comparison hicBuildMatrix.xml @ 4:652fdcbff650 draft

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

3:2a13bfe5bff2

<tool id="hicexplorer_hicbuildmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">
    <description>creates a matrix of interactions</description>
    <macros>
        <token name="@BINARY@">hicBuildMatrix</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" >

            <output name="outFileName" file="small_test_matrix.h5" ftype="h5" compare="sim_size" delta="30000"/>
        </test>
    </tests>
    <help><![CDATA[

**What it does**

Creates a matrix of interactions.

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

4:652fdcbff650

<tool id="hicexplorer_hicbuildmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">
    <description>creates a contact matrix</description>
    <macros>
        <token name="@BINARY@">hicBuildMatrix</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" >

            <output name="outFileName" file="small_test_matrix.h5" ftype="h5" compare="sim_size" delta="30000"/>
        </test>
    </tests>
    <help><![CDATA[

Creation of the contact matrix
===============================

``hicBuildMatrix`` creates a contact matrix based on Hi-C read pairs. It requires two sam or bam files 
corresponding to the first and second mates of the paired-end H-C reads. The sam and bam files should
 not be sorted by position. There are two main options to create the Hi-C contact matrix, either by 
fixed bin size (eg. 10.000 bp) or by bins of variable restriction fragment size length. 
``hicBuildMatrix`` generates a quality control output that can be used to analyze the quality of the Hi-C reads.

Input
-----

`hicBuildMatrix` is having the following parameters:

Parameters
__________


- two input BAM/SAM files
- a bin size
- a restriction cut file as an alternative to the bin size
- restriction sequence: e.g. HindIII: GATC



Output
------

`hicBuildMatrix` creates as an output:
    - the contact matrix
    - a bam file with the accepted alignments
    - a quality report.

Example plot
-----------------------------------------------------------------
.. image:: $PATH_TO_IMAGES/SRR027956.svg
   :width: 70%

Contact matrix created with `hicPlotMatrix`.

Quality report
--------------

The quality report gives you information about:

- how many pairs were used to build the contact matrix
- dangling end pairs: These are reads that start with the restriction site and constitute reads that were digested but no ligated.
- same fragment pairs: These are read mates, facing inward, separated by up to 800 bp that do not have a restriction enzyme in between. These read pairs are not valid Hi-C pairs.
- self circles: Self circles are defined as pairs within 25kb with 'outward' read orientation
- self ligations: These are read pairs with a restriction site in between that are within 800 bp.

Contact distance:
_________________
- inter chromosomal
- short range < 20 kb
- long range

Read orientation:
_________________
- inward pairs
- outward pairs
- left pairs
- right pairs 

.. image:: $PATH_TO_IMAGES/hicQC.png
   :width: 70 %

| 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>