diff hicFindTADs.xml @ 4:8b60271e7e54 draft

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

--- a/hicFindTADs.xml	Mon Nov 27 11:12:30 2017 -0500
+++ b/hicFindTADs.xml	Sat Dec 16 16:32:17 2017 -0500
@@ -111,11 +111,66 @@
         </test>
     </tests>
     <help><![CDATA[
+Calculate TADs
+==============
 
-**What it does**
+Topological associated domains (TADs) are regions on the DNA which tend to interact within the region a lot, but not outside their boundaries. More information_.
+
+Calculation
+------------
+``hicFindTADs`` computes the TAD regions in two steps: In a first step it computes a TAD-separation score based on a z-score matrix for all bins. The z-score is defined as:
+
+“The absolute value of z represents the distance between the raw score and the population mean in 
+units of the standard deviation. z is negative when the raw score is below the mean, positive when above.” 
+[Source_].
+
+.. image:: $PATH_TO_IMAGES/z-score.svg
+   :width: 150
+   
+`Source of image <https://wikimedia.org/api/rest_v1/media/math/render/svg/5ceed701c4042bb34618535c9a902ca1a937a351>`_
+
+In our case the distribution describes the counts per bin of a genomic distance. In a second step the local minima of the TAD-separation score is evaluated with respect to the surrounding bins to assign a p-value. Two multiple testing corrections can be applied to filter the results: `Bonferroni <https://en.wikipedia.org/wiki/Bonferroni_correction>`_ or the `false discovery rate <https://en.wikipedia.org/wiki/False_discovery_rate>`_.
+
+
+Input
+-----
 
-Uses the graph clustering measure "conductance" to find minimum cuts that correspond to boundaries.
+Parameters
+__________
+- contact matrix to compute the TADs on
+- minimum window length
+- maximum window length
+- step size
+- multiple testing correction
+- minimum threshold
+- minimum distance
+
+
+hicFindTADs tries to identify sensible parameters but those can be change to identify more stringent set of boundaries.
+
+Output
+------
 
+- Boundary positions as a bed file
+- Matrix with multi-scale TAD scores as a bedgraph 
+- TAD domains as a bed file
+- Boundary information plus score as gff
+- TAD information in bm file
+- Z-score matrix in h5
+
+The calulated TAD regions can be plotted with ``hicPlotTADs``.
+
+
+.. 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
+.. _Source: https://en.wikipedia.org/wiki/Standard_score#Calculation_from_raw_score 
+.. _information: https://en.wikipedia.org/wiki/Topologically_associating_domain_
 ]]></help>
     <expand macro="citations" />
 </tool>