Mercurial > repos > bgruening > deeptools_plot_profile

annotate plotProfiler.xml @ 16:a3d4a84b8c47 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c
author bgruening
date Wed, 09 Mar 2016 17:45:47 -0500
parents d2205d523d83
children 36947e3103a0
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1 <tool id="deeptools_plot_profile" name="plotProfile" version="@WRAPPER_VERSION@.0">
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2 <description>
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3 creates a profile plot for score distributions across genomic regions
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4 </description>
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5 <macros>
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6 <token name="@BINARY@">plotProfile</token>
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7 <import>deepTools_macros.xml</import>
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8 </macros>
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9 <expand macro="requirements" />
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10 <command>
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11 <![CDATA[
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12 @BINARY@
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13 --matrixFile "$matrixFile"
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14 --outFileName "$outFileName"
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16 #if $output.showOutputSettings == "yes"
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17 --plotFileFormat $output.outFileFormat
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19 #if $output.saveSortedRegions:
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20 --outFileSortedRegions '$outFileSortedRegions'
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21 #end if
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22 #else
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23 --plotFileFormat 'png'
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24 #end if
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26 #if $scaleRegions.showScaleRegionsOpt == "yes":
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27 --startLabel '$scaleRegions.startLabel'
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28 --endLabel '$scaleRegions.endLabel'
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29 #end if
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31 #if $advancedOpt.showAdvancedOpt == "yes":
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32 #if $advancedOpt.averageType:
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33 --averageType '$advancedOpt.averageType'
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34 #end if
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35 --plotHeight $advancedOpt.plotHeight
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36 --plotWidth $advancedOpt.plotWidth
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37 --plotType $advancedOpt.plotType
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38 #if $advancedOpt.samplesLabel and str($advancedOpt.samplesLabel).strip() != "":
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39 --samplesLabel $advancedOpt.samplesLabel
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40 #end if
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41
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42 #if $advancedOpt.regionsLabel and str($advancedOpt.regionsLabel).strip() != "":
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43 --regionsLabel $advancedOpt.regionsLabel
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44 #end if
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46 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle).strip() != "":
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47 --plotTitle '$advancedOpt.plotTitle'
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48 #end if
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49
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50 #if str($advancedOpt.colors).strip() != "":
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51 --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )#
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52 #end if
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53
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54 $advancedOpt.perGroup
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55
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56 #if $advancedOpt.yMin:
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57 --yMin $advancedOpt.yMin
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58 #end if
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59 #if $advancedOpt.yMax:
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60 --yMax $advancedOpt.yMax
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61 #end if
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62
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63 #if $advancedOpt.outFileNameData:
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64 --outFileNameData "$output_outFileNameData"
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65 #end if
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66
0
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67 @KMEANS_CLUSTERING@
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68
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69 #end if
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70 ]]>
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71 </command>
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72 <inputs>
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73 <param argument="--matrixFile" format="deeptools_compute_matrix_archive" type="data" label="Matrix file from the computeMatrix tool"/>
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74 <conditional name="scaleRegions">
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75 <param name="showScaleRegionsOpt" type="select" label="The input matrix was computed in scale-regions mode">
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76 <option value="no" selected="true">no</option>
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77 <option value="yes">yes</option>
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78 </param>
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79 <when value="no" />
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80 <when value="yes">
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81 <param argument="--startLabel" type="text" value="TSS" size="10"
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82 label="Label for the region start"
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83 help ="Label shown in the plot
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84 for the start of the region. Default is TSS (transcription start site),
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85 but could be changed to anything, e.g. &quot;peak start&quot;." />
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86 <param argument="--endLabel" type="text" value="TES" size="10"
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87 label="Label for the region end"
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88 help="Label shown in the plot for the region end. Default is TES (transcription end site)."/>
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89 </when>
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90 </conditional>
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91
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92 <expand macro="input_graphic_output_settings">
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93 <expand macro="input_image_file_format" />
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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 <param name="averageType" type="select" label="Define the type of statistic that should be used for the profile.">
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104 <option value="mean" selected="true">mean</option>
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105 <option value="median">median</option>
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106 <option value="min">min</option>
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107 <option value="max">max</option>
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108 <option value="sum">sum</option>
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109 <option value="std">std</option>
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110 </param>
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111 <param argument="--plotHeight" type="integer" value="5" min="3"
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112 label="Plot height"
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113 help="Height in cm. The default for the plot height is 5 centimeters. The minimum value is 3 cm." />
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114
13
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115 <param argument="--plotWidth" type="integer" value="11" min="1"
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116 label="Plot width"
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117 help="Width in cm. The default value is 11 centimeters. The minimum value is 1 cm." />
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118
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119 <param argument="--plotType" type="select" label="Plot type"
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120 help="The &quot;lines&quot; option will
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121 plot the profile line based on the average type selected. The &quot;fill&quot;
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122 option fills the region between zero and the profile curve. The filled in color is
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123 semi-transparent. The &quot;add standard error&quot;
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124 option colors the region between the profile and the standard error of the data.
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125 As in the case of fill, a semi-transparent color is used.
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126 The option &quot;overlapped_lines&quot; plots each region's value, one on top of
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127 the other.">
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128 <option value="lines" selected="true">lines</option>
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129 <option value="fill">fill</option>
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130 <option value="se">add standard error</option>
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131 <option value="overlapped_lines">overlapped lines</option>
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132 </param>
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133 <param argument="--samplesLabel" type="text" size="30"
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134 label="Labels for the samples (each bigwig) plotted"
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135 help="The default is to use the file name of the sample. The sample labels should be separated by
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136 spaces and quoted if a label itself contains a space, e.g., label-1 &quot;label 2&quot;">
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137 <sanitizer>
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138 <valid initial="string.printable">
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139 </valid>
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140 </sanitizer>
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141 </param>
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142 <param argument="--regionsLabel" type="text" size="30"
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143 label="Labels for the regions plotted in the heatmap"
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144 help="If more than one region is being plotted a list of labels separated by space is required.
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145 If a label itself contains a space, then quotes are needed.
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146 For example, label_1, &quot;label 2&quot;" />
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147
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148 <expand macro="plotTitle" />
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149 <param argument="--colors" type="text" value="" size="40"
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150 label="List of colors to use for the plotted lines"
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151 help="Color names and html hex strings (e.g. #eeff22) are accepted.
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152 The color names should be separated by spaces. (--colors red blue green)">
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153 <validator type="expression"
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154 message="Only numbers, digits, '#' and spaces are allowed.">all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value)</validator>
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155 </param>
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156
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157 <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue=""
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158 label="Make one plot per group of regions"
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159 help="The default is to make one plot per bigWig file, i.e., all samples next to each other. Choosing this option will make one plot per group of regions. " />
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160
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161 <param argument="--outFileNameData" type="boolean" label="Save the data underlying the average profile"
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162 help="This option will create an additional output file." />
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163
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164 <param argument="--yMin" type="float" value="" size="3" optional="true"
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165 label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values"/>
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166 <param argument="--yMax" type="float" value="" size="3" optional="true"
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167 label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" />
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168
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169 <expand macro="kmeans_clustering" />
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170
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171 </when>
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172 </conditional>
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173 </inputs>
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174 <outputs>
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175 <expand macro="output_image_file_format" />
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176 <expand macro="output_graphic_outputs" />
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177
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178 <data format="tabular" name="output_outFileNameData" label="${tool.name} on ${on_string}: Underlying data">
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179 <filter>outFileNameData</filter>
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180 </data>
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181
0
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182 </outputs>
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183 <tests>
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184 <test>
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185 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
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186 <output name="outFileName" file="profiler_result1.png" ftype="png" compare="sim_size" delta="4000" />
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187 </test>
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188 <test>
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189 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
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190 <param name="showAdvancedOpt" value="yes" />
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191 <param name="showScaleRegionsOpt" value="yes" />
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192 <param name="outFileNameData" value="True" />
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193 <output name="outFileName" file="profiler_result2.png" ftype="png" compare="sim_size" delta="4000" />
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194 <output name="output_outFileNameData" file="profiler_result2.tabular" ftype="tabular" />
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195 </test>
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196 </tests>
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197 <help>
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198 <![CDATA[
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199
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200 What it does
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201 -------------
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202
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203 This tool plots the average enrichments over all genomic
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204 regions supplied to ``computeMarix``. It requires that ``computeMatrix`` was successfully run.
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205 It is a very useful complement to ``plotHeatmap``, especially in cases where you want to
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206 compare the scores for many different groups. Like ``plotHeatmap``, ``plotProfile`` does not change the
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207 values that were computed by ``computeMatrix``, but you can modify the color and other display properties of the plots.
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208
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209 Output
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210 -------------
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211
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212 .. image:: $PATH_TO_IMAGES/plotProfiler_examples.png
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213 :width: 600
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214 :height: 858
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215
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216 =======
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217
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218 In addition to the image, ``plotProfile`` can also generate the values underlying the profile.
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219
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220 See the following table for the **optional output** options:
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221
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222 +-----------------------------------+--------------------+-----------------+-----------------+
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223 | **optional output type** | **computeMatrix** | **plotHeatmap** | **plotProfile** |
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224 +-----------------------------------+--------------------+-----------------+-----------------+
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225 | values underlying the heatmap | yes | yes | no |
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226 +-----------------------------------+--------------------+-----------------+-----------------+
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227 | values underlying the profile | no | no | yes |
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228 +-----------------------------------+--------------------+-----------------+-----------------+
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229 | sorted and/or filtered regions | yes | yes | yes |
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230 +-----------------------------------+--------------------+-----------------+-----------------+
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231
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232 -----
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233
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234 @REFERENCES@
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235 ]]>
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236 </help>
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237 <expand macro="citations" />
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238 </tool>