Mercurial > repos > bgruening > deeptools_plot_heatmap

annotate plotHeatmap.xml @ 42:2f2cd7085835 draft default tip

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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 810c1359b884661d3f5c7372be0f0f88c859a3b9
author bgruening
date Thu, 01 Jun 2023 10:18:08 +0000
parents 375e7508e571
children
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1 <tool id="deeptools_plot_heatmap" name="plotHeatmap" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
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2 <description>creates a heatmap for score distributions across 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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14 #if $output.showOutputSettings == "yes"
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15 --plotFileFormat '$output.outFileFormat'
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17 #if $outFileNameMatrix:
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18 --outFileNameMatrix '$outFileNameMatrix'
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19 #end if
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21 #if $outFileSortedRegions:
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22 --outFileSortedRegions '$outFileSortedRegions'
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23 #end if
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25 #if $output.dpi:
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26 --dpi '$output.dpi'
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27 #end if
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28 #else
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29 --plotFileFormat 'png'
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30 #end if
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32 #if $advancedOpt.showAdvancedOpt == "yes"
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33 #if $advancedOpt.sortRegions:
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34 --sortRegions '$advancedOpt.sortRegions'
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35 #end if
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37 #if $advancedOpt.linesAtTickMarks:
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38 --linesAtTickMarks
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39 #end if
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40
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41 #if $advancedOpt.sortUsing:
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42 --sortUsing '$advancedOpt.sortUsing'
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43 #end if
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45 #if $advancedOpt.averageTypeSummaryPlot:
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46 --averageTypeSummaryPlot '$advancedOpt.averageTypeSummaryPlot'
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47 #end if
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49 --plotType '$advancedOpt.plotType'
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51 #if str($advancedOpt.missingDataColor.value) != "None":
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52 --missingDataColor '$advancedOpt.missingDataColor'
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53 #end if
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54
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55 #set colorMap = []
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56 #for $cmap in $advancedOpt.colorMapRepeat:
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57 #silent $colorMap.append(str($cmap.colorMap))
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58 #end for
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59 #if len($colorMap) > 0:
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60 --colorMap #echo " ".join($colorMap)#
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61 #end if
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62
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63 --alpha '$advancedOpt.alpha'
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64 #if str($advancedOpt.colorList).strip() != "":
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65 --colorList $advancedOpt.colorList
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66 #end if
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68 #if str($advancedOpt.zMin).strip() != "":
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69 --zMin $advancedOpt.zMin
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70 #end if
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71 #if str($advancedOpt.zMax).strip() != "":
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72 --zMax $advancedOpt.zMax
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73 #end if
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75 #if str($advancedOpt.yMin).strip() != "":
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76 --yMin $advancedOpt.yMin
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77 #end if
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78 #if str($advancedOpt.yMax).strip() != "":
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79 --yMax $advancedOpt.yMax
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80 #end if
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81 #if str($advancedOpt.sortUsingSamples).strip() != "":
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82 --sortUsingSamples $advancedOpt.sortUsingSamples
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83 #end if
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84 #if str($advancedOpt.clusterUsingSamples).strip() != "":
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85 --clusterUsingSamples $advancedOpt.clusterUsingSamples
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86 #end if
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88 --xAxisLabel '$advancedOpt.xAxisLabel'
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89 --yAxisLabel '$advancedOpt.yAxisLabel'
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91 --heatmapWidth $advancedOpt.heatmapWidth
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92 --heatmapHeight $advancedOpt.heatmapHeight
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93
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94 --whatToShow '$advancedOpt.whatToShow'
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95
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96 --startLabel '$advancedOpt.startLabel'
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97 --endLabel '$advancedOpt.endLabel'
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98
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99 --refPointLabel '$advancedOpt.referencePointLabel'
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100
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101 #if $advancedOpt.samplesLabel and str($advancedOpt.samplesLabel).strip() != "":
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102 --samplesLabel $advancedOpt.samplesLabel
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103 #end if
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104
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105 #if $advancedOpt.regionsLabel and str($advancedOpt.regionsLabel).strip() != "":
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106 --regionsLabel $advancedOpt.regionsLabel
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107 #end if
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108
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109 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
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110 --plotTitle '$advancedOpt.plotTitle'
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111 #end if
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112
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113 --legendLocation '$advancedOpt.legendLocation'
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114
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115 --labelRotation '$advancedOpt.labelRotation'
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116
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117 $advancedOpt.perGroup
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118
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119 @KMEANS_CLUSTERING@
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120
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121 #end if
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122 ]]>
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123 </command>
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124 <inputs>
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125 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
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126 label="Matrix file from the computeMatrix tool" help=""/>
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127
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128 <expand macro="input_graphic_output_settings">
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129 <expand macro="input_image_file_format" />
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130 <expand macro="output_dpi" />
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131 <expand macro="input_save_matrix_values" />
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132 </expand>
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133
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134 <conditional name="advancedOpt" >
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135 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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136 <option value="no" selected="true">no</option>
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137 <option value="yes">yes</option>
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138 </param>
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139 <when value="no" />
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140 <when value="yes">
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141 <expand macro="sortRegions" />
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142 <expand macro="sortUsing" />
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143 <param argument="--sortUsingSamples" type="text"
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144 label="List of samples to be used for sorting"
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145 help="List of sample numbers (order as in matrix), which are used by --sortUsing for sorting.
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146 If no value is set, it uses all samples. Example: 1 3 (space separated!)" />
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147 <sanitizer>
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148 <valid initial="string.printable">
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149 <add value=" "/>
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150 </valid>
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151 </sanitizer>
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152 <param argument="--linesAtTickMarks" type="boolean" truevalue="--linesAtTickMarks" falsevalue=""
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153 label="Draw dashed lines in heatmap above all tick marks?" />
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154 <param argument="--averageTypeSummaryPlot" type="select"
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155 label="Type of statistic that should be plotted in the summary image above the heatmap"
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156 help="">
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157 <option value="mean" selected="true">mean</option>
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158 <option value="median">median</option>
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159 <option value="min">min</option>
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160 <option value="max">max</option>
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161 <option value="sum">sum</option>
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162 <option value="std">std</option>
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163 </param>
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164 <param argument="--plotType" type="select" label="Type of summary plot">
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165 <option value="lines">plot the profile line based on the statistic selected above.</option>
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166 <option value="fill">fills the region between zero and the profile.</option>
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167 <option value="se">color the region between the profile and the standard error.</option>
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168 <option value="std">color the region between the profile and the standard deviation.</option>
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169 </param>
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170 <param argument="--missingDataColor" type="text" value="black" optional="true" label="Missing data color"
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171 help="If 'Represent missing data as zero' is not set, such cases will be colored in black by default.
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172 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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173 Also color names can be used, see a list here: http://packages.python.org/ete2/reference/reference_svgcolors.html.
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174 Alternatively colors can be specified using the #rrggbb notation." />
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175
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176 <repeat name="colorMapRepeat" title="Colormap to use for each sample"
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177 help="A different colormap can be applied to each column of the heatmap. If you select fewer colormaps than you have samples in your matrix, then the select colormap(s) will be repeated (e.g., if you select one colormap then it will be applied to all samples).">
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178 <expand macro="colorMap" />
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179 </repeat>
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180 <param argument="--alpha" type="float" value="1.0" min="0.0"
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181 max="1.0" optional="True"
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182 label="Alpha channel (transparency)"
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183 help="The alpha channel (transparency) to use for the heatmaps. The default is 1.0 and values must
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184 be between 0 and 1. A value of 0.0 would be fully transparent." />
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185
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186 <param argument="--colorList" type="text" value="" optional="True"
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187 label="List of colors for each heatmap. Separate lists by spaces and the colors in the list by comas"
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188 help="The color of the heatmaps can be specified as a list of colors separated by comas with
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189 not space in between. For example: white,blue white,green will set a color map from white
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190 to blue for the first heatmap and for white to green for the next heatmap."/>
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191 <expand macro="zMin_zMax" />
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192 <param argument="--yMin" type="float" value="" optional="True"
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193 label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" help=""/>
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194 <param argument="--yMax" type="float" value="" optional="True"
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195 label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" help=""/>
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196 <param argument="--xAxisLabel" type="text" value="distance from TSS (bp)"
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197 label="The x-axis label" help="" />
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198 <param argument="--yAxisLabel" type="text" value="genes"
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199 label="The y-axis label for the top panel" help="" />
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200
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201 <param argument="--heatmapWidth" type="float" value="7.5" min="1" max="100"
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202 label="Heatmap width in cm" help="The minimum value is 1 and the maximum is 100."/>
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203 <param argument="--heatmapHeight" type="float" value="25" min="3" max="100"
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204 label="Heatmap height in cm" help="The minimum value is 3 and the maximum is 100."/>
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205
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206 <param argument="--whatToShow" type="select" label="What to show"
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207 help ="The default is to include a summary or profile plot on top of the heatmap and a heatmap colorbar.">
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208 <option value="plot, heatmap and colorbar" selected="true">summary plot, heatmap and colorbar</option>
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209 <option value="plot and heatmap">summary plot and heatmap (no colorbar)</option>
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210 <option value="heatmap and colorbar">heatmap and colorbar</option>
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211 </param>
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212
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213 <param argument="--startLabel" type="text" value="TSS"
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214 label="Label for the region start"
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215 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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216 <param argument="--endLabel" type="text" value="TES"
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217 label="Label for the region end"
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218 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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219
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220 <param argument="--referencePointLabel" type="text" value="TSS"
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221 label="Reference point label"
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222 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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223 <param argument="--samplesLabel" type="text"
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224 label="Labels for the samples (each bigwig) plotted"
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225 help="The default is to use the file name of the sample. The sample labels should be separated by
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226 spaces and quoted if a label itself contains a space E.g. label-1 &quot;label 2&quot;">
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227 <sanitizer>
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228 <valid initial="string.printable">
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229 </valid>
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230 </sanitizer>
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231 </param>
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232 <param argument="--regionsLabel" type="text"
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233 label="Labels for the regions plotted in the heatmap"
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234 help="If more than one region is being plotted a list of labels separated by space is required.
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235 If a label itself contains a space, then quotes are needed.
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236 For example, label_1 &quot;label 2&quot;" />
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237
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238 <expand macro="plotTitle" />
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239 <expand macro="legendLocation" />
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240 <expand macro="labelRotation" />
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241 <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue=""
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242 label="Make one plot per group of regions"
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243 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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244
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245 <expand macro="kmeans_clustering" />
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246 <param argument="--clusterUsingSamples" type="text"
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247 label="List of samples to be used for clustering"
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248 help="List of sample numbers (order as in matrix), which are used by --kmeans or --hclust for clustering.
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249 If no value is set, it uses all samples. Example: 1 3 (space separated!)"/>
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250 <sanitizer>
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251 <valid initial="string.printable">
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252 <add value=" "/>
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253 </valid>
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254 </sanitizer>
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255 </when>
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256 </conditional>
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257 </inputs>
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258 <outputs>
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259 <expand macro="output_image_file_format" />
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260 <expand macro="output_graphic_outputs" />
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261 <expand macro="output_save_matrix_values" />
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262 </outputs>
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263 <tests>
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264 <test>
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265 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
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266 <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="4000" />
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267 </test>
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268 <test>
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269 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
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270 <param name="showAdvancedOpt" value="yes" />
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271 <param name="whatToShow" value="heatmap and colorbar" />
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272 <output name="outFileName" file="heatmapper_result2.png" ftype="png" compare="sim_size" delta="4000" />
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273 </test>
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274 </tests>
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275 <help>
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276 <![CDATA[
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277
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278 What it does
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279 --------------
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280
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281 ``plotHeatmap`` visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes.
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282 Like ``plotProfile``, it requires that computeMatrix was run first to calculate the values.
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283
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284 We have implemented a number of optional parameters to optimize the visual output and we encourage you to play around with the min/max values
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285 displayed in the heatmap as well as with the different coloring options.
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286
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287 **TIP:** *If your data is rather sparse and the resulting heatmap is too black, change the "Missing data color" to white (via "Advanced options").*
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288
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289 The most powerful option is probably the **k-means/hierarchical clustering** where you can sort your regions into groups of regions with similar score distributions.
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290
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291 **NOTE:** *The clustering will only work if you supplied a single BED file to computeMatrix. plotHeatmap cannot cluster regions within pre-defined groups. Moreover, k-means will be much faster than hierarchical clustering.*
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292
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293 Output
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294 --------------
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295
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296 This is a heatmap based on two bigWig files generated with default settings and k-means clustering.
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297
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298 .. image:: $PATH_TO_IMAGES/plotHeatmap_example.png
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299 :width: 600
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300 :height: 694
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301
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302 .. image:: $PATH_TO_IMAGES/plotHeatmap_example02.png
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303 :width: 600
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304 :height: 694
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305
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306 In addition to the image, ``plotHeatmap`` can also generate the values underlying both the heatmap.
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307
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308 See the following table for the optional output options:
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309
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310 +-----------------------------------+--------------------+-----------------+-----------------+
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311 | **optional output type** | **computeMatrix** | **plotHeatmap** | **plotProfile** |
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312 +-----------------------------------+--------------------+-----------------+-----------------+
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313 | values underlying the heatmap | yes | yes | no |
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314 +-----------------------------------+--------------------+-----------------+-----------------+
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315 | values underlying the profile | no | no | yes |
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316 +-----------------------------------+--------------------+-----------------+-----------------+
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317 | sorted and/or filtered regions | yes | yes | yes |
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318 +-----------------------------------+--------------------+-----------------+-----------------+
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319
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320 **More examples** can be found in our `Gallery <http://deeptools.readthedocs.org/en/latest/content/example_gallery.html#normalized-chip-seq-signals-and-peak-regions>`_.
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321
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322 -----
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323
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324 @REFERENCES@
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325 ]]>
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326 </help>
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327 <expand macro="citations" />
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328 </tool>