Mercurial > repos > bgruening > deeptools_bam_coverage

annotate bamCoverage.xml @ 0:19a6007845cc draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
author bgruening
date Mon, 25 Jan 2016 20:19:01 -0500
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children 36f655a04a57
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1 <tool id="deeptools_bam_coverage" name="bamCoverage" version="@WRAPPER_VERSION@.0">
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2 <description>generates a coverage bigWig file from a given BAM file</description>
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3 <macros>
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4 <token name="@BINARY@">bamCoverage</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 ln -s '$bamInput' one.bam &&
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11 ln -s '${bamInput.metadata.bam_index}' one.bam.bai &&
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12
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13 @BINARY@
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14 @THREADS@
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16 --bam one.bam
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17 --outFileName '$outFileName'
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18 --outFileFormat '$outFileFormat'
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19
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20 --binSize $binSize
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22 #if $scaling.type=='rpkm':
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23 --normalizeUsingRPKM
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24 #elif $scaling.type=='1x':
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25 #if $scaling.effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
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26 --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize
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27 #else:
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28 --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize_opt
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29 #end if
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30 #elif $scaling.type=='own':
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31 --scaleFactor $scaling.scaleFactor
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32 #end if
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33
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34 #if str($region).strip() != '':
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35 --region '$region'
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36 #end if
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37
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38 #if $advancedOpt.showAdvancedOpt == "yes":
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39 #if $advancedOpt.smoothLength:
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40 --smoothLength '$advancedOpt.smoothLength'
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41 #end if
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42
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43 @ADVANCED_OPTS_READ_PROCESSING@
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44 $advancedOpt.skipNAs
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45
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46 #if str($advancedOpt.ignoreForNormalization).strip() != '':
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47 --ignoreForNormalization $advancedOpt.ignoreForNormalization
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48 #end if
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49 #end if
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50 ]]>
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51 </command>
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52
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53 <inputs>
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54 <param name="bamInput" format="bam" type="data" label="BAM file"
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55 help="The BAM file must be sorted."/>
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56
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57 <param name="binSize" type="integer" value="50" min="1"
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58 label="Bin size in bases"
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59 help="The genome will be divided into bins of the specified size. For each bin, the overlaping number of fragments (or reads) will be reported. If only half a fragment overlaps, this fraction will be reported. "/>
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60
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61 <conditional name="scaling">
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62 <param name="type" type="select" label="Scaling/Normalization method" >
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63 <option value="1x">Normalize coverage to 1x</option>
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64 <option value="rpkm">Normalize to fragments (reads) per kilobase per million (RPKM)</option>
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65 <option value="no">Do not normalize or scale</option>
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66 </param>
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67 <when value="rpkm">
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68 <expand macro="scaleFactor" />
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69 </when>
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70 <when value="no"/>
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71 <when value="1x">
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72 <expand macro="effectiveGenomeSize" />
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73 <expand macro="scaleFactor" />
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74 </when>
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75 </conditional>
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76
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77 <param name="outFileFormat" type="select" label="Coverage file format">
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78 <option value="bigwig" selected="true">bigwig</option>
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79 <option value="bedgraph">bedgraph</option>
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80 </param>
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81
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82 <expand macro="region_limit_operation" />
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83
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84 <conditional name="advancedOpt">
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85 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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86 <option value="no" selected="true">no</option>
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87 <option value="yes">yes</option>
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88 </param>
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89 <when value="no" />
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90 <when value="yes">
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91 <expand macro="smoothLength" />
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92
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93 <param argument="ignoreForNormalization" type="text" value=""
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94 label="Regions that should be excluded for normalization"
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95 help="A list of chromosome names separated by spaces
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96 containing those chromosomes that should be excluded
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97 during normalization. This is useful when
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98 considering samples with unequal coverage across
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99 chromosomes, like male and female samples. Example: chrX chrM" />
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100
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101 <expand macro="skipNAs" />
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102 <expand macro="read_processing_options" />
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103
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104 <param argument="--MNase" type="boolean" truevalue="--MNase" falsevalue=""
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105 label="Determine nucleosome positions from MNase-seq data"
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106 help="Only the 3 nucleotides at the center of each fragment are counted. The fragment ends are defined by the two mate reads. *NOTE*: Requires paired-end data." />
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107
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108 </when>
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109 </conditional>
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110 </inputs>
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111 <outputs>
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112 <data format="bigwig" name="outFileName">
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113 <change_format>
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114 <when input="outFileFormat" value="bigwig" format="bigwig" />
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115 <when input="outFileFormat" value="bedgraph" format="bedgraph" />
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116 </change_format>
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117 </data>
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118 </outputs>
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119 <tests>
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120 <test>
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121 <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
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122 <param name="outFileFormat" value="bigwig" />
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123 <param name="showAdvancedOpt" value="no" />
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124 <param name="binSize" value="10" />
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125 <param name="type" value="no" />
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126 <output name="outFileName" file="bamCoverage_result1.bw" ftype="bigwig" />
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127 </test>
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128 <test>
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129 <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
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130 <param name="outFileFormat" value="bigwig" />
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131 <param name="showAdvancedOpt" value="no" />
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132 <param name="binSize" value="10" />
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133 <output name="outFileName" file="bamCoverage_result2.bw" ftype="bigwig" />
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134 </test>
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135 <test>
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136 <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
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137 <param name="outFileFormat" value="bedgraph" />
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138 <param name="showAdvancedOpt" value="no" />
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139 <param name="binSize" value="10" />
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140 <output name="outFileName" file="bamCoverage_result3.bg" ftype="bedgraph" />
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141 </test>
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142 <test>
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143 <param name="bamInput" value="phiX.bam" ftype="bam" />
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144 <param name="outFileFormat" value="bigwig" />
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145 <param name="showAdvancedOpt" value="no" />
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146 <param name="binSize" value="10" />
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147 <output name="outFileName" file="bamCoverage_result4.bw" ftype="bigwig" />
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148 </test>
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149 <test>
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150 <param name="bamInput" value="phiX.bam" ftype="bam" />
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151 <param name="outFileFormat" value="bedgraph" />
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152 <param name="showAdvancedOpt" value="yes" />
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153 <param name="binSize" value="10" />
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154 <output name="outFileName" file="bamCoverage_result4.bg" ftype="bedgraph" />
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155 </test>
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156 </tests>
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157 <help>
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158 <![CDATA[
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159 **What it does**
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160
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161 Given a BAM file, this tool generates a bigWig or bedGraph file of fragment or
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162 read coverages. The way the method works is by first calculating all the
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163 number of reads (either extended to match the fragment length or not) that
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164 overlap each bin in the genome. The resulting read counts can be normalized
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165 using either a given scaling factor, the RPKM formula or to get a 1x depth of
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166 coverage (RPGC). In the case of paired-end mapping, each read mate is treated
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167 independently to avoid a bias when a mixture of concordant and discordant
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168 pairs is present. This means that *each end* will be extended to match the
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169 fragment length.
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170
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171 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png
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172
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173
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174 You can find more details on the bamCoverage doc page: https://deeptools.readthedocs.org/en/master/content/tools/bamCoverage.html
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175
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176
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177 **Output files**:
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178
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179 - coverage file either in bigWig or bedGraph format
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181 -----
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183 @REFERENCES@
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184 ]]>
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185 </help>
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186 <expand macro="citations" />
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187 </tool>