Mercurial > repos > bgruening > deeptools_compute_matrix_operations

annotate computeMatrixOperations.xml @ 7:20daeedf5ed5 draft

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author bgruening
date Mon, 05 Feb 2018 11:35:15 -0500
parents db94d629b9eb
children fd7e4d6a5d68
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1 <tool id="deeptools_compute_matrix_operations" name="computeMatrixOperations" version="@WRAPPER_VERSION@.0">
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2 <description>Modify or combine the output of computeMatrix in a variety of ways.</description>
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3 <macros>
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4 <token name="@BINARY@">computeMatrixOperations</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 #if $submodule.command == "info":
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12 info
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13 -m $submodule.matrixFile
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14 > $outFileTxt
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15 #else if $submodule.command == "subset":
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16 subset
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17 -m $submodule.matrixFile
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18 #if $submodule.groups is not None and str($submodule.groups) != '':
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19 --groups $submodule.groups
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20 #end if
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21 #if $submodule.samples is not None and str($submodule.samples) != '':
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22 --samples $submodule.samples
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23 #end if
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24 -o $outFileName
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25 #else if $submodule.command == "filterStrand":
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26 filterStrand
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27 -m $submodule.matrixFile
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28 --strand $submodule.strand
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29 -o $outFileName
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30 #else if $submodule.command == "rbind":
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31 #set $files=[]
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32 #for $f in $submodule.matrixFiles:
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33 #silent $files.append(str($f.matrixFile))
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34 #end for
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35 rbind
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36 -m '#echo "' '".join($files)#'
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37 -o $outFileName
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38 #else if $submodule.command == "cbind":
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39 cbind
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40 #set $files=[]
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41 #for $f in $submodule.matrixFiles:
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42 #silent $files.append(str($f.matrixFile))
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43 #end for
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44 -m '#echo "' '".join($files)#'
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45 -o $outFileName
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46 #else if $submodule.command == "sort":
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47 sort
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48 #set $files=[]
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49 #for $f in $submodule.regionsFiles:
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50 #silent $files.append(str($f.regionsFile))
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51 #end for
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52 -m $submodule.matrixFile
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53 -R '#echo "' '".join($files)#'
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54 -o $outFileName
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55 #end if
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56 ]]>
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57 </command>
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58 <inputs>
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59 <conditional name="submodule">
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60 <param name="command" type="select" label="Operation type">
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61 <option value="info" selected="true">Print information (info)</option>
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62 <option value="subset">Subset by samples and/or groups of regions (subset)</option>
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63 <option value="filterStrand">Filter by strand (filterStrand)</option>
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64 <option value="rbind">Bind matrices, top to bottom (rbind)</option>
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65 <option value="cbind">Bind matrices, left to right (cbind)</option>
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66 <option value="sort">Sort by region order in specified files (sort)</option>
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67 </param>
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68 <when value="info">
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69 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
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70 label="Matrix file from the computeMatrix tool" help=""/>
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71 </when>
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72
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73 <when value="subset">
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74 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
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75 label="Matrix file from the computeMatrix tool" help=""/>
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76 <param argument="groups" type="text" optional="true" label="Region groups to include."
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77 help="If blank, all region groups are output. Alternatively, one or more groups listed in the output of the 'info' command can be used (separate groups by a space and enclose in quotes if needed)" />
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78 <param argument="samples" type="text" optional="true" label="Samples to include."
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79 help="If blank, all samples are output. Alternatively, one or more samples listed in the output of the 'info' command can be used (separate sample names by a space and enclose in quotes if needed)" />
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80 </when>
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81
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82 <when value="filterStrand">
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83 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
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84 label="Matrix file from the computeMatrix tool" help=""/>
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85 <param argument="strand" type="select" label="Only include regions on this strand."
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86 help="Only regions on the desired strand will be included in the output. If you desire to instead remove regions on only one strand (or the . strand), separately run this on the other strand and then use the rbind operation.">
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87 <option value="+">+</option>
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88 <option value="-">-</option>
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89 <option value=".">. (no annotated strand)</option>
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90 </param>
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91 </when>
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92
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93 <when value="rbind">
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94 <repeat name="matrixFiles" title="Matrix files from computeMatrix" min="2">
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95 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
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96 label="Matrix file from the computeMatrix tool" help=""/>
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97 </repeat>
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98 </when>
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99
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100 <when value="cbind">
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101 <repeat name="matrixFiles" title="Matrix files from computeMatrix" min="2">
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102 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
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103 label="Matrix file from the computeMatrix tool" help=""/>
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104 </repeat>
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105 </when>
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106
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107 <when value="sort">
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108 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
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109 label="Matrix file from the computeMatrix tool" help=""/>
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110 <repeat name="regionsFiles" title="BED or GTF files of regions" min="1">
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111 <param name="regionsFile" format="bed,gtf" type="data" label="Regions to plot"
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112 help="File, in BED format, containing the regions to plot."/>
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113 </repeat>
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114 </when>
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115 </conditional>
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116 </inputs>
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117 <outputs>
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118 <data format="deeptools_compute_matrix_archive" name="outFileName" label="${tool.name} ${submodule.command} on ${on_string}">
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119 <filter>
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120 ((
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121 submodule['command'] != "info"
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122 ))
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123 </filter>
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124 </data>
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125 <data format="txt" name="outFileTxt" label="${tool.name} info on ${on_string}">
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126 <filter>
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127 ((
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128 submodule['command'] == "info"
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129 ))
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130 </filter>
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131 </data>
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132 </outputs>
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133 <tests>
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134 <test>
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135 <param name="command" value="info" />
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136 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
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137 <output name="outFileTxt" file="computeMatrixOperations.txt" ftype="txt" />
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138 </test>
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139 <test>
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140 <param name="command" value="rbind" />
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141 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
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142 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
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143 <output name="outFileName" file="computeMatrixOperations_result2.mat.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" delta="100"/>
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144 </test>
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145 </tests>
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146 <help>
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147 <![CDATA[
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148
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149 What it does
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150 ------------
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151
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152 ``computeMatrixOperations`` can perform a variety of operations on one or more files produced by ``computeMatrix`` (N.B., the output is always written to a new file):
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153
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154 +----------------+--------------------------------------------------------------------------------------------------------------------------+
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155 + **Subcommand** | **What it does** |
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156 +----------------+--------------------------------------------------------------------------------------------------------------------------+
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157 + info | Prints out the sample and region group names in the order in which they appear. |
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158 +----------------+--------------------------------------------------------------------------------------------------------------------------+
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159 + subset | Subsets a file by the desired samples/region group names. This can also change the order of these samples/region groups. |
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160 +----------------+--------------------------------------------------------------------------------------------------------------------------+
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161 + filterStrand | Filters the file to only include regions annotated as being on a particular strand. |
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162 +----------------+--------------------------------------------------------------------------------------------------------------------------+
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163 + rbind | Concatenates multiple matrices together, top to bottom. |
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164 +----------------+--------------------------------------------------------------------------------------------------------------------------+
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165 + cbind | Merges multiple matrices, left to right. |
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166 +----------------+--------------------------------------------------------------------------------------------------------------------------+
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167 + sort | Sorts the given file so regions are in the order of occurence in the input BED/GTF file(s). |
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168 +----------------+--------------------------------------------------------------------------------------------------------------------------+
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169
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170
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171 These operations are useful when you want to run computeMatrix on multiple files (thereby keeping all of the values together) and later exclude regions/samples or add new ones. Another common use would be if you require the output of computeMatrix to be sorted to match the order of regions in the input file.
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172
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173 -----
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174
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175 @REFERENCES@
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176 ]]>
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177 </help>
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178 <expand macro="citations" />
db94d629b9eb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
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179 </tool>