Mercurial > repos > bgruening > deeptools_plot_heatmap

annotate plotHeatmap.xml @ 8:8ed7e3b6a16c draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69
author bgruening
date Wed, 23 Dec 2015 07:28:42 -0500
parents aaf01404686f
children f509604dbf06
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1 <tool id="deeptools_plot_heatmap" name="plotHeatmap" version="@WRAPPER_VERSION@.0">
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2 <description>creates a heatmap for a score associated to genomic regions</description>
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3 <macros>
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4 <token name="@BINARY@">plotHeatmap</token>
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5 <import>deepTools_macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command>
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9 <![CDATA[
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10 @BINARY@
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11 --matrixFile "$matrixFile"
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12 --outFileName "$outFileName"
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13
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14 #if $output.showOutputSettings == "yes"
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15 --plotFileFormat "$output.outFileFormat"
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16 #if $outFileNameData:
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17 --outFileNameData "$outFileNameData"
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18 #end if
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20 #if $outFileNameMatrix:
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21 --outFileNameMatrix "$outFileNameMatrix"
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22 #end if
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24 #if $outFileSortedRegions:
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25 --outFileSortedRegions "$outFileSortedRegions"
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26 #end if
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27 #else
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28 --plotFileFormat 'png'
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29 #end if
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30
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31 #if $advancedOpt.showAdvancedOpt == "yes"
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32 #if $advancedOpt.sortRegions:
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33 --sortRegions '$advancedOpt.sortRegions'
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34 #end if
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35
0
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36 #if $advancedOpt.sortUsing:
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37 --sortUsing '$advancedOpt.sortUsing'
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38 #end if
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39
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40 #if $advancedOpt.averageTypeSummaryPlot:
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41 --averageTypeSummaryPlot '$advancedOpt.averageTypeSummaryPlot'
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42 #end if
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43
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44 #if str($advancedOpt.missingDataColor.value) != "None":
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45 --missingDataColor '$advancedOpt.missingDataColor'
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46 #end if
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47
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48 --colorMap '$advancedOpt.colorMap'
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49
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50 #if str($advancedOpt.zMin).strip() != "":
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51 --zMin $advancedOpt.zMin
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52 #end if
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53 #if $advancedOpt.zMax:
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54 --zMax $advancedOpt.zMax
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55 #end if
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56
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57 #if str($advancedOpt.yMin).strip() != "":
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58 --yMin $advancedOpt.yMin
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59 #end if
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60 #if $advancedOpt.yMax:
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61 --yMax $advancedOpt.yMax
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62 #end if
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63
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64 --xAxisLabel '$advancedOpt.xAxisLabel'
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65 --yAxisLabel '$advancedOpt.yAxisLabel'
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66
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67 --heatmapWidth $advancedOpt.heatmapWidth
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68 --heatmapHeight $advancedOpt.heatmapHeight
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69
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70 --whatToShow '$advancedOpt.whatToShow'
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71
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72 --startLabel '$advancedOpt.startLabel'
0
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73 --endLabel '$advancedOpt.endLabel'
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74 --refPointLabel '$advancedOpt.referencePointLabel'
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75 --regionsLabel '$advancedOpt.regionsLabel'
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76
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77 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
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78 --plotTitle '$advancedOpt.plotTitle'
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79 #end if
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80
8
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81 $advancedOpt.perGroup
0
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82
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83 @KMEANS_CLUSTERING@
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84
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85 #end if
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86 ]]>
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87 </command>
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88 <inputs>
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89 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data" label="Matrix file from the computeMatrix tool" help=""/>
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90
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91 <expand macro="input_graphic_output_settings">
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92 <expand macro="input_image_file_format" />
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93 <expand macro="input_save_matrix_values" />
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94 </expand>
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95
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96 <conditional name="advancedOpt" >
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97 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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98 <option value="no" selected="true">no</option>
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99 <option value="yes">yes</option>
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100 </param>
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101 <when value="no" />
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102 <when value="yes">
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103 <expand macro="sortRegions" />
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104 <expand macro="sortUsing" />
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105 <param argument="--averageTypeSummaryPlot" type="select"
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106 label="Type of statistic that should be plotted in the summary image above the heatmap"
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107 help="">
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108 <option value="mean" selected="true">mean</option>
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109 <option value="median">median</option>
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110 <option value="min">min</option>
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111 <option value="max">max</option>
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112 <option value="sum">sum</option>
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113 <option value="std">std</option>
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114 </param>
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115
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116 <param argument="--missingDataColor" type="text" value="black" optional="true" label="Missing data color"
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117 help="If 'Represent missing data as zero' is not set, such cases will be colored in black by default.
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118 By using this parameter a different color can be set. A value between 0 and 1 will be used for a gray scale (black is 0).
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119 Also color names can be used, see a list here: http://packages.python.org/ete2/reference/reference_svgcolors.html.
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120 Alternatively colors can be specified using the #rrggbb notation." />
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121
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122 <expand macro="colorMap" />
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123
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124 <param argument="--zMin" type="float" value="" size="3" optional="True"
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125 label="Minimum value for the heatmap intensities. Leave empty for automatic values" help=""/>
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126 <param argument="--zMax" type="float" value="" size="3" optional="True"
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127 label="Maximum value for the heatmap intensities. Leave empty for automatic values" help=""/>
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128 <param argument="--yMin" type="float" value="" size="3" optional="True"
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129 label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" help=""/>
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130 <param argument="--yMax" type="float" value="" size="3" optional="True"
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131 label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" help=""/>
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132 <param argument="--xAxisLabel" type="text" value="distance from TSS (bp)" size="200"
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133 label="Description for the x-axis label" help="" />
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134 <param argument="--yAxisLabel" type="text" value="genes" size="30"
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135 label="Description for the y-axis label for the top panel" help="" />
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136
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137 <param argument="--heatmapWidth" type="float" value="7.5" min="1" max="100"
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138 label="Heatmap width in cm" help="The minimum value is 1 and the maximum is 100."/>
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139 <param argument="--heatmapHeight" type="float" value="25" min="3" max="100"
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140 label="Heatmap height in cm" help="The minimum value is 3 and the maximum is 100."/>
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141
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142 <param argument="--whatToShow" type="select" label="What to show"
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143 help ="The default is to include a summary or profile plot on top of the heatmap and a heatmap colorbar.">
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144 <option value="plot, heatmap and colorbar" selected="true">summary plot, heatmap and colorbar</option>
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145 <option value="plot and heatmap">summary plot and heatmap (no colorbar)</option>
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146 <option value="heatmap and colorbar">heatmap and colorbar</option>
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147 </param>
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148
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149 <param argument="--startLabel" type="text" value="TSS" size="10"
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150 label="Label for the region start"
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151 help ="Only for scale-regions mode. Label shown in the plot for the start of the region. Default is TSS (transcription start site), but could be changed to anything, e.g. &quot;peak start&quot;." />
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152 <param argument="--endLabel" type="text" value="TES" size="10"
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153 label="Label for the region end"
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154 help="Only for scale-regions mode. Label shown in the plot for the region end. Default is TES (transcription end site)."/>
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155
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156 <param argument="--referencePointLabel" type="text" value="TSS" size="10"
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157 label="Reference point label"
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158 help ="Label shown in the plot for the reference-point. Default is the same as the reference point selected (e.g. TSS), but could be anything, e.g. &quot;peak start&quot; etc." />
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159 <param argument="--regionsLabel" type="text" value="genes" size="30"
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160 label="Labels for the regions plotted in the heatmap"
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161 help="If more than one region is being plotted a list of labels separated by comma and limited by quotes, is required. For example, label1, label2.">
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162 <sanitizer>
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163 <valid initial="string.printable">
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164 </valid>
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165 </sanitizer>
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166 </param>
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167 <expand macro="plotTitle" />
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168 <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue=""
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169 label="Do one plot per group"
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170 help="When clustering is applied to the data, or the computematrix was performed on file containing
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171 groups separated by &quot;#&quot;, plot the groups next to each other. The default is to plot
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172 the samples next to each other. If this option is set, each group (or cluster) will get its own plot,
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173 with different samples stacked on top of each other."/>
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174
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175 <expand macro="kmeans_clustering" />
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176 </when>
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177 </conditional>
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178 </inputs>
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179 <outputs>
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180 <expand macro="output_image_file_format" />
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181 <expand macro="output_graphic_outputs" />
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182 <expand macro="output_save_matrix_values" />
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183 </outputs>
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184 <tests>
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185 <test>
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186 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
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187 <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="100" />
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188 </test>
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189 <test>
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190 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
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191 <param name="showAdvancedOpt" value="yes" />
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192 <param name="whatToShow" value="heatmap and colorbar" />
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193 <output name="outFileName" file="heatmapper_result2.png" ftype="png" compare="sim_size" delta="100" />
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194 </test>
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195 </tests>
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196 <help>
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197 <![CDATA[
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198 **What it does**
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199
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200 The heatmapper visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes.
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201 Like profiler, it requires that computeMatrix was run first to calculate the values.
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202
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203 We implemented vast optional parameters to optimize the visual output and we encourage you to play around with the min/max values
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204 displayed in the heatmap as well as with the different coloring options. The most powerful option is the k-means/hirarchichal clustering
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205 where you simply need to indicate the number of groups with similar read distributions that you expect and the algorithm will do the sorting for you.
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206
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207
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208 .. image:: $PATH_TO_IMAGES/visual_hm_DmelPolII.png
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209 :alt: Heatmap of RNA Polymerase II ChIP-seq
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210
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211
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212 You can find more details on the tool on the plotHeatmap doc page: https://deeptools.readthedocs.org/en/release-1.6/content/tools/plotHeatmap.html
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213
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214
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215 -----
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216
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217 @REFERENCES@
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218 ]]>
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219 </help>
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220 <expand macro="citations" />
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221 </tool>