annotate computeMatrixOperations.xml @ 16:ee3a1b0f45f1 draft default tip

"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
author bgruening
date Sat, 25 Jan 2020 04:55:34 -0500
parents 848ce8f81e6e
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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 == "relabel":
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16 relabel
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17 -m $submodule.matrixFile
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18 #if $submodule.groupLabels is not None and str($submodule.groupLabels) != '':
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19 --groupLabels $submodule.groupLabels
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20 #end if
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21 #if $submodule.sampleLabels is not None and str($submodule.sampleLabels) != '':
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22 --sampleLabels $submodule.sampleLabels
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23 #end if
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24 #else if $submodule.command == "subset":
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25 subset
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26 -m $submodule.matrixFile
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27 #if $submodule.groups is not None and str($submodule.groups) != '':
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28 --groups $submodule.groups
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29 #end if
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30 #if $submodule.samples is not None and str($submodule.samples) != '':
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31 --samples $submodule.samples
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32 #end if
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33 -o $outFileName
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34 #else if $submodule.command == "filterStrand":
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35 filterStrand
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36 -m $submodule.matrixFile
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37 --strand $submodule.strand
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38 -o $outFileName
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39 #else if $submodule.command == "filterValues":
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40 filterValues
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41 -m $submodule.matrixFile
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42 #if $submodule.minValue is not None and str($submodule.minValue) != '':
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43 --min $submodule.minValue
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44 #end if
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45 #if $submodule.maxValue is not None and str($submodule.maxValue) != '':
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46 --max $submodule.maxValue
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47 #end if
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48 -o $outFileName
0
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49 #else if $submodule.command == "rbind":
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50 #set $files=[]
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51 #for $f in $submodule.matrixFiles:
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52 #silent $files.append(str($f.matrixFile))
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53 #end for
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54 rbind
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55 -m '#echo "' '".join($files)#'
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56 -o $outFileName
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57 #else if $submodule.command == "cbind":
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58 cbind
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59 #set $files=[]
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60 #for $f in $submodule.matrixFiles:
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61 #silent $files.append(str($f.matrixFile))
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62 #end for
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63 -m '#echo "' '".join($files)#'
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64 -o $outFileName
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65 #else if $submodule.command == "sort":
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66 sort
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67 #set $files=[]
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68 #for $f in $submodule.regionsFiles:
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69 #silent $files.append(str($f.regionsFile))
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70 #end for
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71 -m $submodule.matrixFile
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72 -R '#echo "' '".join($files)#'
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73 -o $outFileName
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74 #end if
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75 ]]>
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76 </command>
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77 <inputs>
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78 <conditional name="submodule">
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79 <param name="command" type="select" label="Operation type">
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80 <option value="info" selected="true">Print information (info)</option>
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81 <option value="relabel">Relabel the samples and/or groups (relabel)</option>
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82 <option value="subset">Subset by samples and/or groups of regions (subset)</option>
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83 <option value="filterStrand">Filter by strand (filterStrand)</option>
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84 <option value="filterValues">Filter by min/max value (filterValues)</option>
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85 <option value="rbind">Bind matrices, top to bottom (rbind)</option>
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86 <option value="cbind">Bind matrices, left to right (cbind)</option>
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87 <option value="sort">Sort by region order in specified files (sort)</option>
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88 </param>
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89 <when value="info">
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90 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
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91 label="Matrix file from the computeMatrix tool" help=""/>
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92 </when>
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93
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94 <when value="relabel">
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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 <param argument="groupLabels" type="text" optional="true" label="New Region/Group Labels."
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98 help="If blank, the labels are left unchanged, otherwise they're changed to be those provided here. Multiple labels should be separated by spaces. If you provide labels, you must provide exactly one label for each group of regions."/>
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99 <param argument="sampleLabels" type="text" optional="true" label="New Sample Labels."
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100 help="If blank, the labels are left unchanged, otherwise they're changed to be those provided here. Multiple labels should be separated by spaces. If you provide labels, you must provide exactly one label for each sample."/>
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101 </when>
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102
0
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103 <when value="subset">
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104 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
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105 label="Matrix file from the computeMatrix tool" help=""/>
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106 <param argument="groups" type="text" optional="true" label="Region groups to include."
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107 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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108 <param argument="samples" type="text" optional="true" label="Samples to include."
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109 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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110 </when>
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111
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112 <when value="filterStrand">
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113 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
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114 label="Matrix file from the computeMatrix tool" help=""/>
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115 <param argument="--strand" type="select" label="Only include regions on this strand."
0
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116 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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117 <option value="+">+</option>
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118 <option value="-">-</option>
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119 <option value=".">. (no annotated strand)</option>
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120 </param>
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121 </when>
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122
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123 <when value="filterValues">
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124 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
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125 label="Matrix file from the computeMatrix tool" help=""/>
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126 <param argument="--min" type="float" optional="true" label="Minimum value"
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127 help="Exclude any row in the matrix with a value below this. By default there is no minimum value." />
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128 <param argument="--max" type="float" optional="true" label="Maximum value"
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129 help="Exclude any row in the matrix with a value above this. By default there is no maximum value." />
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130 </when>
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131
0
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132 <when value="rbind">
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133 <repeat name="matrixFiles" title="Matrix files from computeMatrix" min="2">
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134 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
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135 label="Matrix file from the computeMatrix tool" help=""/>
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136 </repeat>
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137 </when>
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138
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139 <when value="cbind">
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140 <repeat name="matrixFiles" title="Matrix files from computeMatrix" min="2">
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141 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
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142 label="Matrix file from the computeMatrix tool" help=""/>
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143 </repeat>
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144 </when>
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145
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146 <when value="sort">
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147 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
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148 label="Matrix file from the computeMatrix tool" help=""/>
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149 <repeat name="regionsFiles" title="BED or GTF files of regions" min="1">
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150 <param name="regionsFile" format="bed,gtf" type="data" label="Regions to plot"
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151 help="File, in BED format, containing the regions to plot."/>
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152 </repeat>
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153 </when>
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154 </conditional>
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155 </inputs>
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156 <outputs>
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157 <data format="deeptools_compute_matrix_archive" name="outFileName" label="${tool.name} ${submodule.command} on ${on_string}">
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158 <filter>
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159 ((
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160 submodule['command'] != "info"
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161 ))
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162 </filter>
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163 </data>
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164 <data format="txt" name="outFileTxt" label="${tool.name} info on ${on_string}">
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165 <filter>
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166 ((
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167 submodule['command'] == "info"
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168 ))
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169 </filter>
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170 </data>
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171 </outputs>
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172 <tests>
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173 <test>
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174 <param name="command" value="info" />
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175 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
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176 <output name="outFileTxt" file="computeMatrixOperations.txt" ftype="txt" />
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177 </test>
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178 <test>
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179 <param name="command" value="rbind" />
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180 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
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181 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
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182 <output name="outFileName" file="computeMatrixOperations_result2.mat.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" delta="100"/>
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183 </test>
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184 </tests>
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185 <help>
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186 <![CDATA[
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187
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188 What it does
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189 ------------
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190
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191 ``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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192
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193 +----------------+--------------------------------------------------------------------------------------------------------------------------+
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194 + **Subcommand** | **What it does** |
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195 +----------------+--------------------------------------------------------------------------------------------------------------------------+
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196 + info | Prints out the sample and region group names in the order in which they appear. |
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197 +----------------+--------------------------------------------------------------------------------------------------------------------------+
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198 + 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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199 +----------------+--------------------------------------------------------------------------------------------------------------------------+
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200 + filterStrand | Filters the file to only include regions annotated as being on a particular strand. |
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201 +----------------+--------------------------------------------------------------------------------------------------------------------------+
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202 + rbind | Concatenates multiple matrices together, top to bottom. |
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203 +----------------+--------------------------------------------------------------------------------------------------------------------------+
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204 + cbind | Merges multiple matrices, left to right. |
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205 +----------------+--------------------------------------------------------------------------------------------------------------------------+
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206 + sort | Sorts the given file so regions are in the order of occurence in the input BED/GTF file(s). |
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207 +----------------+--------------------------------------------------------------------------------------------------------------------------+
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208
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209
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210 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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211
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212 -----
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213
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214 @REFERENCES@
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215 ]]>
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216 </help>
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217 <expand macro="citations" />
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218 </tool>