Mercurial > repos > bgruening > hicexplorer_hiccomparematrices
annotate hicCompareMatrices.xml @ 4:6d2c4187805b draft
"planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 91a0182476a7fc26be7bef1677790518c4e88348-dirty"
author | bgruening |
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date | Mon, 16 Dec 2019 08:39:14 -0500 |
parents | 08e157ceda6f |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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1 <tool id="hicexplorer_hiccomparematrices" name="@BINARY@" version="@WRAPPER_VERSION@.0"> |
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08e157ceda6f
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
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2 <description>normalize and compare two Hi-C contact matrices</description> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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3 <macros> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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4 <token name="@BINARY@">hicCompareMatrices</token> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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5 <import>macros.xml</import> |
a0ab04565c73
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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6 </macros> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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7 <expand macro="requirements" /> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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8 <command detect_errors="exit_code"><![CDATA[ |
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9 |
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10 @BINARY@ |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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11 --matrices '$matrix1' '$matrix2' |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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12 --operation $operation |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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13 --outFileName matrix.$outputFormat |
a0ab04565c73
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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14 |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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15 && mv matrix.$outputFormat matrix |
a0ab04565c73
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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16 ]]> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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17 </command> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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18 <inputs> |
a0ab04565c73
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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19 <param name='matrix1' type="data" format="h5,cool" |
a0ab04565c73
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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20 label="First matrix"/> |
a0ab04565c73
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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21 <param name='matrix2' type="data" format="h5,cool" |
a0ab04565c73
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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22 label="Second matrix to compare against the first"/> |
a0ab04565c73
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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23 |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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24 <param name='operation' type='select' label="Operation to be used for the comparison"> |
a0ab04565c73
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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25 <option value='diff'>diff</option> |
a0ab04565c73
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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26 <option value="ratio">ratio</option> |
a0ab04565c73
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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27 <option value="log2ratio">log2ratio</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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28 </param> |
a0ab04565c73
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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29 <param name='outputFormat' type='select' label="Output file format"> |
a0ab04565c73
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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30 <option value='h5'>HiCExplorer format</option> |
a0ab04565c73
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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31 <option value="cool">cool</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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32 </param> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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33 </inputs> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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34 <outputs> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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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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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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36 <change_format> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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37 <when input="outputFormat" value="cool" format="cool" /> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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38 </change_format> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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39 </data> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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40 </outputs> |
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41 <tests> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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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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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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46 <param name="outputFormat" value="h5" /> |
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"planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 91a0182476a7fc26be7bef1677790518c4e88348-dirty"
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47 <output name="outFileName" file="compare_matrices_log2ratio.h5" ftype="h5" compare="sim_size" delta='10000'/> |
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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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56 |
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57 </tests> |
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58 <help><![CDATA[ |
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59 Comparison of Hi-C matrices |
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60 =========================== |
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61 |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
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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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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
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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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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
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75 on the downstream analyses to perform (visualisation of a whole chromosome, or of a small region, etc). |
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76 |
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77 _________________ |
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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 |
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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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96 |
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97 | For more information about HiCExplorer please consider our documentation on readthedocs.io_ |
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98 |
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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> |