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1 <tool id="deeptools_profiler" name="profiler" version="@WRAPPER_VERSION@.0">
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2 <description>
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3 creates a profile plot for a score associated to genomic regions
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4 </description>
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5 <expand macro="requirements" />
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6 <expand macro="stdio" />
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7 <macros>
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8 <token name="@BINARY@">profiler</token>
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9 <import>deepTools_macros.xml</import>
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10 </macros>
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11 <command>
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12 <![CDATA[
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13 profiler
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14
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15 --matrixFile $matrixFile
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16 --outFileName $outFileName
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17
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18 #if $output.showOutputSettings == "yes"
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19 --plotFileFormat $output.outFileFormat
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20
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21 #if $output.saveData:
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22 --outFileNameData '$outFileNameData'
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23 #end if
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24
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25 #if $output.saveSortedRegions:
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26 --outFileSortedRegions '$outFileSortedRegions'
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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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31
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32 #if $scaleRegions.showScaleRegionsOpt == "yes":
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33 --startLabel '$scaleRegions.startLabel'
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34 --endLabel '$scaleRegions.endLabel'
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35 #end if
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36
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37 #if $advancedOpt.showAdvancedOpt == "yes":
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38 #if $advancedOpt.averageType:
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39 --averageType '$advancedOpt.averageType'
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40 #end if
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41 --plotHeight $advancedOpt.plotHeight
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42 --plotWidth $advancedOpt.plotWidth
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43 --plotType $advancedOpt.plotType
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44
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45 --regionsLabel '$advancedOpt.regionsLabel'
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46
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47 #if str($advancedOpt.plotTitle).strip() != "":
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48 --plotTitle '$advancedOpt.plotTitle'
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49 #end if
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50
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51 #if str($advancedOpt.colors).strip() != "":
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52 --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )#
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53 #end if
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54
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55 $advancedOpt.onePlotPerGroup
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56
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57 #if $advancedOpt.yMin:
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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 #if str($advancedOpt.yAxisLabel.value) != "None":
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66 --yAxisLabel '$advancedOpt.yAxisLabel'
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67 #end if
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68
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69 @KMEANS_CLUSTERING@
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70
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71 #end if
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72 ]]>
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73 </command>
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74 <inputs>
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75 <param name="matrixFile" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/>
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76 <conditional name="scaleRegions">
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77 <param name="showScaleRegionsOpt" type="select" label="The input matrix was computed in scale-regions mode">
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78 <option value="no" selected="true">no</option>
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79 <option value="yes">yes</option>
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80 </param>
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81 <when value="no" />
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82 <when value="yes">
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83 <param name="startLabel" type="text" value="TSS" size="10"
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84 label="Label for the region start"
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85 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. "peak start"." />
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86 <param name="endLabel" type="text" value="TES" size="10"
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87 label="Label for the region end"
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88 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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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 name="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 <param name="plotWidth" type="integer" value="8" min="1"
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115 label="Plot width"
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116 help="Width in cm. The default value is 8 centimeters. The minimum value is 1 cm." />
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117 <param name="plotType" type="select" label="Plot type"
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118 help="For the summary plot (profile) only. The "lines" option will plot the profile line based on the average type selected. The "fill" option fills the region between zero and the profile curve. The fill in color is semi transparent to distinguish different profiles. The "add standard error" option colors the region between the profile and the standard error of the data. As in the case of fill, a semi-transparent color is used. The option "overlapped_lines" plots each region values, one on top of the other; this option only works if "one plot per proup" is set.">
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119 <option value="lines" selected="true">lines</option>
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120 <option value="fill">fill</option>
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121 <option value="se">add standard error</option>
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122 <option value="overlapped_lines">overlapped lines</option>
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123 </param>
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124 <param name="regionsLabel" type="text" value="genes" size="30"
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125 label="Labels for the regions plotted in the heatmap"
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126 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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127 <param name="plotTitle" type="text" value="" size="30"
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128 label="Title of the plot"
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129 help="Title of the plot, to be printed on top of the generated image. Leave blank for no title." />
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130 <param name="colors" type="text" value="" size="40"
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131 label="List of colors to use for the plotted lines"
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132 help="Color names and html hex strings (e.g. #eeff22) are accepted. The color names should be given separated by spaces. (--colors red blue green)">
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133 <validator type="expression"
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134 message="Only numbers, digits, '#' and spaces are allowed.">all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value)</validator>
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135 </param>
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136
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137 <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue=""
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138 label="Do one plot per group"
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139 help="When the region file contains groups separated by "#", the default is to plot the averages for the distinct plots in one plot. If this option is set, each group will get its own plot, stacked on top of each other."/>
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140 <param name="yMin" type="float" value="" size="3" optional="true"
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141 label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values"/>
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142 <param name="yMax" type="float" value="" size="3" optional="true"
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143 label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" />
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144 <param name="xAxisLabel" type="text" value="gene distance (bp)" size="50"
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145 label="Description for the x-axis label" />
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146 <param name="yAxisLabel" type="text" value="" size="50"
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147 label="Description for the y-axis label for the top panel" />
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148
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149 <expand macro="kmeans_clustering" />
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150
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151 </when>
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152 </conditional>
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153 </inputs>
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154 <outputs>
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155 <expand macro="output_image_file_format" />
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156 <expand macro="output_graphic_outputs" />
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157 </outputs>
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158 <help>
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159 <![CDATA[
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160 **What it does**
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161
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162 This tool plots the average enrichments over all genomic
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163 regions supplied to computeMarix. It requires that computeMatrix was successfully run.
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164 It is a very useful complement to the heatmapper, especially in cases when you want to
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165 compare the scores for many different groups. Like heatmapper, profiler does not change the
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166 values that were compute by computeMatrix, but you can choose between
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167 many different ways to color and display the plots.
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168
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169
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170 .. image:: $PATH_TO_IMAGES/visual_profiler_DmelPolII.png
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171 :alt: Meta-gene profile of Rna Polymerase II
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172
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173
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174 You can find more details on the profiler wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-profiler
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175
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176
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177 -----
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178
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179 @REFERENCES@
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180 ]]>
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181 </help>
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182 <expand macro="citations" />
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183 </tool>
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