Mercurial > repos > bgruening > hicexplorer_hicmergematrixbins

annotate hicMergeMatrixBins.xml @ 13:4d8f5bb39a78 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
author iuc
date Mon, 16 Dec 2019 22:46:46 +0000
parents 5b298225b9b4
children 566cc39d8d04
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1 <tool id="hicexplorer_hicmergematrixbins" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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2 <description>merge adjacent bins from a Hi-C contact matrix to reduce its resolution</description>
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3 <macros>
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4 <token name="@BINARY@">hicMergeMatrixBins</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
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10 @BINARY@
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11 --matrix 'matrix.$matrix_h5_cooler.ext'
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12 --numBins $numBins
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13 $runningWindow
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14 --outFileName 'matrix.$matrix_h5_cooler.ext'
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15 && mv 'matrix.$matrix_h5_cooler.ext' matrix
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17 ]]>
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18 </command>
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19 <inputs>
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20 <expand macro='matrix_h5_cooler_macro' />
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21
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22 <param argument="--numBins" type="integer" min="1" value="3" label="Number of bins to merge" />
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23 <param argument="--runningWindow" type="boolean" falsevalue="" truevalue="--runningWindow" label="Set to merge for using a running window of length --numBins. Usually not set." />
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24 </inputs>
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25 <outputs>
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26 <data name="outFileName" from_work_dir="matrix" format="cool">
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27 <change_format>
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28 <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5"/>
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29 </change_format>
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30 </data>
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
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35 <param name="numBins" value="5" />
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36 <output name="outFileName" ftype="h5">
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37 <assert_contents>
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38 <has_h5_keys keys='intervals,matrix,nan_bins'/>
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39 </assert_contents>
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40 </output>
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41 </test>
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42 </tests>
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43 <help><![CDATA[
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44
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45 Change matrix resolution
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46 ========================
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48 **hicMergeMatrixBins** is used to decrease the resolution of a matrix. With this tool, you can for example create out of a 100 kb
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49 contact matrix a 1000 kb one:
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51 Number of bins to merge = 10
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53 100 kb * 10 = 1000 kb = 1 Mb
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55 Depending on the downstream analyses to perform on a Hi-C matrix generated with HiCExplorer, one might need different bin resolutions. For example using ``hicPlotMatrix`` to display chromatin interactions of a whole chromosome will not produce any meaningful vizualisation if it is performed on a matrix at restriction sites resolution (unmerged). Furthermore, the higher the resolution of a matrix, the more detailed it is, which can make it
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56 difficult to interpret, especially if the read depth of the Hi-C data is not high enough. **hicMergeMatrixBins** address these issues by merging a given number of adjacent bins to reduce Hi-C matrices resolution.
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58 _________________
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60 Usage
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61 -----
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63 To limit the loss of information, it is mandatory to perform **hicMergeMatrixBins** on matrices prior to any correction and any other bin merging (direct output from ``hicBuildMatrix``). After bin merging, ``hicCorrectMatrix`` must be used for downstream analyses requiring corrected matrices.
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65 _________________
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67 Output
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68 ------
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69
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70 **hicMergeMatrixBins** outputs a Hi-C matrix with reduced resolution.
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72 Below, we will develop the example of a Hi-C matrix in *Drosophila melanogaster* that we want to display at the whole X-chromosome scale and at the scale of a 1Mb region of the X chromosome. To do this, we performed two different bin merging using **hicMergeMatrixBins** on an uncorrected matrix built at the restiction sites resolution using ``hicBuildMatrix``.
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74 Starting from a matrix with bins of a median length of 529bp (restriction enzyme resolution, here DpnII), running **hicMergeMatrixBins** with a number of bins to merge of 3 produced a matrix with bins of a median length of 1661bp, while **hicMergeMatrixBins** with a number of bins to merge of 50 produced a matrix with bins of a median length of 29798bp.
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76 After the correction of these three matrices using ``hicCorrectMatrix``, we plotted them using ``hicPlotMatrix`` at the scale of the whole X-chromosome and at the scale of the X:2000000-3000000 region to see the effect of bin merging on the interactions visualization.
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78 - **Effect of bins merging at the scale of a chromosome:**
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80 .. image:: $PATH_TO_IMAGES/hicMergeMatrixBins_Xchr.png
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81 :width: 60 %
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82
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83 When observed altogether, the plots above show that the merging of bins by 50 is the most adequate way to plot interactions for a whole chromosome in *Drosophila melanogaster* when starting from a matrix with bins of a median length of 529bp.
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84
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85 - **Effect of bins merging at the scale of a specific region:**
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86
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87 .. image:: $PATH_TO_IMAGES/hicMergeMatrixBins_Xregion.png
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88 :width: 60 %
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89
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90 When observed altogether, the plots above show that the merging of bins by 3 is the most adequate way to plot interactions for a region of 1Mb in Drosophila melanogaster when starting from a matrix with bins of a median length of 529bp.
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91
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92 _________________
2
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93
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94 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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95
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96 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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97 ]]></help>
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98 <expand macro="citations" />
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99 </tool>