Mercurial > repos > bgruening > hicexplorer_hiccomparematrices

annotate hicCompareMatrices.xml @ 12:826a6ac07f93 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa140a9f660eab2459e21b0b637b129d7de24c02
author iuc
date Tue, 10 Jan 2023 19:14:50 +0000
parents 80abd5e2922a
children 3ee5332bf57c
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1 <tool id="hicexplorer_hiccomparematrices" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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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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12 @BINARY@
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13 --matrices 'matrix1.$matrix1.ext' 'matrix2.$matrix2.ext'
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14 --operation $operation
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15 --outFileName 'matrix.$matrix1.ext'
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17 && mv 'matrix.$matrix1.ext' matrix
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18 ]]>
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19 </command>
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20 <inputs>
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21 <param name='matrix1' type="data" format="h5,cool" label="First matrix" />
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22 <param name='matrix2' type="data" format="h5,cool" label="Second matrix to compare against the first" />
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24 <param name='operation' type='select' label="Operation to be used for the comparison">
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25 <option value='diff'>diff</option>
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26 <option value="ratio">ratio</option>
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27 <option value="log2ratio">log2ratio</option>
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28 </param>
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29 </inputs>
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30 <outputs>
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31 <data name="outFileName" from_work_dir="matrix" format="cool" label="${tool.name} MATRIX on ${on_string}">
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32 <change_format>
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33 <when input_dataset="matrix1" attribute="ext" value="h5" format="h5" />
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34 </change_format>
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35 </data>
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36 </outputs>
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37 <tests>
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38 <test>
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39 <param name="matrix1" value="small_test_matrix.h5" />
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40 <param name="matrix2" value="small_test_matrix.h5" />
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41 <param name="operation" value='log2ratio' />
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42 <output name="outFileName" ftype="h5">
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43 <assert_contents>
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44 <has_h5_keys keys='intervals,matrix' />
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45 </assert_contents>
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46 </output>
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47 </test>
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49 </tests>
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50 <help><![CDATA[
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52 Comparison of Hi-C matrices
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53 ===========================
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55 This tool is useful to compare two matrices by applying operations like difference, ratio or log2ratio after normalization. To
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56 normalize the matrices, each element is divided by the sum of the matrix.
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58 **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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59 or to see TAD structure modifications near differentially expressed genes between two conditions when followed by ``hicPlotMatrix``.
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60 It can also be used to compare two biological replicates.
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62 _________________
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64 Usage
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65 -----
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67 **hicCompareMatrices** is usually perfomed on corrected matrices (``hicCorrectMatrix``) with bins merged (``hicMergeMatrixBins``) depending
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68 on the downstream analyses to perform (visualisation of a whole chromosome, or of a small region, etc).
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70 _________________
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72 Output
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73 ------
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75 Here is an example of a log2ratio comparison between M1BP Knockdown and GST cells in
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76 *Drosophila melanogaster* on corrected matrices with 50 bins merged (about 30kb bins) plotted using ``hicPlotMatrix``.
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78 .. image:: $PATH_TO_IMAGES/hicCompareMatrices_m1bp_over_gst_log2_m50_matrix_plot.png
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79 :width: 50%
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81 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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82
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83 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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85 .. image:: $PATH_TO_IMAGES/hicCompareMatrices_QC_log2_m50_matrix_plot.png
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86 :width: 50%
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88 _________________
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90 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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92 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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80abd5e2922a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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93 ]]> </help>
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94 <expand macro="citations" />
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95 </tool>