Mercurial > repos > bgruening > hicexplorer_hicdetectloops

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 79133bc3739fbcc6c2055d589679aae312161d03
author iuc
date Mon, 04 Nov 2024 23:21:56 +0000
parents ffc33339cd3e
children
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ffc33339cd3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
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1 <tool id="hicexplorer_hicdetectloops" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>searches for enriched regions</description>
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3 <macros>
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4 <token name="@BINARY@">hicDetectLoops</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 '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
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10 @BINARY@
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12 --matrix 'matrix.$matrix_h5_cooler.ext'
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13 #if $peakWidth:
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14 --peakWidth $peakWidth
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15 #end if
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17 #if $windowSize:
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18 --windowSize $windowSize
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19 #end if
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21 #if $pValuePreselection:
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22 --pValuePreselection $pValuePreselection
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23 #end if
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25 #if $peakInteractionsThreshold:
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26 --peakInteractionsThreshold $peakInteractionsThreshold
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27 #end if
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28
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29 #if $obsExpThreshold:
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30 --obsExpThreshold $obsExpThreshold
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31 #end if
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32
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33 #if $pValue:
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34 --pValue $pValue
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35 #end if
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36 #if $maxLoopDistance:
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37 --maxLoopDistance $maxLoopDistance
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38 #end if
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39
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40 #if $region:
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41 --region '$region'
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42 #end if
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43
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44 #if $chromosomes:
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45 #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
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46 --chromosomes $chromosome
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47 #end if
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48
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49 --expected $expected
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50 --outFileName output_loop.bedgraph
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51 --threads @THREADS@ -tpc @THREADS@
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52 ]]>
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53 </command>
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54 <inputs>
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55 <expand macro="matrix_h5_cooler_macro" />
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56 <param argument="--peakWidth" type="integer" optional="true" label="Peak width" help= "The width of the peak region in bins. The square around the peak will include (2 * peakWidth)^2 bins." />
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57 <param argument="--windowSize" type="integer" optional="true" label="Window size" help= "The window size for the neighborhood region the peak is located in. All values from this region (exclude the values from the peak
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58 region) are tested against the peak region for significant difference. The square will have the size of (2 * windowSize)^2 bins" />
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59 <param argument="--pValuePreselection" type="float" label="P-value preselection" help= "Only candidates with p-values less the given threshold will be considered as candidates.
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60 For each genomic distance a negative binomial distribution is fitted and for each pixel a p-value given by the cumulative density function is given.
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61 This does NOT influence the p-value for the neighborhood testing." value="0.05" />
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62 <param argument="--peakInteractionsThreshold" type="integer" label="Minimum interaction number" help= "The minimum number of interactions a detected peaks needs to have to be considered." value="5" />
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63
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64 <!-- new-->
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65 <param argument="--obsExpThreshold" type="float" label="Obs/exp interaction threshold" help= "The minimum number of obs/exp interactions a detected peaks needs to have to be considered" value="1.5" />
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66
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67 <param argument="--pValue" type="float" label="P-value" help= "Rejection level for the statistical test for H0. H0 is peak region and background have the same distribution." value="0.05" />
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68 <param argument="--maxLoopDistance" optional="true" type="integer" label="Maximal loop distance" help= "Maximum genomic distance of a loop, usually loops are within a distance of ~2MB." value="2000000" />
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69 <param argument="--chromosomes" optional="true" type="text" label="Chromosomes to include" help= "Chromosomes to include in the analysis. If not set, all chromosomes are included." />
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70 <param argument="--region" optional="true" type="text" label="Chromosomes to include" help= "The format is chr:start-end." />
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71 <param argument="--expected" type="select" label="Method to compute the expected value">
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72 <option value="mean" selected="True">mean</option>
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73 <option value="mean_nonzero">mean_nonzero</option>
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74 <option value="mean_nonzero_ligation">mean_nonzero_ligation</option>
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75 </param>
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76 </inputs>
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77 <outputs>
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78 <data name="output_loops" from_work_dir="output_loop.bedgraph" format="bedgraph" label="Computed loops" />
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79 </outputs>
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80 <tests>
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81 <test>
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82 <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
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83 <param name="maxLoopDistance" value="30000000" />
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84 <param name="windowSize" value="5" />
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85 <param name="peakWidth" value="2" />
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86 <param name="pValue" value="0.5" />
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87 <param name="pValuePreselection" value="0.55" />
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88 <output name="output_loops" file="hicDetectLoops/loops.bedgraph" ftype="bedgraph" compare="sim_size" />
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89 </test>
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90 </tests>
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91 <help><![CDATA[
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92
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93 Loop detection
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94 ==============
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95
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96 Computes enriched regions (peaks) or long range contacts on the given contact matrix.
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97
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98 hicDetectLoops can detect enriched interaction regions (peaks / loops) based on a strict candidate selection, negative binomial distributions and Wilcoxon rank-sum tests.
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99
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100 The algorithm was mainly develop on GM12878 cells from Rao 2014 on 10kb and 5kb fixed bin size resolution.
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101
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102 _________________
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103
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104 Usage
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105 -----
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106
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107 A command line example is available below (easily matchable in Galaxy using each field information):
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108
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109 ̀`$ hicDetectLoops -m matrix.cool -o loops.bedgraph --maxLoopDistance 2000000 --windowSize 10 --peakWidth 6 --pValuePreselection 0.05 --pValue 0.05 --peakInteractionsThreshold 20`
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110
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111 The candidate selection is based on the restriction of the maximum genomic distance, here 2MB. This distance is given by Rao 2014. For each genomic distance a negative binomial distribution is computed and only interaction pairs with a threshold less than ``--pValuePreselection`` are accepted. Detected candidates need to have at least an interaction count of ``--maximumInteractionPercentageThreshold`` times the maximum value for their genomic distance. Please note that ``--maximumInteractionPercentageThreshold`` was introduced with HiCExplorer release 3.2. Earlier versions did not have this parameter yet and therefore their outputs may differ. In a second step, each candidate is considered compared to its neighborhood. This neighborhood is defined by the ``--windowSize`` parameter in the x and y dimension. Per neighborhood only one candidate is considered, therefore only the candidate with the highest peak values is accepted. As a last step, the neighborhood is split into a peak and background region (parameter ``--peakWidth``). The peakWidth can never be larger than the windowSize. However, we recommend for 10kb matrices a windowSize of 10 and a peakWidth of 6.
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112
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113 The output file (´´-o loops.bedgraph``) contains the x and y position of each loop and its corresponding p-value of the Anderson-Darling test.
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114
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115 `1 120000000 122500000 1 145000000 147500000 0.001`
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116
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117 The results can visualized via hicPlotMatrix:
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118
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119 `$ hicPlotMatrix -m matrix.cool -o plot.png --log1p --region 1:18000000-22000000 --loops loops.bedgraph`
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120
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121 .. image:: $PATH_TO_IMAGES/hicDetectLoops.png
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122 :width: 50%
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123
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124
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125 For more information about HiCExplorer please consider our documentation on readthedocs.io_.
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126
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127 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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128
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129 ]]> </help>
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130 <expand macro="citations" />
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131 </tool>