Mercurial > repos > bgruening > hicexplorer_hiccomparematrices

annotate hicCompareMatrices.xml @ 2:915015cbcc0a draft

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author iuc
date Fri, 27 Apr 2018 08:41:21 -0400
parents 08e157ceda6f
children 6d2c4187805b
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1 <tool id="hicexplorer_hiccomparematrices" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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2 <description>normalize and compare two Hi-C contact matrices</description>
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3 <macros>
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4 <token name="@BINARY@">hicCompareMatrices</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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10 @BINARY@
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11 --matrices '$matrix1' '$matrix2'
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12 --operation $operation
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13 --outFileName matrix.$outputFormat
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15 && mv matrix.$outputFormat matrix
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16 ]]>
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17 </command>
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18 <inputs>
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19 <param name='matrix1' type="data" format="h5,cool"
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20 label="First matrix"/>
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21 <param name='matrix2' type="data" format="h5,cool"
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22 label="Second matrix to compare against the first"/>
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23
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24 <param name='operation' type='select' label="Operation to be used for the comparison">
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25 <option value='diff'>diff</option>
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26 <option value="ratio">ratio</option>
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27 <option value="log2ratio">log2ratio</option>
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28 </param>
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29 <param name='outputFormat' type='select' label="Output file format">
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30 <option value='h5'>HiCExplorer format</option>
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31 <option value="cool">cool</option>
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32 </param>
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33 </inputs>
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34 <outputs>
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35 <data name="outFileName" from_work_dir="matrix" format="h5" label="${tool.name} MATRIX on ${on_string}">
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36 <change_format>
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37 <when input="outputFormat" value="cool" format="cool" />
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38 </change_format>
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39 </data>
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40 </outputs>
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41 <tests>
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42 <test>
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43 <param name="matrix1" value="small_test_matrix.h5"/>
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44 <param name="matrix2" value="small_test_matrix.h5"/>
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45 <param name="operation" value='log2ratio' />
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46 <param name="outputFormat" value="h5" />
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47 <output name="outFileName" file="compare_matrices_log2ratio.h5" ftype="h5" compare="sim_size" delta='2000'/>
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48 </test>
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49 <test>
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50 <param name="matrix1" value="pearson_small_50kb.cool"/>
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51 <param name="matrix2" value="pearson_small_50kb.cool"/>
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52 <param name="operation" value='ratio' />
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53 <param name="outputFormat" value="cool" />
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54 <output name="outFileName" file="compare_matrices_pearson_ratio.cool" ftype="cool" compare="sim_size" delta='2000'/>
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55 </test>
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57 </tests>
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58 <help><![CDATA[
1
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59 Comparison of Hi-C matrices
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60 ===========================
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61
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62 This tool is useful to compare two matrices by applying operations like difference, ratio or log2ratio after normalization. To
08e157ceda6f planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
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63 normalize the matrices, each element is divided by the sum of the matrix.
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64
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65 **hicCompareMatrices** can be used for example to determine the effect of a mutation compared to wild-type samples on contact enrichment,
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66 or to see TAD structure modifications near differentially expressed genes between two conditions when followed by ``hicPlotMatrix``.
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67 It can also be used to compare two biological replicates.
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68
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69 _________________
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70
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71 Usage
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72 -----
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73
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74 **hicCompareMatrices** is usually perfomed on corrected matrices (``hicCorrectMatrix``) with bins merged (``hicMergeMatrixBins``) depending
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75 on the downstream analyses to perform (visualisation of a whole chromosome, or of a small region, etc).
0
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76
1
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77 _________________
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78
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79 Output
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80 ------
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81
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82 Here is an example of a log2ratio comparison between M1BP Knockdown and GST cells in
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83 *Drosophila melanogaster* on corrected matrices with 50 bins merged (about 30kb bins) plotted using ``hicPlotMatrix``.
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84
1
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85 .. image:: $PATH_TO_IMAGES/hicCompareMatrices_m1bp_over_gst_log2_m50_matrix_plot.png
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86 :width: 50%
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87
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88 In this plot we see that the cells with a M1BP Knockdown display a negative log2ratio compared to the wild-type. Depletion of M1BP thus show a dramatic effect on the distribution of Hi-C contacts in which short range contacts decrease (Ramirez *et al.* 2017, High-resolution TADs reveal DNA sequences underlying genome organization in flies, https://doi.org/10.1038/s41467-017-02525-w).
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89
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90 Below you can find an example of a log2ratio plot between Hi-C matrices of two biological replicates, no differences are observable which means that the replicates are well correlated.
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91
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92 .. image:: $PATH_TO_IMAGES/hicCompareMatrices_QC_log2_m50_matrix_plot.png
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93 :width: 50%
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94
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95 _________________
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97 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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99 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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100 ]]></help>
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101 <expand macro="citations" />
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102 </tool>