comparison hicPlotTADs.xml @ 4:50502e2beaaa draft

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

3:6323d728dbab

            <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="35000" />
        </test>
    </tests>
    <help><![CDATA[

**What it does**

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.

]]></help>
    <expand macro="citations" />
</tool>

4:50502e2beaaa

            <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="35000" />
        </test>
    </tests>
    <help><![CDATA[

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.

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
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</tool>