tracks">
                 <conditional name="track_file_style_conditional">
                     <param name="track_file_style_selector" value="spacer_option" />
                     <param name="spacer_width" value="0.5" />
@@ -540,9 +540,9 @@
                     <param name="title" value="genes" />
                     <param name="width_bed" value="5" />
                     <param name="fontsize" value="10" />
-                </conditional>   
+                </conditional>
             </repeat>
-            <repeat name="tracks">             
+            <repeat name="tracks">
                 <conditional name="track_file_style_conditional">
                     <param name="track_file_style_selector" value="spacer_option" />
                     <param name="spacer_width" value="1" />
@@ -556,9 +556,9 @@
                     <param name="width_bed" value="3" />
                     <param name="fontsize" value="8" />
                     <param name="gene_rows" value="3" />
-                </conditional>   
+                </conditional>
             </repeat>
-            <repeat name="tracks">             
+            <repeat name="tracks">
                 <conditional name="track_file_style_conditional">
                     <param name="track_file_style_selector" value="spacer_option" />
                     <param name="spacer_width" value="1" />
@@ -572,14 +572,14 @@
                     <param name="width_bed" value="20" />
                     <param name="fontsize" value="10" />
                     <param name="global_max_row" value="True" />
-                </conditional>   
+                </conditional>
             </repeat>
             <repeat name="tracks">
                 <conditional name="track_file_style_conditional">
                     <param name="track_file_style_selector" value="vlines_track_option" />
                     <param name="track_input_bed" value="domains.bed" ftype="bed" />
                     <param name="type" value="vlines" />
-                </conditional>   
+                </conditional>
             </repeat>
             <param name="image_file_format" value="png" />
             <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="35000" />
@@ -587,38 +587,47 @@
     </tests>
     <help><![CDATA[
 
-Plot TADs
-=========
+Plot Topologic Associated Domains
+=================================
 
-``hicPlotTADs`` is a visualization tool to plot the topologically associating domains (TADs) in a given region. Additional tracks can be added to enable the comparisons with other data like gene tracks.
+**hicPlotTADs** is a visualization tool to plot the topologically associating domains (TADs) in a given region. Additional tracks can be added to enable the comparisons with other data like gene, ChIP-seq, RNA-seq or other tracks, including TAD seperation scores computed by ``hicFindTADs``.
 
-Input
+_________________
+
+Usage
 -----
-- the region to plot: chr1:1000-2000
-- the tracks:
-    - the contact matrix
-    - Boundaries file: The result of ``hicFindTADs``.
-- different tracks for comparison:
-    - Chromatine states: 
-    - TAD score
-    - gene tracks
-    - Generic bigwig, bedgraph or bedgraph matrix files
-    - Vlines: vertical lines as a visual support where regions start / end over all tracks
-    - Spacer: Add some space between the different tracks
+
+This tool takes various types of tracks as input:
 
-For each track parameters for the color, the width or the font size can be defined.
+    - **TAD vizualisation:** corrected Hi-C contact matrix to plot a contact heatmap. It is recommended to follow ``hicPlotMatrix`` instructions. Boundaries file can used, which is the output of ``hicFindTADs`` in bed format. If selected, TADs will be drawn directly on the contact heatmap.
+    - **Chromatin states:** display blocks of different colors following a bed file.
+    - **TAD score:** display TAD seperation score computed by ``hicFindTADs``.
+    - **Gene track / Bed Track:** display genes or bed files. Labels like gene names can be toggled on or off.
+    - **Bigwig track:** generic bigwig track plotting.
+    - **Bedgraph track:** generic bedgraph track plotting.
+    - **Bedgraph matrix track** is used to specifically plot bm files computed by ``hicFindTADs`` (TAD seperation scores).
+    - **Vlines:** vertical lines drawn on top of all tracks following a bed file. It is used as a visual support where regions start / end over all tracks, for example to display TAD boundaries computed by ``hicFindTADs``.
+    - **Spacer:** Add some space between two tracks.
+
+For each track, parameters for the color, the width or the font size can be defined.
+
+_________________
 
 Output
 ------
-An output looks like this:
 
+**hicPlotTADs** output is similar to a genome browser screen-shot that besides the usual genes, and score data (like bigwig or bedgraph files) also contains Hi-C data. The plot is composed of tracks that need to be specified.
+Below is represented the 85 Mb to 110 Mb region from human chromosome 2 visualized using **hicPlotTADs**. TADs were computed by ``hicFindTADs``. The additional tracks added correspond to: TAD-separation score (as reported by ``hicFindTADs``), chromatin states, principal component 1 (A/B compartment) computed using ``hicPCA``, ChIP-seq coverage for the H3K27ac mark, DNA methylation, and a gene track. Data are from mouse cardiac myocytes, published by `Nothjunge et al. (2017)`_.
 
-.. image:: $PATH_TO_IMAGES/master_TADs_plot.png
-   :width: 80 %
+.. image:: $PATH_TO_IMAGES/hicPlotTADs.png
+   :width: 70 %
+
+_________________
 
 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
 
 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
+.. _`Nothjunge et al. (2017)`: https://www.nature.com/articles/s41467-017-01724-9
 ]]></help>
     <expand macro="citations" />
 </tool>