Mercurial > repos > bgruening > deeptools_plot_enrichment

annotate plotEnrichment.xml @ 21:c03c3384cd81 draft

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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 14:47:18 +0000
parents e65d16fb2724
children
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21
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1 <tool id="deeptools_plot_enrichment" name="plotEnrichment" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
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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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30
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31 #if $advancedOpt.showAdvancedOpt == "yes"
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32 #if $advancedOpt.attributeKey:
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33 --attributeKey '$advancedOpt.attributeKey'
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34 #end if
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35
0
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36 #if $advancedOpt.labels and str($advancedOpt.labels).strip() != "":
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37 --labels $advancedOpt.labels
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38 #end if
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39
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40 #if $advancedOpt.regionLabels and str($advancedOpt.regionLabels).strip() != "":
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41 --regionLabels $advancedOpt.regionLabels
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42 #end if
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44 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
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45 --plotTitle '$advancedOpt.plotTitle'
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46 #end if
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47
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48 $advancedOpt.perSample
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50 $advancedOpt.variableScales
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51
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52 $advancedOpt.perSample
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54 $advancedOpt.variableScales
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56 --plotWidth '$advancedOpt.plotWidth'
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58 --plotHeight '$advancedOpt.plotHeight'
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60 #if str($advancedOpt.colors).strip() != "":
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61 --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )#
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62 #end if
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64 --numPlotsPerRow '$advancedOpt.numPlotsPerRow'
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66 --alpha '$advancedOpt.alpha'
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68 @ADVANCED_OPTS_READ_PROCESSING@
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69
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70 #if $advancedOpt.Offset:
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71 --Offset $advancedOpt.Offset
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72 #end if
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73
0
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74 @blacklist@
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76 $advancedOpt.keepExons
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78 #end if
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79 ]]>
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80 </command>
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82 <inputs>
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83 <expand macro="multiple_input_bams" MIN="1"/>
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84 <expand macro="custom_sample_labels" />
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85 <expand macro="multiple_bed" />
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87 <expand macro="region_limit_operation" />
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88 <expand macro="input_image_file_format" />
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89
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90 <expand macro="advancedOpt_scaffold">
18
e65d16fb2724 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
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91 <param argument="--attributeKey" type="text" optional="true" size="20" label="Optional attribute key"
17
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92 help="Instead of deriving the feature label from the feature column, use the value of the given
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93 attribute key. For example, the gene_biotype. Note that 'None' is used for BED files
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94 or entries where the attributeKey is not found." />
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95
0
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96 <param argument="--plotHeight" type="integer" value="20" min="3"
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97 label="Plot height"
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98 help="Height in cm. The default for the plot height is 20 centimeters. The minimum value is 3 cm." />
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99
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100 <param argument="--plotWidth" type="integer" value="20" min="1"
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101 label="Plot width"
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102 help="Width in cm. The default value is 20 centimeters. The minimum value is 1 cm." />
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103
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104 <param argument="--labels" type="text" size="30"
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105 label="Labels for the samples (each BAM file) plotted"
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106 help="The default is to use the file name of the sample. The sample labels should be separated by
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107 spaces and quoted if a label itself contains a space, e.g., label-1 &quot;label 2&quot;">
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108 <sanitizer>
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109 <valid initial="string.printable" />
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110 </sanitizer>
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111 </param>
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112
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113 <param argument="--regionLabels" type="text" size="30"
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114 label="Labels for the features"
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115 help="For BED files, this sets the label for all entries in each file.
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116 For GTF files this is ignored." />
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117
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118 <expand macro="plotTitle" />
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119
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120 <param argument="--alpha" type="float" value="0.9" min="0.0" max="1.0"
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121 label="Alpha channel"
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122 help="The alpha channel value (between 0 and 1). A value of 0 is transparent. Default: 0.9" />
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123
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124 <param argument="--colors" type="text" value="" size="40"
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125 label="List of colors to use for the plotted bars"
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126 help="Color names and html hex strings (e.g. #eeff22) are accepted.
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127 The color names should be separated by spaces. (--colors red blue green)">
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128 <validator type="expression"
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129 message="Only numbers, digits, '#' and spaces are allowed.">all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value)</validator>
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130 </param>
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131
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132 <param argument="--perSample" type="boolean" truevalue="--perSample" falsevalue=""
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133 label="Create one plot per-sample"
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134 help="Plot per-sample, rather than per-feature." />
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135
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136 <param argument="--variableScales" type="boolean" truevalue="--variableScales" falsevalue=""
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137 label="Allow variable scales"
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138 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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139
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140 <param argument="--numPlotsPerRow" type="integer" value="4" min="1"
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141 label="Number of plots/row"
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142 help="" />
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143
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144 <expand macro="read_processing_options" />
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145
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146 <param argument="--keepExons" type="boolean" truevalue="--keepExons" falsevalue=""
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147 label="Include BED12 exons"
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148 help="Only for BED12 files, include columns 10-12 rather than just 2 and 3." />
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149
4
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150 <param argument="--Offset" type="text" value="" optional="True"
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151 label="Offset inside each alignment to use for the signal location."
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152 help="Uses this offset inside of each read as the signal. This is useful in
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153 cases like RiboSeq or GROseq, where only the 12th, 15th or 1st base aligned
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154 should be used to denote where the signal is (rather than the span of the
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155 whole alignment). This can be paired with the --filterRNAstrand option. Note
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156 that negative values indicate offsets from the end of each read. A value of
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157 1 indicates the first base of the alignment (taking alignment orientation
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158 into account). Likewise, a value of -1 is the last base of the alignment. An
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159 offset of 0 is not permitted. If two values (separated by spaces) are specified, then they will be
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160 used to specify a range of positions. Note that specifying something like
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161 --Offset 5 -1 will result in the 5th through last position being used, which
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162 is equivalent to trimming 4 bases from the 5-prime end of alignments." />
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163
0
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164 <expand macro="blacklist" />
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165
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166 </expand>
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167
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168 <param argument="--outRawCounts" type="boolean" label="Save percentages to a file" help=""/>
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169
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170 </inputs>
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171 <outputs>
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172 <expand macro="output_image_file_format_not_nested" />
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173 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: percentages">
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174 <filter>outRawCounts is True</filter>
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175 </data>
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176 </outputs>
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177 <tests>
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178 <test>
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179 <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
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180 <param name="BED" value="multiBamSummary_regions.bed,multiBamSummary_regions.bed" ftype="bed" />
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181 <param name="outRawCounts" value="true" />
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182 <param name="showAdvancedOpt" value="yes" />
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183 <param name="minMappingQuality" value="0" />
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184 <param name="regionLabels" value="up down" />
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185 <output name="outFileName" file="plotEnrichment_output.png" ftype="png" compare="sim_size" delta="1000" />
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186 <output name="outFileRawCounts" file="plotEnrichment_output.txt" ftype="tabular" />
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187 </test>
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188 </tests>
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189
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190 <help>
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191 <![CDATA[
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192
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193 What it does
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194 -------------
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195
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196 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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197
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198 Output
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199 --------
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200
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201 The output file is a plot in the format specified. A table of the percentages and raw counts can also be created.
0
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202
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203 .. image:: $PATH_TO_IMAGES/plotEnrichment_output.png
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204 :width: 600
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205 :height: 600
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206
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207 -----
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208
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209 @REFERENCES@
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210 ]]>
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211 </help>
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212 <expand macro="citations" />
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213 </tool>