Mercurial > repos > bgruening > hicexplorer_chicviewpoint

annotate chicViewpoint.xml @ 5:889194374660 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3e5c2f8ce3e540b0474746a33ee20b4a374dd38c"
author iuc
date Fri, 11 Dec 2020 21:00:03 +0000
parents 78b70d78a596
children dbfd2cfc0f66
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1 <tool id="hicexplorer_chicviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.1">
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2 <description>computes viewpoints with the given reference points and a background model.</description>
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3 <macros>
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4 <token name="@BINARY@">chicViewpoint</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 mkdir interactionFiles &&
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12 #for $m in $matrix_h5_cooler_multiple:
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13 #set identifier = @ESCAPE_IDENTIFIER_M@
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14 ln -s '$m' '$identifier' &&
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15 #end for
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16 #set $m = ' '.join([ '\'%s\'' % @ESCAPE_IDENTIFIER_MATRIX@ for $matrix in $matrix_h5_cooler_multiple ])
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17
0
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18 @BINARY@
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20 --matrices $m
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21 --range $rangeUpstream $rangeDownstream
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22 --referencePoints '$referencePoints'
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23 --averageContactBin $averageContactBin
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24 --fixateRange $fixateRange
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25 --decimalPlaces $decimalPlaces
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26 --threads @THREADS@
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27 --backgroundModelFile '$backgroundModelFile'
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28 --outputFolder interactionFiles
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29 $writeFileNamesToFile
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31 #if $tar:
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32 && cd interactionFiles
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33 && tar -cvf ../viewpoints.tar .
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34 && cd ..
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35 && rm -rf interactionFiles
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36 #end if
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37
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38 ]]></command>
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39 <inputs>
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40 <expand macro="matrix_h5_cooler_multiple_macro" />
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41
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42 <param argument="--referencePoints" type="data" format='interval'
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43 label="Reference points"
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44 help="Bed file contains all reference points which should be used to create viewpoints." />
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45 <param name="rangeUpstream" type="integer" value="500000" label="Upstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' />
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46 <param name="rangeDownstream" type="integer" value="500000" label="Downstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' />
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47
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48 <param argument="--backgroundModelFile" type="data" format='tabular'
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49 label="Background model"
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50 help="The background file computed by chicViewpointBackgroundModel" />
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51 <param argument="--averageContactBin" type="integer" value="5" label="Average contacts window size" help='Average the contacts of n bins via a sliding window approach.'/>
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52 <param argument="--fixateRange" type="integer" value="500000" label="Clip background distance" help='Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.'/>
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53 <param argument="--decimalPlaces" type="integer" value="12" label="Decimal places for output" help='Decimal places for all floating value in the output.'/>
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54
0
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55 <param name='writeFileNamesToFile' type='boolean' truevalue='--writeFileNamesToFile interactionFiles.txt' falsevalue="" checked="false" label="Save interaction file names (batch processing)"
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56 help="Set this parameter if you want to use the batch processing mode for the further analysis."/>
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57 <param name='tar' type='boolean' checked="false" label="tar output to one file"
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58 help="The output is tarred to one file and not written to a collection. Set this option if the number of files is large."/>
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59
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60 </inputs>
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61 <outputs>
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62 <collection name="interactionFilesCollection" type="list" label="Interaction files">
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63 <discover_datasets pattern="__name__" format="interval" directory="interactionFiles" />
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64 </collection>
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65 <data name="interactionFileNames" from_work_dir="interactionFiles.txt" format="txt" label="${tool.name} interaction file names">
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66 <filter>writeFileNamesToFile</filter>
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67 </data>
4
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68 <data name="interactionFilesTar" from_work_dir="viewpoints.tar" format="tar" label="${tool.name} interaction file names tar">
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69 <filter>tar</filter>
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70 </data>
0
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71 </outputs>
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72 <tests>
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73 <test>
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74 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/>
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75
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76 <param name="referencePoints" value="cHi-C/referencePoints_chicViewpoint.bed"/>
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77 <param name="backgroundModelFile" value="cHi-C/background.txt"/>
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78 <param name="fixateRange" value="500000"/>
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79 <param name="rangeUpstream" value="200000"/>
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80 <param name="rangeDownstream" value="200000"/>
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81 <param name="writeFileNamesToFile" value="True"/>
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82
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83
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84 <output_collection name="interactionFilesCollection" type="list" count="6">
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85 <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt" ftype="interval" lines_diff="3"/>
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86 <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt" ftype="interval" lines_diff="3"/>
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87 <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt" ftype="interval" lines_diff="3"/>
0
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88
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89 <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt" ftype="interval" lines_diff="3"/>
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90 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt" ftype="interval" lines_diff="3"/>
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91 <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" ftype="interval" lines_diff="3"/>
0
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92 </output_collection>
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93 <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0'/>
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94
0
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95 </test>
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96 <test>
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97 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/>
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98
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99 <param name="referencePoints" value="cHi-C/referencePoints_chicViewpoint.bed"/>
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100 <param name="backgroundModelFile" value="cHi-C/background.txt"/>
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101 <param name="fixateRange" value="500000"/>
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102 <param name="rangeUpstream" value="200000"/>
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103 <param name="rangeDownstream" value="200000"/>
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104 <param name="writeFileNamesToFile" value="False"/>
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105
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106
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107 <output_collection name="interactionFilesCollection" type="list" count="6">
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108 <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt" ftype="interval" lines_diff="3"/>
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109 <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt" ftype="interval" lines_diff="3"/>
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110 <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt" ftype="interval" lines_diff="3"/>
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111
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112 <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt" ftype="interval" lines_diff="3"/>
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113 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt" ftype="interval" lines_diff="3"/>
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114 <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" ftype="interval" lines_diff="3"/>
1
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115 </output_collection>
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116 <!-- <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0'/> -->
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117
1
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118 </test>
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119 <test>
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120 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/>
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121
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122 <param name="referencePoints" value="cHi-C/referencePoints_chicViewpoint.bed"/>
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123 <param name="backgroundModelFile" value="cHi-C/background.txt"/>
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124 <param name="fixateRange" value="500000"/>
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125 <param name="rangeUpstream" value="200000"/>
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126 <param name="rangeDownstream" value="200000"/>
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127 <param name="writeFileNamesToFile" value="True"/>
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128 <param name='tar' value='True'/>
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129
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130 <output name="interactionFilesTar" file="cHi-C/chicViewpoint/viewpoints.tar" ftype='tar' compare="sim_size" delta='40000' />
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131 <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0'/>
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132
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133 </test>
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134 </tests>
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135 <help><![CDATA[
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136
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137 Compute viewpoints for all given reference points
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138 =================================================
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139
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140 Computes per input matrix all viewpoints which are defined in the reference points file. All files are stored in the folder defined by `--outputFolder`, the files
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141 are named by the name of the reference point, the sample name and the location of the reference point:
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142
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143 gene_matrix_name_chr_start_end.txt
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144
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145 If multiple reference points are used and the processing downstream should be automated via batch processing mode, please activate `--writeFileNamesToFile`. In this
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146 file, all the file names will be written to; in the case of multiple samples two consecutive lines are considered as treatment vs control in the differential analysis.
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147
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148 For more information about HiCExplorer please consider our documentation on readthedocs.io_
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149
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150 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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151 ]]></help>
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152 <expand macro="citations" />
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153 </tool>