Mercurial > repos > bgruening > deeptools_plot_enrichment

annotate plotEnrichment.xml @ 9:618c05a02bef draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e071ca1cc84da473ecc209c9d5e633d90cbc6a78
author bgruening
date Mon, 15 May 2017 03:57:26 -0400
parents f8b1d1ae388e
children 4039432f51fc
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1 <tool id="deeptools_plot_enrichment" name="plotEnrichment" version="@WRAPPER_VERSION@.0">
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2 <description>plots read/fragment coverage over sets of regions</description>
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3 <macros>
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4 <token name="@BINARY@">plotEnrichment</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 @multiple_input_bams@
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11 @BINARY@
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12 @THREADS@
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14 --plotFile '$outFileName'
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16 --bamfiles #echo " ".join($files)#
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17 --labels #echo " ".join($labels)#
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19 @multiple_bed@
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21 #if $outRawCounts:
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22 --outRawCounts "$outFileRawCounts"
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23 #end if
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25 --plotFileFormat "$outFileFormat"
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27 #if str($region).strip() != "":
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28 --region '$region'
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29 #end if
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31 #if $advancedOpt.showAdvancedOpt == "yes"
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32 #if $advancedOpt.labels and str($advancedOpt.labels).strip() != "":
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33 --labels $advancedOpt.labels
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34 #end if
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35
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36 #if $advancedOpt.regionLabels and str($advancedOpt.regionLabels).strip() != "":
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37 --regionLabels $advancedOpt.regionLabels
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38 #end if
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39
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40 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
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41 --plotTitle '$advancedOpt.plotTitle'
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42 #end if
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44 $advancedOpt.perSample
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46 $advancedOpt.variableScales
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48 $advancedOpt.perSample
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49
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50 $advancedOpt.variableScales
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52 --plotWidth '$advancedOpt.plotWidth'
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53
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54 --plotHeight '$advancedOpt.plotHeight'
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55
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56 #if str($advancedOpt.colors).strip() != "":
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57 --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )#
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58 #end if
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59
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60 --numPlotsPerRow '$advancedOpt.numPlotsPerRow'
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61
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62 --alpha '$advancedOpt.alpha'
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64 @ADVANCED_OPTS_READ_PROCESSING@
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65
6
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66 #if $advancedOpt.Offset:
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67 --Offset $advancedOpt.Offset
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68 #end if
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69
0
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70 @blacklist@
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71
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72 $advancedOpt.keepExons
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74 #end if
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75 ]]>
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76 </command>
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78 <inputs>
8
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79 <expand macro="multiple_input_bams" MIN="1"/>
0
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80 <expand macro="multiple_bed" />
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81
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82 <expand macro="region_limit_operation" />
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83 <expand macro="input_image_file_format" />
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84
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85 <expand macro="advancedOpt_scaffold">
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86 <param argument="--plotHeight" type="integer" value="20" min="3"
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87 label="Plot height"
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88 help="Height in cm. The default for the plot height is 20 centimeters. The minimum value is 3 cm." />
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89
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90 <param argument="--plotWidth" type="integer" value="20" min="1"
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91 label="Plot width"
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92 help="Width in cm. The default value is 20 centimeters. The minimum value is 1 cm." />
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93
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94 <param argument="--labels" type="text" size="30"
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95 label="Labels for the samples (each BAM file) plotted"
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96 help="The default is to use the file name of the sample. The sample labels should be separated by
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97 spaces and quoted if a label itself contains a space, e.g., label-1 &quot;label 2&quot;">
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98 <sanitizer>
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99 <valid initial="string.printable" />
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100 </sanitizer>
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101 </param>
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102
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103 <param argument="--regionLabels" type="text" size="30"
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104 label="Labels for the features"
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105 help="For BED files, this sets the label for all entries in each file.
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106 For GTF files this is ignored." />
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107
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108 <expand macro="plotTitle" />
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109
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110 <param argument="--alpha" type="float" value="0.9" min="0.0" max="1.0"
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111 label="Alpha channel"
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112 help="The alpha channel value (between 0 and 1). A value of 0 is transparent. Default: 0.9" />
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113
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114 <param argument="--colors" type="text" value="" size="40"
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115 label="List of colors to use for the plotted bars"
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116 help="Color names and html hex strings (e.g. #eeff22) are accepted.
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117 The color names should be separated by spaces. (--colors red blue green)">
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118 <validator type="expression"
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119 message="Only numbers, digits, '#' and spaces are allowed.">all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value)</validator>
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120 </param>
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121
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122 <param argument="--perSample" type="boolean" truevalue="--perSample" falsevalue=""
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123 label="Create one plot per-sample"
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124 help="Plot per-sample, rather than per-feature." />
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125
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126 <param argument="--variableScales" type="boolean" truevalue="--variableScales" falsevalue=""
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127 label="Allow variable scales"
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128 help="By default, the y-axis always goes from 0 to 100. If this option is selected, then the maximum value will vary with the dataset." />
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129
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130 <param argument="--numPlotsPerRow" type="integer" value="4" min="1"
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131 label="Number of plots/row"
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132 help="" />
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133
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134 <expand macro="read_processing_options" />
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135
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136 <param argument="--keepExons" type="boolean" truevalue="--keepExons" falsevalue=""
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137 label="Include BED12 exons"
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138 help="Only for BED12 files, include columns 10-12 rather than just 2 and 3." />
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139
6
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140 <param argument="--Offset" type="text" value="" optional="True"
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141 label="Offset inside each alignment to use for the signal location."
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142 help="Uses this offset inside of each read as the signal. This is useful in
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143 cases like RiboSeq or GROseq, where only the 12th, 15th or 1st base aligned
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144 should be used to denote where the signal is (rather than the span of the
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145 whole alignment). This can be paired with the --filterRNAstrand option. Note
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146 that negative values indicate offsets from the end of each read. A value of
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147 1 indicates the first base of the alignment (taking alignment orientation
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148 into account). Likewise, a value of -1 is the last base of the alignment. An
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149 offset of 0 is not permitted. If two values (separated by spaces) are specified, then they will be
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150 used to specify a range of positions. Note that specifying something like
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151 --Offset 5 -1 will result in the 5th through last position being used, which
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152 is equivalent to trimming 4 bases from the 5-prime end of alignments." />
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153
0
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154 <expand macro="blacklist" />
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155
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156 </expand>
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157
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158 <param argument="--outRawCounts" type="boolean" label="Save percentages to a file" help=""/>
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159
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160 </inputs>
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161 <outputs>
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162 <expand macro="output_image_file_format_not_nested" />
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163 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: percentages">
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164 <filter>outRawCounts is True</filter>
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165 </data>
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166 </outputs>
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167 <tests>
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168 <test>
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169 <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
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170 <param name="BED" value="multiBamSummary_regions.bed,multiBamSummary_regions.bed" ftype="bed" />
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171 <param name="outRawCounts" value="true" />
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172 <param name="showAdvancedOpt" value="yes" />
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173 <param name="minMappingQuality" value="0" />
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174 <param name="regionLabels" value="up down" />
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175 <output name="outFileName" file="plotEnrichment_output.png" ftype="png" compare="sim_size" delta="1000" />
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176 <output name="outFileRawCounts" file="plotEnrichment_output.txt" ftype="tabular" />
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177 </test>
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178 </tests>
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179
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180 <help>
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181 <![CDATA[
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182
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183 What it does
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184 -------------
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185
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186 This tool determines read/fragment coverage of regions. The regions (e.g., exons, genes or peaks) can be specified in one or more BED or GTF files. For GTF files, the feature type is taken from column 3. For BED files, the file name is used. For BED files, the feature labels can be changed.
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187
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188 Output
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189 --------
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190
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191 The output file is a plot in the format specified. A table of the percentages can also be created.
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192
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193 .. image:: $PATH_TO_IMAGES/plotEnrichment_output.png
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194 :width: 600
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195 :height: 600
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196
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197 -----
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198
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199 @REFERENCES@
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200 ]]>
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201 </help>
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202 <expand macro="citations" />
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203 </tool>