Mercurial > repos > bgruening > hicexplorer_hicplotsvl

annotate hicPlotSVL.xml @ 6:b75f87deaa15 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
author iuc
date Tue, 16 Mar 2021 15:14:22 +0000
parents 3a7752b8d2cb
children 279fb179dae7
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6
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1 <tool id="hicexplorer_hicplotsvl" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>plots the relation of short vs long range contacts</description>
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3 <macros>
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4 <token name="@BINARY@">hicPlotSVL</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 #import re
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11 #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
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12 #set identifier = @ESCAPE_IDENTIFIER_M@
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13 ln -s '$m' '${counter}_$identifier' &&
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14 #end for
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15 #set $m = ' '.join([ '\'%s_%s\'' % ($counter, @ESCAPE_IDENTIFIER_MATRIX@) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
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16
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17 @BINARY@
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18 --matrices $m
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19 #if $distance:
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20 --distance $distance
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21 #end if
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23 @CHROMOSOME_LIST@
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24
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25 #if $colorList:
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26 #set $colorList_new = ' '.join([ '\'%s\'' % $color for $color in str($colorList).split(' ') ])
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27 --colorList $colorList_new
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28 #end if
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29
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30 #if $dpi:
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31 --dpi $dpi
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32 #end if
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33 --plotFileName plot.$image_file_format
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34 --outFileName p_values.txt
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35 --outFileNameData ratios.txt
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36 --threads @THREADS@
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37
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38 && mv plot.$image_file_format plot
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39 ]]>
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40 </command>
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41 <inputs>
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42 <expand macro='matrix_h5_cooler_multiple_macro' />
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43 <param argument="--distance" optional='true' type="integer" label="Short range distance" help="Distance which should be considered as short range. Default 2MB." value='2000000' />
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44 <expand macro="chromosome_list" />
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45 <param argument="--colorList" optional='true' type="text" label="Colorlist" help="Colorlist for the boxplots." />
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46 <expand macro="dpi" />
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47 <param name="image_file_format" type="select" label="Image output format">
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48 <option value="png" selected="True">png</option>
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49 <option value="svg">svg</option>
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50 <option value="pdf">pdf</option>
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51 </param>
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52 </inputs>
2
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53 <outputs>
0
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54 <data name='output_plot' from_work_dir='plot' format='png' label='Plot SVL'>
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55 <change_format>
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56 <when input="image_file_format" value="svg" format="svg" />
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57 <when input="image_file_format" value="pdf" format="pdf" />
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58 </change_format>
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59 </data>
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60 <data name='output_p_values' from_work_dir='p_values.txt' format='txt' label='P values svl' />
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61 <data name='output_ratios' from_work_dir='ratios.txt' format='txt' label='Ratios svl' />
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62
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63 </outputs>
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64 <tests>
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65 <test>
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66 <param name="matrix_h5_cooler_multiple" value="small_test_matrix.h5,small_test_matrix.h5" />
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67 <param name="distance" value="2000000" />
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68 <param name="dpi" value="10" />
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69 <param name="color" value="y m c" />
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70 <repeat name="chromosome_list">
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71 <param name="chromosomes" value="chr2L" />
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72 </repeat>
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73 <repeat name="chromosome_list">
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74 <param name="chromosomes" value="chr3L" />
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75 </repeat>
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76 <repeat name="chromosome_list">
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77 <param name="chromosomes" value="chr4" />
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78 </repeat>
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79
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80 <param name="image_file_format" value="png" />
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81
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82 <output name="output_plot" file="hicPlotSVL/plot.png" ftype="png" compare="sim_size" />
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83 <output name="output_p_values" file="hicPlotSVL/p_values.txt" ftype="txt" />
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84 <output name="output_ratios" file="hicPlotSVL/ratios.txt" ftype="txt" />
2
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85
0
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86 </test>
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87 </tests>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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88 <help><![CDATA[
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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89
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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90 Short vs long range contacts
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91 ============================
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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92
2
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93 hicPlotSVL computes the ratio between short range and long range contacts per chromosome independently. Per sample one box plot is created and,
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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94 if more than one sample is given, the computed ratios are assumed to be one distribution and a Wilcoxon rank-sum test under H0 'distributions are equal'
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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95 is computed. All used data is written to a third raw data file.
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96
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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97 The distance to distinct short and long range contacts can be set via the –distance parameter; for short range the sum for all contacts smaller or equal this distance are computed, for long range contacts all contacts greater this distance.
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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98
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99
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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100
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101 Usage
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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102 -----
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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103
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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104
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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105 .. code-block:: text
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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106
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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107 $ hicPlotSVL -m hmec_10kb.cool nhek_10kb.cool hmec_10kb.cool --distance 2000000 --threads 4 --plotFileName plot.png --outFileName pvalues.txt --outFileNameData rawData.txt
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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108
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109
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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110 This results in three files:
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111
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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112 The raw data containing the sums for short range, long range and ratio per sample and chromosome.
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113
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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114
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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115 .. code-block:: text
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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116
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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117 # Created with HiCExplorer's hicPlotSVL 3.3
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118 # Short range vs long range contacts per chromosome: raw data
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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119 # Short range contacts: <= 2000000
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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120 # hmec_10kb.cool nhek_10kb.cool hmec_10kb.cool
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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121 # Chromosome Ratio Sum <= 2000000 Sum > 2000000 Ratio Sum <= 2000000 Sum > 2000000 Ratio Sum <= 2000000 Sum > 2000000
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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122 1 3.0399769346724543 33476834 11012200 2.79740105237572 44262902 15822866 3.0399769346724543 33476834 11012200
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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123 2 2.7532203542810625 31723954 11522490 2.5007877714355438 47468438 18981394 2.7532203542810625 31723954 11522490
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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124 3 2.922650759458664 26251027 8981924 2.6235211241878442 39640848 15109788 2.922650759458664 26251027 8981924
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
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125 4 2.7235598858451637 22474680 8251950 2.5572455199457864 37486882 14659086 2.7235598858451637 22474680 8251950
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
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126 5 2.9585962905193712 22716268 7678056 2.752922527526723 35445722 12875670 2.9585962905193712 22716268 7678056
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
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127 6 3.168274165465025 22872690 7219290 2.8602111006131703 33990211 11883812 3.168274165465025 22872690 7219290
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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128 7 3.1093346580597516 19603416 6304698 2.8021236966788887 29712823 10603680 3.1093346580597516 19603416 6304698
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
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129 8 3.135391026076832 18355087 5854162 2.7964394470859024 28660624 10248970 3.135391026076832 18355087 5854162
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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130 9 4.1147978383348125 15395763 3741560 3.819940066283481 21994046 5757694 4.1147978383348125 15395763 3741560
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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131 10 3.448063050802953 17964043 5209894 3.1116673856502253 26270171 8442474 3.448063050802953 17964043 5209894
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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132 11 3.5924666993070407 18651850 5191934 3.1364875011923035 26240350 8366158 3.5924666993070407 18651850 5191934
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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133 12 3.6817551043464416 18640866 5063038 3.306662109403207 26101554 7893626 3.6817551043464416 18640866 5063038
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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134 13 3.476204237522881 11018462 3169682 3.0976674036654805 18922281 6108558 3.476204237522881 11018462 3169682
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
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135 14 3.70550850832778 11164875 3013048 3.6226817463785164 17245704 4760480 3.70550850832778 11164875 3013048
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
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136 15 4.607631079612186 11165313 2423222 4.567998349104569 15273742 3343640 4.607631079612186 11165313 2423222
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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137 16 4.397874357146307 10745775 2443402 3.890983210350018 14666462 3769346 4.397874357146307 10745775 2443402
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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138 17 5.809374740402161 12168235 2094586 5.3360710927739285 14154110 2652534 5.809374740402161 12168235 2094586
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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139 18 3.7647349280938895 9339833 2480874 3.485487446356812 15019063 4309028 3.7647349280938895 9339833 2480874
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
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140 19 6.492239632778196 8466283 1304062 5.774337450385819 9368978 1622520 6.492239632778196 8466283 1304062
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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141 20 5.542933774973686 8962935 1617002 4.977679877778358 12009479 2412666 5.542933774973686 8962935 1617002
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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142 21 6.665622315255486 3910374 586648 6.1843701763589225 6554715 1059884 6.665622315255486 3910374 586648
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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143 22 8.063663557923096 4992327 619114 7.433759425439728 5932928 798106 8.063663557923096 4992327 619114
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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144 X 2.208752982178897 14424173 6530460 2.3130534357407995 27628734 11944702 2.208752982178897 14424173 6530460
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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145 Y 4.165021803993573 36294 8714 3.8063291139240505 45105 11850 4.165021803993573 36294 8714
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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146 MT
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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147
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148
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149
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150 The p-values between the samples:
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151
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152 .. code-block:: text
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153
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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154 # Created with HiCExplorer's hicPlotSVL 3.3
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155 # Short range vs long range contacts per chromosome, p-values of each distribution against each other distribution with Wilcoxon rank-sum
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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156 # Short range contacts: <= 2000000
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157 hmec_10kb.cool nhek_10kb.cool 0.28362036331636575
3a7752b8d2cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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158 hmec_10kb.cool hmec_10kb.cool 1.0
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159 nhek_10kb.cool hmec_10kb.cool 0.28362036331636575
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160
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161
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163 The box plot:
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164
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165 .. image:: $PATH_TO_IMAGES/plot_svl.png
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166 :width: 50%
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167
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168 For more information about HiCExplorer please consider our documentation on readthedocs.io_.
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169
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170 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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172 ]]> </help>
0
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173 <expand macro="citations" />
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174 </tool>