view hicMergeMatrixBins.xml @ 2:cdff00acac0f draft

planemo upload for repository commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
author iuc
date Sat, 16 Dec 2017 16:33:36 -0500
parents a1cf508bff84
children 5186eda61ca4
line wrap: on
line source

<tool id="hicexplorer_hicmergematrixbins" name="@BINARY@" version="@WRAPPER_VERSION@.0">
    <description>Merges bins from a Hi-C matrix</description>
        <token name="@BINARY@">hicMergeMatrixBins</token>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[

        ln -s '$matrix' input.npz.h5 &&

            --matrix input.npz.h5
            --numBins $numBins
            --outFileName ./out.npz.h5

        <param argument="--matrix" type="data" format="h5" label="Matrix to reduce" />
        <param argument="--numBins" type="integer" min="1" value="3" label="Number of bins to merge" />
        <param argument="--runningWindow" type="boolean" falsevalue="" truevalue="--runningWindow" label="Merge using a running window of length --numBins" />
        <data name="outFileName" from_work_dir="out.npz.h5" format="h5"/>
            <param name="matrix" value="small_test_matrix.h5" />
            <param name="numBins" value="5" />
            <output name="outFileName" file="hicMergeMatrixBins_result1.npz.h5" ftype="h5" compare="sim_size" delta="24000" />

Change matrix resolution

``hicMergeMatrixBins`` is used to decrease the resolution of a matrix. With this tool you can create out of a 100 kb 
contact matrix a 1000 kb one:

Number of bins to merge = 10

100 kb * 10 = 1000 kb = 1 Mb

This functionality is useful especially for plotting. The higher the resolution of an contact matrix is, the more likely it is to run out of memory while plotting. This is caused by the circumstances that we compute internally with a sparse matrices but to plot we need a dense one. Furthermore, the higher the resolution of a matrix the more detailed it is which can make it difficult to interpret, especially if the read depth of the Hi-C data is not high.


- contact matrix to change the resolution on
- Number of bins to merge
- running window


A contact matrix with the resolution ``original resolution * number of bins``.

| For more information about HiCExplorer please consider our documentation on readthedocs.io_

    <expand macro="citations" />