Mercurial > repos > bgruening > hicexplorer_hicplotmatrix

annotate hicPlotMatrix.xml @ 5:c3703afea1b1 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
author bgruening
date Sat, 30 Dec 2017 09:21:50 -0500
parents fd5e51d2b558
children f93a78bc045e
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1 <tool id="hicexplorer_hicplotmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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2 <description>Plots a HiC matrix heatmap</description>
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3 <macros>
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4 <token name="@BINARY@">hicPlotMatrix</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
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10 #if str($pca_conditional.pca_type) == 'bedgraph':
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11 ln -s $pca_conditional.pca_bedgraph pca.bedgraph &&
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12 #set $pca = '--pca pca.bedgraph'
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13 #elif str($pca_conditional.pca_type) == 'bigwig':
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14 ln -s $pca_conditional.pca_bigwig pca.bw &&
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15 #set $pca = '--pca pca.bw'
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16 #elif str($pca_conditional.pca_type) == '':
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17 #set $pca = ''
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18 #end if
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19
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20 @BINARY@
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22 --matrix '$matrix_h5_cooler'
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24 #if $title and $title is not None:
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25 --title '$title'
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26 #end if
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28 #if $scoreName and $scoreName is not None:
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29 --scoreName '$scoreName'
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30 #end if
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31
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32 --outFileName plot.$image_file_format
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34 $perChromosome
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35 $clearMaskedBins
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36
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37 ## special: --chromosomeOrder is optional, but if given needs at least one argument
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38 #set chroms = '" "'.join([ str($var.chromosome) for $var in $chromosomeOrder ])
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39 #if chroms:
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40 --chromosomeOrder '$chroms'
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41 #end if
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42
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43 #if $region:
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44 --region '$region'
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45 #end if
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46
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47 #if $region2:
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48 --region2 '$region2'
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49 #end if
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50 $log1p
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51 $log
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52
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53 #if $colormap:
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54 --colorMap $colormap
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55 #end if
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56
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57 #if $vMin:
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58 --vMin $vMin
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59 #end if
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60
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61 #if $vMax:
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62 --vMax $vMax
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63 #end if
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64
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65 $pca
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66
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67 && mv plot.$image_file_format plot
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68 ]]>
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69 </command>
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70 <inputs>
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71 <expand macro='matrix_h5_cooler_macro' />
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72
0
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73 <param argument="--title" type="text" optional="true" label="Plot title"/>
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74 <param argument="--scoreName" type="text" optional="true" label="Score name"/>
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75 <param argument="--perChromosome" type="boolean" truevalue="--perChromosome" falsevalue="" checked="false"
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76 label="Plot per chromosome"
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77 help="Instead of plotting the whole matrix each chromosome is plotted next to the other. This parameter is not compatible with --region" />
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78 <param argument="--clearMaskedBins" type="boolean" truevalue="--clearMaskedBins" falsevalue="" checked="false"
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79 label="Remove masked bins from the matrix" />
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80
2
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81 <repeat name="chromosomeOrder" min="0" title="Chromosomes to include (and order to plot in):"
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82 help="This option overrides --region and --region2" >
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83 <param name="chromosome" type="text" >
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84 <validator type="empty_field" />
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85 </param>
0
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86 </repeat>
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87
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88 <param argument="--region" type="text" optional="True" label="Plot only this region"
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89 help="The format is chr:start-end The plotted region contains the main diagonal and is symmetric unless --region2 is given"/>
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90 <param argument="--region2" type="text" optional="True" label="Region two to plot"
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91 help="If given then only the region defined by --region and --region2 is plotted. The format is the same as --region"/>
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92 <param argument="--log1p" type="boolean" truevalue="--log1p" falsevalue="" checked="false" label="Plot the log1p of the matrix values."/>
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93 <param argument="--log" type="boolean" truevalue="--log" falsevalue="" checked="false" label="Plot the log of the matrix values."/>
0
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94
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95 <expand macro="colormap" />
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96
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97 <param argument="--vMin" type="float" optional="true" label="vMin"/>
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98 <param argument="--vMax" type="float" optional="true" label="vMax"/>
5
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99
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100 <conditional name="pca_conditional">
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101 <param name='pca_type' label='Datatype of eigenvector file' type='select'>
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102 <option value='' selected="true"></option>
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103 <option value='bedgraph'>bedgraph</option>
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104 <option value='bigwig'>bigwig</option>
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105 </param>
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106 <when value='' />
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107 <when value='bedgraph'>
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108 <param name='pca_bedgraph' type="data" format="bedgraph"
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109 label="Eigenvector file"/>
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110 </when>
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111 <when value='bigwig'>
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112 <param name='pca_bigwig' type="data" format="bigwig"
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113 label="Eigenvector file"/>
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114 </when>
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115 </conditional>
2
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116 <param name="image_file_format" type="select" label="Image output format">
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117 <option value="png" selected="True">png</option>
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118 <option value="svg">svg</option>
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119 </param>
0
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120 </inputs>
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121 <outputs>
2
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122 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on ${on_string}">
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123 <change_format>
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124 <when input="image_file_format" value="svg" format="svg" />
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125 </change_format>
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126 </data>
0
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127 </outputs>
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128 <tests>
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129 <test>
5
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130 <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/>
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131 <conditional name="pca_conditional">
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132 <param name="pca_type" value=''/>
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133 </conditional>
0
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134 <param name="region" value="chrX:3000000-3500000"/>
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135 <param name="region2" value="chrX:3100000-3600000"/>
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136 <param name="log1p" value="True"/>
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137 <param name="clearMaskedBins" value="True"/>
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138 <param name="image_file_format" value="png" />
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139 <output name="outFileName" file="master_matrix_plot.png" ftype="png" compare="sim_size"/>
0
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140 </test>
5
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141 <test>
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142 <param name="matrix_h5_cooler" value="Li_et_al_2015.cool"/>
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143 <conditional name="pca_conditional">
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144 <param name="pca_type" value=''/>
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145 </conditional>
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146 <param name="region" value="X:3000000-3500000"/>
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147 <param name="image_file_format" value="png" />
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148 <output name="outFileName" file="Li_chrX30-35_cool.png" ftype="png" compare="sim_size"/>
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149 </test>
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150 <test>
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151 <param name="matrix_h5_cooler" value="pearson_small_50kb.cool"/>
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152 <param name="perChromosome" value="True"/>
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153 <conditional name="pca_conditional">
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154 <param name="pca_type" value='bedgraph'/>
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155 <param name="pca_bedgraph" value="pca1.bedgraph"/>
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156 </conditional>
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157 <param name='colormap' value='hot'/>
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158 <param name="image_file_format" value="svg" />
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159 <output name="outFileName" file="small_matrix_50kb_pearson_pca1_plot.svg" ftype="svg" compare="sim_size" delta='35000'/>
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160 </test>
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161 <test>
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162 <param name="matrix_h5_cooler" value="pearson_small_50kb.h5"/>
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163 <param name="perChromosome" value="True"/>
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164 <conditional name="pca_conditional">
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165 <param name="pca_type" value='bigwig'/>
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166 <param name="pca_bigwig" value="pca1.bw"/>
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167 </conditional>
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168 <param name='colormap' value='hot'/>
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169
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170 <param name="image_file_format" value="svg" />
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171 <output name="outFileName" file="small_matrix_50kb_pearson_pca1_plot.svg" ftype="svg" compare="sim_size" delta='35000'/>
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172 </test>
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173 </tests>
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174 <help><![CDATA[
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175 Contact matrix plot
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176 =======================
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177
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178 ``hicPlotMatrix`` is a visualization tool for a contact matrix. It supports to plot the whole contact matrix, one or more chromosomes, a region or two regions against each other.
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179 Additional it can plot the result of a principal component analysis to have a better understanding of A / B compartments.
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180
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181 Input
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182 -----
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183
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184 Parameters
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185 __________
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186 - the contact matrix: h5 or cool file format.
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187 - A title for the plot
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188 - Score name
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189 - per chromosome
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190 - The chromosomes to include in the plot.
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191 - What to show:
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192 - The region(s) to plot. This parameter overrides 'chromosome'. If either 'chromosomes' or 'region' is given the full contact matrix is used.
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193 - log / log1p of the values: It is recommended to use log1p.
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194 - Colormaps_ for the heatmap.
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195 - vMin / vMax
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196 - principal component: a bedgraph or bigwig file containing eigenvector information
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197
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198 Output
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199 ------
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200
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201 The contact matrix plotted for chromosome 1.
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202
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203 .. image:: SRR027956.svg
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204 :width: 60%
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206
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207 The contact matrix used with ``--perChr`` and the first eigenvector from the tool ``hicPCA``. For this plot a pearson correlated matrix was used which is computed by creating first an observed / expected matrix and second a pearson correlation matrix. These matricies can be computed with ``hicChangeMatrixType``. The used Hi-C data were published by `Lieberman-Aiden <https://doi.org/10.1126/science.1181369>`_ in 2009, `GSE18199 <https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18199>`_.
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208
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209 .. image:: $PATH_TO_IMAGES/SRR0279XX_perChr_eigenvector1.png
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210 :width: 70 %
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211
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212 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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213
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214 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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215 .. _Colormaps: https://matplotlib.org/examples/color/colormaps_reference.html
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216 ]]></help>
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217 <expand macro="citations" />
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218 </tool>
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219