Mercurial > repos > bgruening > hicexplorer_hicdetectloops

comparison hicDetectLoops.xml @ 2:ce8d154fc6b5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
author iuc
date Wed, 11 Mar 2020 17:08:20 -0400
parents 2d1f9759fa0e
children 1119cdd14ddb
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1:5759cd7db0d1 2:ce8d154fc6b5
45 #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ]) 45 #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
46 --chromosomes $chromosome 46 --chromosomes $chromosome
47 #end if 47 #end if
48 48
49 --statisticalTest $statisticalTest_selector 49 --statisticalTest $statisticalTest_selector
50 50
51 --outFileName output_loop.bedgraph 51 --outFileName output_loop.bedgraph
52 52
53 --threads @THREADS@ 53 --threads @THREADS@ -tpc @THREADS@
54 ]]> 54 ]]>
55 </command> 55 </command>
56 <inputs> 56 <inputs>
57 <expand macro="matrix_h5_cooler_macro" /> 57 <expand macro="matrix_h5_cooler_macro" />
58 <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." /> 58 <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." />
59 <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 59 <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
60 region) are tested against the peak region for significant difference. The square will have the size of (2 * windowSize)^2 bins" /> 60 region) are tested against the peak region for significant difference. The square will have the size of (2 * windowSize)^2 bins" />
61 <param argument="--pValuePreselection" type="float" label="P-value preselection" help= "Only candidates with p-values less the given threshold will be considered as candidates. 61 <param argument="--pValuePreselection" type="float" label="P-value preselection" help= "Only candidates with p-values less the given threshold will be considered as candidates.
62 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. 62 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.
63 This does NOT influence the p-value for the neighborhood testing." value='0.05'/> 63 This does NOT influence the p-value for the neighborhood testing." value='0.05'/>
64 <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' /> 64 <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' />
65 <param argument="--maximumInteractionPercentageThreshold" type="float" value='0.1' label="Maximum interaction share" help= "For each genomic distance the maximum value is considered and all candidates need to have at least \'max_value * maximumInteractionPercentageThreshold\' interactions." /> 65 <param argument="--maximumInteractionPercentageThreshold" type="float" value='0.1' label="Maximum interaction share" help= "For each genomic distance the maximum value is considered and all candidates need to have at least \'max_value * maximumInteractionPercentageThreshold\' interactions." />
66 <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'/> 66 <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'/>
67 <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'/> 67 <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'/>
71 <param name="statisticalTest_selector" type="select" label="Stistical test"> 71 <param name="statisticalTest_selector" type="select" label="Stistical test">
72 <option value="wilcoxon-rank-sum" selected="True">Wilcoxon rank-sum'</option> 72 <option value="wilcoxon-rank-sum" selected="True">Wilcoxon rank-sum'</option>
73 <option value="anderson-darling">Anderson-Darling</option> 73 <option value="anderson-darling">Anderson-Darling</option>
74 </param> 74 </param>
75 </inputs> 75 </inputs>
76 <outputs> 76 <outputs>
77 <data name='output_loops' from_work_dir='output_loop.bedgraph' format='bedgraph' label='Computed loops'/> 77 <data name='output_loops' from_work_dir='output_loop.bedgraph' format='bedgraph' label='Computed loops'/>
78 </outputs> 78 </outputs>
79 <tests> 79 <tests>
80 <test> 80 <test>
81 <param name="matrix_h5_cooler" value="small_test_matrix.cool"/> 81 <param name="matrix_h5_cooler" value="small_test_matrix.cool"/>
93 Loop detection 93 Loop detection
94 ============== 94 ==============
95 95
96 Computes enriched regions (peaks) or long range contacts on the given contact matrix. 96 Computes enriched regions (peaks) or long range contacts on the given contact matrix.
97 97
98 hicDetectLoops can detect enriched interaction regions (peaks / loops) based on a strict candidate selection, negative binomial distributions and Anderson-Darling / Wilcoxon rank-sum tests.
99
100 The algorithm was mainly develop on GM12878 cells from Rao 2014 on 10kb and 5kb fixed bin size resolution.
101
102 _________________
103
104 Usage
105 -----
106
107 A command line example is available below (easily matchable in Galaxy using each field information):
108
109 ̀`$ hicDetectLoops -m matrix.cool -o loops.bedgraph --maxLoopDistance 2000000 --windowSize 10 --peakWidth 6 --pValuePreselection 0.05 --pValue 0.05 --peakInteractionsThreshold 20 --maximumInteractionPercentageThreshold 0.1 --statisticTest anderson-darling`
110
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.
112
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.
114
115 `1 120000000 122500000 1 145000000 147500000 0.001`
116
117 The results can visualized via hicPlotMatrix:
118
119 `$ hicPlotMatrix -m matrix.cool -o plot.png --log1p --region 1:18000000-22000000 --loops loops.bedgraph`
120
121 .. image:: $PATH_TO_IMAGES/hicDetectLoops.png
122 :width: 50%
123
124
98 For more information about HiCExplorer please consider our documentation on readthedocs.io_. 125 For more information about HiCExplorer please consider our documentation on readthedocs.io_.
99 126
100 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html 127 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
101 128
102 ]]></help> 129 ]]></help>