--- a/hicAggregateContacts.xml	Wed Mar 07 03:37:18 2018 -0500
+++ b/hicAggregateContacts.xml	Fri Apr 27 03:32:37 2018 -0400
@@ -1,5 +1,6 @@
+
 <tool id="hicexplorer_hicaggregatecontacts" name="@BINARY@" version="@WRAPPER_VERSION@.0">
-    <description>Takes a list of positions in the hic-matrix and makes a pooled image</description>
+    <description>allow plotting of aggregated Hi-C contacts between regions specified in a file</description>
     <macros>
         <token name="@BINARY@">hicAggregateContacts</token>
         <import>macros.xml</import>
@@ -64,21 +65,21 @@
     </command>
     <inputs>
         <expand macro='matrix_h5_cooler_macro' />
-        <param argument="--BED" type="data" format="bed" label="Interactions between regions in this BED file are plotted."/>
+        <param argument="--BED" type="data" format="bed" label="Interactions between regions in this BED file are plotted"/>
         <param argument="--BED2" type="data" format="bed" optional="true"
-            label="Interactions between regions in first and second BED file are plotted."/>
+            label="Interactions between regions in first and second BED file are plotted"/>
 
         <expand macro='range' />
 
         <repeat name="chromosomes" title="List of chromosomes to plot" min="0">
-            <param name="chromosome" type="text">
+            <param name="chromosome" type="text" label="chromosome (one per field)">
                 <validator type="empty_field" />
             </param>
         </repeat>
 
         <param argument="--numberOfBins" type="integer" optional="true" label="Number of bins to include in the submatrix"
-            help=" The bed regions will be centered between - half number of bins
-            and the other half number of bins." />
+            help="The bed regions will be centered between -half number of bins
+            and +half number of bins indicated." />
 
         <param argument="--transform" type="select" label="Type of transformation for the matrix"
             help="If total counts are selected, then the sub-matrix values
@@ -99,10 +100,10 @@
         <param name="clustering" type="select" optional="true" label="Number of clusters per chromosome"
             help="When this option is set, then the matrix is split into
                   clusters using the hierarchical clustering algorithm,
-                  using 'ward linkage'. --hclust could be very slow if
+                  using 'ward linkage'. hclust could be very slow if
                   you have >1000 submatrices per chromosome. In those
-                  cases, you might prefer --kmeans">
-            <option value="--kmeans">kmenas</option>
+                  cases, you might prefer kmeans.">
+            <option value="--kmeans">kmeans</option>
             <option value="--hclust">hclust (#clusters per chromosome)</option>
         </param>
 
@@ -111,15 +112,18 @@
             help="Clustering is by default carried out on the whole
                   submatrices. If this parameter is given, the
                   clustering is only carried out based on the submatrix
-                  diagonal (representing values at the same distance to each other)" />
+                  diagonal (representing values at the same distance to each other)." />
 
         <param argument="--plotType" type="select" optional="true" label="Plot type">
             <option value="2d">2D</option>
             <option value="3d">3D</option>
         </param>
         <expand macro="colormap" />
-        <param argument="--vMin" type="float" optional="true" label="vMin"/>
-        <param argument="--vMax" type="float" optional="true" label="vMax"/>
+        <param argument="--vMin" type="float" optional="true" label="vMin"
+            help= "Minimum value of the plotted score." />
+
+        <param argument="--vMax" type="float" optional="true" label="vMax"
+            help= "Maximum value of the plotted score." />
 
         <param name="image_file_format" type="select" label="Image output format">
             <option value="png" selected="True">png</option>
@@ -134,7 +138,7 @@
 
     </inputs>
     <outputs>
-        <data name="outFileName" from_work_dir="plot" format="png" label="${tool.name} on ${on_string}">
+        <data name="outFileName" from_work_dir="plot" format="png" label="${tool.name} on ${on_string}: Plot">
             <change_format>
                 <when input="image_file_format" value="svg" format="svg" />
             </change_format>
@@ -161,34 +165,50 @@
         </test>
     </tests>
     <help><![CDATA[
-  --outFilePrefixMatrix OUTFILEPREFIXMATRIX
-                        If this option is given, then the values underlying
-                        the final matrix will be saved to tab-delimited tables
-                        (one per chromosome) using the indicated prefix, for
-                        example TSS_to_TSS_chrX.tab. If clustering is
-                        performed, then the values are saved including the
-                        cluster_id a in TSS_to_TSS_chrX_cluster_1.tab
-  --outFilePrefixClusterContactPositions OUTFILEPREFIXCLUSTERCONTACTPOSITIONS
-                        If this option is given, then the position of the
-                        contacts is saved as (chrom1, start1, end1, chrom2,
-                        start2, end2) where chrom_n, start_n, end_n correspond
-                        to the pair ofpositions used to compute the submatrix.
-                        The data is saved per chromosome and per cluster
-                        separatedly (one file each)
-  --diagnosticHeatmapFile DIAGNOSTICHEATMAPFILE
-                        If given, a heatmap file (per chromosome) is saved.
-                        Each row in the heatmap contains thediagonal of each
-                        of the submatrices centered on the bed file. This file
-                        is useful to get an idea of the values that are used
-                        for the aggregate matrix and to determine the fraction
-                        of sub-matrices that are aggregated that may have an
-                        enrichment at the center.
+Aggregation of Hi-C contacts
+============================
+
+**hicAggregateContacts** allows plotting of aggregated Hi-C sub-matrices of a specified list of positions. Positions of interest can for example be binding sites of a specific protein that were determined by ChIP-seq or genetic elements as transcription start sites of active genes.
+
+_________________
+
+Usage
+-----
+
+This tool must be used on Hi-C matrices corrected by ``hicCorrectMatrix``. One should also consider bigger bins than restriction enzyme resolution bins using ``hicMergeMatrixBins``.
+
+_________________
+
+Optional parameters
+-------------------
+
+Optional data output can be selected:
 
+    - **Save values underlying the final matrix:** if this option is given, then the values underlying the final matrix will be saved to tab-delimited tables (one per chromosome) using the indicated prefix, for example TSS_to_TSS_chrX.tab. If clustering is performed, then the values are saved including the cluster_id a in TSS_to_TSS_chrX_cluster_1.tab
 
+    - **Save the position of the contacts:** if this option is given, then the position of the contacts is saved as (chrom1, start1, end1, chrom2, start2, end2) where chrom_n, start_n, end_n correspond to the pair of positions used to compute the submatrix. The data is saved per chromosome and per cluster separately (one file each).
+
+    - **Heatmap file per chromosome:** if given, a heatmap file (per chromosome) is saved. Each row in the heatmap contains the diagonal of each of the submatrices centered on the bed file. This file is useful to get an idea of the values that are used for the aggregate matrix and to determine the fraction of submatrices that are aggregated that may have an enrichment at the center.
+
+_________________
+
+Output
+------
+
+**hicAggregateContacts** outputs a plot of aggregated contacts.
+
+Below, you can find an example of an aggregate Hi-C matrix obtained from *Drosophila melanogaster* Hi-C data. The interactions are plotted at binding sites of a protein that were determined by ChIP-seq. We plot sub-matrices of 30 bins (1.5 kb bin size, 45 kb in total). The regions specified in the BED file will be centered between half number of bins and the other half number of bins.The considered range is 300-1000 kb. The range should be adjusted and only contain contacts larger than TAD size to reduce background interactions.
+
+.. image:: $PATH_TO_IMAGES/hicAggregateContacts.png
+
+This example was calculated using mean interactions of an observed vs. expected transformed Hi-C matrix. Additional options for the matrix transformation are total-counts or z-score. Aggregate contacts can be plotted in 2D or 3D.
+
+_________________
 
 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
 
 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
+.. _Colormaps: https://matplotlib.org/examples/color/colormaps_reference.html
 ]]></help>
     <expand macro="citations" />
 </tool>