diff hicPlotTADs.xml @ 4:50502e2beaaa draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04

--- a/hicPlotTADs.xml	Mon Nov 27 11:14:58 2017 -0500
+++ b/hicPlotTADs.xml	Sat Dec 16 16:36:29 2017 -0500
@@ -577,10 +577,38 @@
     </tests>
     <help><![CDATA[
 
-**What it does**
+Plot TADs
+=========
+
+``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.
 
-Plots the diagonal, and some values close to the diagonal of a Hi-C matrix. The diagonal of the matrix is plotted horizontally for a region.
+Input
+-----
+- 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
 
+For each track parameters for the color, the width or the font size can be defined.
+
+Output
+------
+An output looks like this:
+
+
+.. image:: $PATH_TO_IMAGES/master_TADs_plot.png
+   :width: 80 %
+
+| For more information about HiCExplorer please consider our documentation on readthedocs.io_
+
+.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
 ]]></help>
     <expand macro="citations" />
 </tool>