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comparison hicSumMatrices.xml @ 9:0399cd2c25aa draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
author iuc
date Fri, 27 Apr 2018 03:31:58 -0400
parents c109622e0cf5
children e89bc5e38823
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8:c109622e0cf5 9:0399cd2c25aa
1 <tool id="hicexplorer_hicsummatrices" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_hicsummatrices" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>combines Hi-C matrices of the same size</description> 2 <description>combine Hi-C matrices of the same size</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">hicSumMatrices</token> 4 <token name="@BINARY@">hicSumMatrices</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
13 #set $m = '" "'.join([ '%s_matrix' % $counter for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ]) 13 #set $m = '" "'.join([ '%s_matrix' % $counter for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
14 14
15 hicSumMatrices 15 hicSumMatrices
16 --matrices "$m" 16 --matrices "$m"
17 --outFileName matrix.$outputFormat 17 --outFileName matrix.$outputFormat
18 18
19 && mv matrix.$outputFormat matrix 19 && mv matrix.$outputFormat matrix
20 ]]> 20 ]]>
21 </command> 21 </command>
22 <inputs> 22 <inputs>
23 <expand macro='matrix_h5_cooler_multiple_macro'/> 23 <expand macro='matrix_h5_cooler_multiple_macro'/>
24 24
25 <param name='outputFormat' type='select' label="Output file format"> 25 <param name='outputFormat' type='select' label="Output file format">
26 <option value='h5'>HiCExplorer format</option> 26 <option value='h5'>HiCExplorer format</option>
27 <option value="cool">cool</option> 27 <option value="cool">cool</option>
28 </param> 28 </param>
29 </inputs> 29 </inputs>
44 </tests> 44 </tests>
45 <help><![CDATA[ 45 <help><![CDATA[
46 Summation of matrices 46 Summation of matrices
47 ===================== 47 =====================
48 48
49 ``hicSumMatrix`` is combining two (or more) contact matrices of the same size to one. 49 **hicSumMatrix** is combining two (or more) contact matrices of the same size to one.
50 This is useful if replicates of an Hi-C experiment should be merged into one contact matrix to 50 This is useful if replicates of an Hi-C experiment should be merged into one contact matrix to
51 increase the power of the data. It is the nature of Hi-C that real contact cannot be distinguished 51 increase the coverage of the data. With Hi-C, real contacts are sometimes difficult to be distinguished
52 from noise, especially with a low contact count. The more contacts are given, the more likely it is 52 from noise, especially with a low contact count. The more contacts are given, the more likely it is
53 that a high number of contacts are real contact or contain at least a high amount. Therefore it is 53 that a high number of contacts are biologically releveant. It is therefore common to merge biological
54 a common way to merge replicates of Hi-C experiments to increase the validity of the experiment. 54 and technical replicates of Hi-C experiments and **hicSumMatrix** address this concern.
55 55
56 Input 56 _________________
57
58 Usage
57 ----- 59 -----
58 60
59 Parameters 61 This tool takes two or more Hi-C contact matrices and sum the contacts into one matrix. It is recommended to use uncorrected and unmerged matrices as input (use the direct output from ``hicBuildMatrix``). Bin merging (``hicMergeMatrixBins``) and Hi-C contact matrix correction (``hicCorrectMatrix``) must be performed afterwards.
60 __________ 62
61 - two or matrices of the same shape. 63 _________________
62 64
63 Output 65 Output
64 ------ 66 ------
65 The summed matrix. 67 **hicSumMatrix** outputs a Hi-C contact matrix comprising the sum of all the contacts of the Hi-C matrices used as input.
68
69 _________________
66 70
67 | For more information about HiCExplorer please consider our documentation on readthedocs.io_ 71 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
68 72
69 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html 73 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
70 ]]></help> 74 ]]></help>