Mercurial > repos > bgruening > hicexplorer_hictransform

annotate hicTransform.xml @ 18:fd9fcf27561b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
author iuc
date Mon, 01 Jul 2024 19:05:26 +0000
parents e63824ecb435
children
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fd9fcf27561b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
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1 <tool id="hicexplorer_hictransform" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>transform a matrix to obs/exp, pearson and covariance matrices</description>
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3 <macros>
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4 <token name="@BINARY@">hicTransform</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
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10 ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
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11 @BINARY@ --matrix 'matrix.$matrix_h5_cooler.ext'
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12 --method $method_selector
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13 #if $ligation_factor:
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14 $ligation_factor
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15 #end if
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16 $perChromosome
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17 #set chroms = ' '.join([ '\'' + str($var.chromosome) + '\'' for $var in $chromosomeOrder ])
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18 #if chroms:
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19 --chromosomes $chroms
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20 #end if
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21 --outFileName 'out_matrix.$matrix_h5_cooler.ext'
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22
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23 && mv 'out_matrix.$matrix_h5_cooler.ext' matrix
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24 ]]>
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25 </command>
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26 <inputs>
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27 <expand macro="matrix_h5_cooler_macro" />
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28 <param name="method_selector" type="select" label="Choose method to apply">
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29 <option value="obs_exp" selected="True">obs / exp</option>
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30 <option value="obs_exp_lieberman">obs / exp (Lieberman-Aiden 2009)</option>
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31 <option value="obs_exp_non_zero">obs / exp (exclude non-zero from exp)</option>
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32 <option value="pearson">pearson</option>
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33 <option value="covariance">covariance</option>
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34 </param>
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35 <param name="ligation_factor" type="boolean" truevalue="--ligation_factor" falsevalue="" checked="false" label="Multiplies a scaling factor to each entry of the expected matrix to take care of the proximity ligation" />
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36 <param argument="--perChromosome" type="boolean" truevalue="--perChromosome" falsevalue="" checked="false" label="Computation per chromosome" />
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37 <repeat name="chromosomeOrder" min="0" title="Chromosomes to include in the computation">
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38 <param name="chromosome" type="text">
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39 <validator type="empty_field" />
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40 <validator type="expression" message="Only alphanumeric characters and the underscore can be used in chromosome names">value.replace('_', '').isalnum()</validator>
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41 </param>
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42 </repeat>
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43 </inputs>
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44 <outputs>
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45 <data name="matrix_out" from_work_dir="matrix" format="cool" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: $method_selector">
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46 <change_format>
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47 <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5" />
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48 </change_format>
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49 </data>
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50 </outputs>
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51 <tests>
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52 <test>
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53 <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
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54 <param name="method_selector" value="obs_exp_lieberman" />
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55 <output name="matrix_out" ftype="h5">
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56 <assert_contents>
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57 <has_h5_keys keys="intervals,matrix" />
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58 </assert_contents>
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59 </output>
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60 </test>
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61 <test>
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62 <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
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63 <param name="method_selector" value="obs_exp_lieberman" />
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64 <param name="ligation_factor" value="True" />
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65 <output name="matrix_out" ftype="h5">
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66 <assert_contents>
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67 <has_h5_keys keys="intervals,matrix" />
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68 </assert_contents>
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69 </output>
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70 </test>
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71 </tests>
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72 <help><![CDATA[
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73 Transformation of matrix for plotting
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74 =====================================
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75
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76 **hicTransform** computes a matrix based on one Hi-C contact matrix as input:
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77
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78 - An **observed/expected matrix** obtained "by dividing each entry in the contact matrix by the genome-wide average contact probability for loci at that genomic distance" (`Lieberman-Aiden et al. (2009)`_). This transformation allows to better assess long range interactions.
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79 - An **observed/expected norm matrix** which computes the expected matrix as EXP_i,j = sum(diagonal(i-j)) * sum(row(j)) * sum(row(i)) / sum(matrix)
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80 - An **observed/expected non-zero values matrix** which computes the expected matrix as the sum per genomic distance j divided by sum of non-zero contacts: sum(diagonal(j) / number of non-zero elements in diagonal(j)
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81 - A **Pearson correlation matrix** obtained by computing the Pearson correlation between each bin based on observed/expected values. This matrix transformation allows to better identify the bins that are entering in contact together, or not, at long ranges, and thus helps defining compartments in the nucleus (``hicPCA``).
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82 - A **covariance matrix**, which is used as a basis for the Principal Component Analysis (PCA) to compute the eigenvectors outputed by **hicTransform**.
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83
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84 These matrices can be used with ``hicPlotMatrix`` or ``pyGenomeTracks`` for a visualization of the A / B compartment analysis.
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85
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86 _________________
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88 Output
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89 ------
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90
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91 From one Hi-C contact matrix, **hicTransform** outputs a matrix with the selected method applied.
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93 _________________
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95 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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97 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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98 .. _`Lieberman-Aiden et al. (2009)`: https://pubmed.ncbi.nlm.nih.gov/19815776/
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99 ]]> </help>
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100 <expand macro="citations" />
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101 </tool>