diff hicPlotDistVsCounts.xml @ 4:ed96f2fd7e3f draft

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

--- a/hicPlotDistVsCounts.xml	Mon Nov 27 11:16:45 2017 -0500
+++ b/hicPlotDistVsCounts.xml	Sat Dec 16 16:31:27 2017 -0500
@@ -76,15 +76,42 @@
         </test>
     </tests>
     <help><![CDATA[
-
-**What it does**
+Relation of genomic distance and number of contacts
+========================================================
 
-This program makes a distance vs. Hi-C counts plots. It can use several matrix files to compare
-them. If the `--perchr` option is given, each chromosome is plotted independently. In the case
-of more than one matrix, multiple plots are created, one per chromosome. When plotting multiple
-matrices denser matrices are scaled down to match the sum of the smaller matrix.
+| This program makes a distance vs. Hi-C counts plots. It can use several matrix files to compare
+| them. If the ``--perchr`` option is given, each chromosome is plotted independently. In the case
+| of more than one matrix, multiple plots are created, one per chromosome. When plotting multiple
+| matrices denser matrices are scaled down to match the sum of the smaller matrix.
+|
+| For more information about HiCExplorer please consider our documentation on readthedocs.io_
 
 
+Input
+-----
+
+Parameters
+__________
+- contact matrix
+- skip diagonal
+- per chromosome
+- max depth
+- plot size
+- chromosome(s) to exclude
+
+Output
+-------
+Output if all data in the contact matrix is considered:
+
+.. image:: $PATH_TO_IMAGES/hicPlotDistVsCounts_result1.png
+   :width: 70%
+
+Output if the distance vs. Hi-C contact counts is computed and plotted per chromosome:
+
+.. image:: $PATH_TO_IMAGES/hicPlotDistVsCounts_result2.png
+   :width: 80% 
+
+.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
 ]]></help>
     <expand macro="citations" />
 </tool>