Mercurial > repos > bgruening > hicexplorer_hiccomparematrices

annotate hicCompareMatrices.xml @ 6:a54c1b5698fa draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
author bgruening
date Wed, 05 Feb 2020 19:50:41 -0500
parents 55b4b8bc250d
children 80abd5e2922a
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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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9 ln -s '$matrix1' 'matrix1.$matrix1.ext' &&
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10 ln -s '$matrix2' 'matrix2.$matrix2.ext' &&
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13 @BINARY@
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14 --matrices 'matrix1.$matrix1.ext' 'matrix2.$matrix2.ext'
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15 --operation $operation
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16 --outFileName 'matrix.$matrix1.ext'
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18 && mv 'matrix.$matrix1.ext' matrix
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19 ]]>
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20 </command>
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21 <inputs>
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22 <param name='matrix1' type="data" format="h5,cool"
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23 label="First matrix"/>
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24 <param name='matrix2' type="data" format="h5,cool"
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25 label="Second matrix to compare against the first"/>
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27 <param name='operation' type='select' label="Operation to be used for the comparison">
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28 <option value='diff'>diff</option>
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29 <option value="ratio">ratio</option>
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30 <option value="log2ratio">log2ratio</option>
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31 </param>
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32 </inputs>
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33 <outputs>
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34 <data name="outFileName" from_work_dir="matrix" format="cool" label="${tool.name} MATRIX on ${on_string}">
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35 <change_format>
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36 <when input_dataset="matrix1" attribute="ext" value="h5" format="h5"/>
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37 </change_format>
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38 </data>
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39 </outputs>
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40 <tests>
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41 <test>
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42 <param name="matrix1" value="small_test_matrix.h5"/>
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43 <param name="matrix2" value="small_test_matrix.h5"/>
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44 <param name="operation" value='log2ratio' />
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45 <output name="outFileName" ftype="h5">
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46 <assert_contents>
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47 <has_h5_keys keys='intervals,matrix'/>
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48 </assert_contents>
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49 </output>
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50 </test>
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52 </tests>
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53 <help><![CDATA[
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54 Comparison of Hi-C matrices
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55 ===========================
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57 This tool is useful to compare two matrices by applying operations like difference, ratio or log2ratio after normalization. To
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58 normalize the matrices, each element is divided by the sum of the matrix.
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59
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60 **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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61 or to see TAD structure modifications near differentially expressed genes between two conditions when followed by ``hicPlotMatrix``.
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62 It can also be used to compare two biological replicates.
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63
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64 _________________
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65
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66 Usage
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67 -----
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68
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69 **hicCompareMatrices** is usually perfomed on corrected matrices (``hicCorrectMatrix``) with bins merged (``hicMergeMatrixBins``) depending
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70 on the downstream analyses to perform (visualisation of a whole chromosome, or of a small region, etc).
0
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71
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72 _________________
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73
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74 Output
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75 ------
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76
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77 Here is an example of a log2ratio comparison between M1BP Knockdown and GST cells in
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78 *Drosophila melanogaster* on corrected matrices with 50 bins merged (about 30kb bins) plotted using ``hicPlotMatrix``.
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79
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80 .. image:: $PATH_TO_IMAGES/hicCompareMatrices_m1bp_over_gst_log2_m50_matrix_plot.png
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81 :width: 50%
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82
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83 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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85 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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87 .. image:: $PATH_TO_IMAGES/hicCompareMatrices_QC_log2_m50_matrix_plot.png
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88 :width: 50%
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89
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90 _________________
0
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92 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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94 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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95 ]]></help>
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96 <expand macro="citations" />
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97 </tool>