Mercurial > repos > bgruening > deeptools_compute_matrix

annotate computeMatrix.xml @ 4:98d2e2ad3c82 draft

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author bgruening
date Thu, 10 Mar 2016 03:25:44 -0500
parents a842285199d9
children aee77c22123d
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1 <tool id="deeptools_compute_matrix" name="computeMatrix" version="@WRAPPER_VERSION@.0">
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2 <description>prepares data for plotting a heatmap or a profile of given regions</description>
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3 <macros>
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4 <token name="@BINARY@">computeMatrix</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 #import tempfile
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11 #set bw_files=[]
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12 #for $counter, $bigwig in enumerate($scoreFileName):
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13 ln -s "${bigwig}" "file_${counter}.bw" &&
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14 #silent $bw_files.append('file_%s.bw' % $counter)
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15 #end for
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17 #set bed_files=[]
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18 #for $counter, $rf in enumerate($regionsFiles):
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19 ln -s "${rf.regionsFile}" "group_${counter}.bed" &&
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20 #silent $bed_files.append('group_%s.bed' % $counter)
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21 #end for
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23 @BINARY@
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24
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25 $mode.mode_select
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26 --regionsFileName '#echo "' '".join($bed_files)#'
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28 --scoreFileName '#echo "' '".join($bw_files)#'
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30 --outFileName '$outFileName'
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32 @THREADS@
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34 #if $output.showOutputSettings == "yes"
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35 #if $output.saveMatrix:
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36 --outFileNameMatrix '$outFileNameMatrix'
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37 #end if
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39 #if $output.saveSortedRegions:
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40 --outFileSortedRegions '$outFileSortedRegions'
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41 #end if
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42 #end if
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43
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44 #if $mode.mode_select == "reference-point":
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45 --referencePoint $mode.referencePoint
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46 $mode.nanAfterEnd
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47 --beforeRegionStartLength $mode.beforeRegionStartLength
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48 --afterRegionStartLength $mode.afterRegionStartLength
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49 #else
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50 --regionBodyLength $mode.regionBodyLength
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51 #if $mode.regionStartLength.regionStartLength_select == "yes":
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52 --beforeRegionStartLength $mode.regionStartLength.beforeRegionStartLength
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53 --afterRegionStartLength $mode.regionStartLength.afterRegionStartLength
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54
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55 --unscaled5prime $mode.regionStartLength.unscaled5prime
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56 --unscaled3prime $mode.regionStartLength.unscaled3prime
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57
0
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58 #end if
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60 #end if
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61
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62 #if $advancedOpt.showAdvancedOpt == "yes":
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63 --sortRegions '$advancedOpt.sortRegions'
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64 --sortUsing '$advancedOpt.sortUsing'
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65 --averageTypeBins '$advancedOpt.averageTypeBins'
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66 $advancedOpt.skipZeros
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67 $advancedOpt.missingDataAsZero
0
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68 --binSize $advancedOpt.binSize
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69
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70 #if $advancedOpt.minThreshold is not None and str($advancedOpt.minThreshold) != '':
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71 --minThreshold $advancedOpt.minThreshold
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72 #end if
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73 #if $advancedOpt.maxThreshold is not None and str($advancedOpt.maxThreshold) != '':
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74 --maxThreshold $advancedOpt.maxThreshold
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75 #end if
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76 #if $advancedOpt.scale is not None and str($advancedOpt.scale) != '':
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77 --scale $advancedOpt.scale
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78 #end if
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79 #end if
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80 ]]>
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81 </command>
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82 <inputs>
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83
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84 <repeat name="regionsFiles" title="Select regions" min="1">
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85 <param name="regionsFile" format="bed" type="data" label="Regions to plot"
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86 help="File, in BED format, containing the regions to plot."/>
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87 </repeat>
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88
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89 <param name="scoreFileName" format="bigwig" type="data"
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90 label="Score file" multiple="True"
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91 help="You can generate a bigWig file from a BAM file using the
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92 bamCoverage tool. (--scoreFileName)"/>
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93
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94 <conditional name="mode" >
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95 <param name="mode_select" type="select"
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96 label="computeMatrix has two main output options"
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97 help="In the scale-regions mode, all regions in the BED file are
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98 stretched or shrunken to the same length (in bases) that is indicated
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99 by the user. Reference-point refers to a position within the BED
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100 regions (start or end of each region). In the reference-point mode only
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101 those genomic positions before (upstream) and/or after (downstream)
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102 the reference point will be considered.">
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103 <option value="scale-regions" selected="true">scale-regions</option>
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104 <option value="reference-point">reference-point</option>
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105 </param>
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106
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107 <when value="scale-regions" >
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108 <param argument="--regionBodyLength" type="integer" value="500"
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109 label="Distance in bases to which all regions are going to be fit" help=""/>
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110 <conditional name="regionStartLength">
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111 <param name="regionStartLength_select" type="select" label="Set distance up- and downstream of the given regions">
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112 <option value="no" selected="true">no</option>
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113 <option value="yes">yes</option>
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114 </param>
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115 <when value="no" />
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116 <when value="yes">
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117 <param argument="--beforeRegionStartLength" type="integer" value="1000" min="1"
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118 label="Distance upstream of the region start position"
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119 help="If the regions are genes, this would be the
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120 distance upstream of the transcription start site."/>
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121 <param argument="--afterRegionStartLength" type="integer" value="1000" min="1"
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122 label="Distance downstream of the region end position"
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123 help="If the regions are genes, this would be the
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124 distance downstream of the transcription end site."/>
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125 <param argument="--unscaled5prime" type="integer" min="0" value="0"
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126 label="Number of bases within the gene body at the 5-prime end to exclude from scaling."
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127 help="By default, each region is scaled to a given length (see the --regionBodyLength
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128 option). In some cases it is useful to look at unscaled signals around region boundaries, so this
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129 setting specifies the number of unscaled bases on the 5-prime end of each boundary." />
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130 <param argument="--unscaled3prime" type="integer" min="0" value="0"
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131 label="Number of bases within the gene body at the 3-prime end to exclude from scaling."
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132 help="As with --unscaled5prime, but for the 3-prime end." />
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133 </when>
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134 </conditional>
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135 </when>
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136 <when value="reference-point">
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137 <param name="referencePoint" type="select" label="The reference point for the plotting">
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138 <option value="TSS" selected="true">beginning of region (e.g. TSS)</option>
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139 <option value="TES">end of region (e.g. TES)</option>
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140 <option value="center">center of region</option>
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141 </param>
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142 <param name="nanAfterEnd" type="boolean" truevalue="--nanAfterEnd" falsevalue=""
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143 label="Discard any values after the region end"
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144 help="This is useful to visualize the region end when not using the
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145 scale-regions mode and when the reference-point is set to the TSS. (--nanAfterEnd)"/>
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146 <param name="beforeRegionStartLength" type="integer" value="1000" min="1"
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147 label="Distance upstream of the start site of the regions defined in the region file"
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148 help="If the regions are genes, this would be the distance upstream of the transcription start site. (--beforeRegionStartLength)"/>
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149 <param name="afterRegionStartLength" type="integer" value="1000" min="1"
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150 label="Distance downstream of the end site of the given regions"
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151 help="If the regions are genes, this would be the distance downstream of the transcription end site. (--afterRegionStartLength)"/>
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152 </when>
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153 </conditional>
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154
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155 <expand macro="input_graphic_output_settings">
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156 <expand macro="input_save_matrix_values" />
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157 </expand>
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158
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159 <conditional name="advancedOpt" >
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160 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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161 <option value="no" selected="true">no</option>
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162 <option value="yes">yes</option>
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163 </param>
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164 <when value="no" />
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165 <when value="yes">
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166 <param name="binSize" type="integer" value="50" min="1"
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167 label="Length, in bases, of non-overlapping bins used for averaging the score over the regions length"
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168 help="(--binSize)"/>
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169
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170 <expand macro="sortRegions" />
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171 <expand macro="sortUsing" />
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172
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173 <param name="averageTypeBins" type="select"
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174 label="Define the type of statistic that should be displayed."
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175 help="The value is computed for each bin. (--averageTypeBins)">
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176 <option value="mean" selected="true">mean</option>
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177 <option value="median">median</option>
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178 <option value="min">min</option>
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179 <option value="max">max</option>
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180 <option value="sum">sum</option>
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181 <option value="std">std</option>
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182 </param>
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183
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184 <param name="missingDataAsZero" type="boolean" truevalue="--missingDataAsZero" falsevalue="" checked="False"
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185 label="Convert missing values to 0?"
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186 help="If set to 'yes', missing values (NAs) are converted
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187 to 0. If you want to use clustering with plotHeatmap
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188 or plotProfile, set this to 'yes'.
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189 The default is to ignore missing values, which will be
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190 depicted as black areas once a heatmap is created.
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191 (--missingDataAsZero)" />
0
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192
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193 <expand macro="skipZeros" />
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194
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195 <param name="minThreshold" type="float" optional="True"
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196 label="Minimum threshold"
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197 help="Any region containing a value that is equal or less than this numeric
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198 value will be skipped. This is useful to skip, for example, genes where the
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199 read count is zero for any of the bins which could be the result of
0
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200 unmappable areas and can bias the overall results. (--minThreshold)"/>
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201 <param name="maxThreshold" type="float" optional="True"
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202 label="Maximum threshold"
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203 help="Any region containing a value that is equal or higher that this
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204 numeric value will be skipped. The max threshold is useful to skip those
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205 few regions with very high read counts (e.g. major satellites) that may
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206 bias the average values. (--maxThreshold)"/>
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207 <param name="scale" type="float" optional="True" label="Scaling factor"
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208 help="If set, all values are multiplied by this number. (--scale)"/>
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209 </when>
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210 </conditional>
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211 </inputs>
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212 <outputs>
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213 <data format="deeptools_compute_matrix_archive" name="outFileName" label="${tool.name} on ${on_string}: Matrix" />
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214 <expand macro="output_graphic_outputs" />
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215 <expand macro="output_save_matrix_values" />
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216 </outputs>
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217 <tests>
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218 <test>
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219 <param name="regionsFile" value="computeMatrix1.bed" ftype="bed" />
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220 <param name="scoreFileName" value="bamCoverage_result4.bw" ftype="bigwig" />
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221 <param name="showAdvancedOpt" value="yes" />
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222 <param name="mode_select" value="reference-point" />
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223 <param name="binSize" value="10" />
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224 <param name="sortUsing" value="sum" />
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225 <param name="averageTypeBins" value="sum" />
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226 <param name="beforeRegionStartLength" value="10" />
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227 <param name="afterRegionStartLength" value="10" />
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228 <output name="outFileName" file="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
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229 </test>
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230 <test>
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231 <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" />
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232 <param name="scoreFileName" value="computeMatrix2.bw" ftype="bigwig" />
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233 <param name="showAdvancedOpt" value="yes" />
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234 <param name="mode_select" value="reference-point" />
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235 <param name="binSize" value="10" />
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236 <param name="beforeRegionStartLength" value="10" />
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237 <param name="afterRegionStartLength" value="10" />
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238 <output name="outFileName" file="computeMatrix_result2.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
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239 </test>
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240 <test>
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241 <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" />
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242 <param name="scoreFileName" value="computeMatrix2.bw" ftype="bigwig" />
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243 <param name="showAdvancedOpt" value="yes" />
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244 <param name="mode_select" value="scale-regions" />
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245 <param name="endLabel" value="END" />
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246 <param name="regionStartLength" value="yes" />
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247 <output name="outFileName" file="computeMatrix_result3.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
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248 </test>
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249 </tests>
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250 <help>
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251 <![CDATA[
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252
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253 What it does
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254 ----------------
0
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255
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256 This tool prepares an intermediate file (a gzipped table of values)
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257 that contains scores associated with genomic regions.
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258 The regions can either be scaled to the same size (using the ``scale-regions`` mode) or you can choose the start, end, or center of each region as the focus point for the score calculations.
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259 For more details, check out the explanation `here <file:///Users/frd2007/Documents/MPI/deepTools/docs/_build/html/content/tools/computeMatrix.html#details>`_.
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260
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261 The intermediate file produced by ``computeMatrix`` is meant to be used with ``plotHeatmap`` and ``plotProfile``.
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262 See the descriptions of ``plotHeatmap`` and ``plotProfile`` for example plots.
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263
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264 .. image:: $PATH_TO_IMAGES/computeMatrix_overview.png
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265 :alt: Relationship between computeMatrix, heatmapper and profiler
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266 :width: 600
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267 :height: 418
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268
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269 =======
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270
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271 Usage hints
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272 -------------
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273
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274 The supplied genomic regions can really be anything - genes, parts of genes, ChIP-seq peaks, favorite genome regions... as long as you provide a proper file
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275 in BED or INTERVAL format. If you would like to compare different groups of regions (e.g., genes from chromosome 2 and 3), you can supply more than 1 regions file, one for each group by selecting "Insert Select regions".
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276
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277 .. image:: $PATH_TO_IMAGES/computeMatrix_selectRegions.png
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278 :width: 600
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279 :height: 150
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280
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281 You can select as many score (bigWig) files as you like. Simply use the Shift and/or Command key while clicking on the files of interest.
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282
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283 .. image:: $PATH_TO_IMAGES/computeMatrix_selectScores.png
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284 :width: 600
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285 :height: 136
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286
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287 The multitude of parameters can seem daunting at first - here are the options that we tend to tune most often:
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288
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289 * ``bin Size`` -- The default value works well most of the time, but if you want to have a more finely grained image, decrease the default value (but not smaller than your bigWig file(s)' bin size). If you want to reduce the computation time, increase it.
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290 * ``Skip zeros`` -- useful to avoid completely blank lines in the heatmap.
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291 * ``Convert missing values to 0?`` -- If you want to identify clusters of similar regions in an unsupervised fashion using ``plotHeatmap`` and/or ``plotProfile``, you should definitely set this to 'yes'.
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292
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293
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294 Output files
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295 ---------------
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296
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297 The default output is a **gzipped table of values** that is used by both ``plotHeatmap`` and ``plotProfile``.
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298
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299 The optional output files include a) the **regions after sorting and filtering (if selected)** as they were used to calculate the values for the plotting, and b) the uncompressed table that **underlies the heatmap**.
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300
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301 **TIP:** ``computeMatrix`` can also be used to filter and sort regions according to their score by making use of the "advanced output settings".
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302
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303 .. image:: $PATH_TO_IMAGES/computeMatrix_advancedOutput.png
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304 :width: 600
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305 :height: 189
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306
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307 .. image:: $PATH_TO_IMAGES/computeMatrix_output.png
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308 :width: 600
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309 :height: 297
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310
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311 Note that these advanced output options are available for ``plotHeatmap`` and ``plotProfile``, too.
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312
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313 See the following table for the optional output options:
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314
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315 +-----------------------------------+--------------------+-----------------+-----------------+
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316 | **optional output type** | **computeMatrix** | **plotHeatmap** | **plotProfile** |
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317 +-----------------------------------+--------------------+-----------------+-----------------+
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318 | values underlying the heatmap | yes | yes | no |
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319 +-----------------------------------+--------------------+-----------------+-----------------+
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320 | values underlying the profile | no | no | yes |
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321 +-----------------------------------+--------------------+-----------------+-----------------+
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322 | sorted and/or filtered regions | yes | yes | yes |
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323 +-----------------------------------+--------------------+-----------------+-----------------+
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324
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325 **More examples** can be found in our `Gallery <http://deeptools.readthedocs.org/en/latest/content/example_gallery.html#normalized-chip-seq-signals-and-peak-regions>`_.
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326
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327 -----
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328
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329 @REFERENCES@
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330 ]]>
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331 </help>
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332 <expand macro="citations" />
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333 </tool>