Mercurial > repos > bgruening > hicexplorer_hiccorrectmatrix

annotate hicCorrectMatrix.xml @ 0:aa854293da07 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
author bgruening
date Sun, 09 Oct 2016 17:35:21 -0400
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children c041d564e6cc
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0
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1 <tool id="hicexplorer_hiccorrectmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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2 <description>Runs Dekker's iterative correction over a hic matrix.</description>
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3 <macros>
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4 <token name="@BINARY@">hicCorrectMatrix</token>
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5 <import>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 '$matrix' temp_matrix.npz.h5 &&
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11
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12 hicCorrectMatrix
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13 $mode.mode_selector
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14 --matrix temp_matrix.npz.h5
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15
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16 ## special: --chromosomes is optional, but if given needs at least one argument
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17 #set chroms = '" "'.join([ str($var.chromosome) for $var in $chromosomes ])
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18 #if chroms
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19 --chromosomes "$chroms"
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20 #end if
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21
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22 #if $mode.mode_selector == 'correct':
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23
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24 --iterNum $mode.iterNum
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25 --outFileName corrected_matrix.npz.h5
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26
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27 #if $mode.filterThreshold_low and $mode.filterThreshold_large:
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28 --filterThreshold $mode.filterThreshold_low $mode.filterThreshold_large
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29 #end if
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30
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31 #if $mode.inflationCutoff:
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32 --inflationCutoff $mode.inflationCutoff
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33 #end if
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34
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35 #if $mode.transCutoff:
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36 --transCutoff $mode.transCutoff
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37 #end if
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38
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39 #if $mode.sequencedCountCutoff:
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40 --sequencedCountCutoff $mode.sequencedCountCutoff
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41 #end if
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42
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43 $mode.skipDiagonal
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44 $mode.perchr
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45
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46 #elif $mode.mode_selector == 'merge_failed':
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47 --plotName diagnostic_plot.png
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48 --outMatrixFile corrected_matrix.npz.h5
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49 #if $mode.xMax:
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50 --xMax $mode.xMax
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51 #end if
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52 #if $mode.filterThreshold_low and $mode.filterThreshold_large:
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53 --filterThreshold $mode.filterThreshold_low $mode.filterThreshold_large
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54 #end if
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55 #else:
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56 --plotName diagnostic_plot.png
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57 #if $mode.xMax:
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58 --xMax $mode.xMax
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59 #end if
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60 #end if
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61
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62 ]]>
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63 </command>
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64 <inputs>
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65 <param argument="--matrix" name="matrix" type="data" format="h5"
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66 label="Hi-C matrix" />
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67
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68 <conditional name="mode">
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69 <param name="mode_selector" type="select" label="Range restriction (in bp)" argument="--range">
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70 <option value="diagnostic_plot">Diagnostic plot</option>
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71 <option value="correct">Correct matrix</option>
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72 <option value="merge_failed">Merges together failed bins</option>
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73 </param>
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74 <when value="diagnostic_plot">
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75 <expand macro="xMax" />
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76 </when>
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77 <when value="correct">
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78 <param argument="--iterNum" name="iterNum" type="integer" optional="true" value="500"
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79 label="Number of iterations" />
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80
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81 <param argument="--inflationCutoff" name="inflationCutoff" type="float" optional="true"
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82 label="Inflation cutoff" value=""
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83 help="Value corresponding to the maximum number of times a bin can be scaled up during the iterative correction.
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84 For example, a inflationCutoff of 3 will filter out all bins that were expanded 3 times or more during the iterative correction."/>
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85
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86 <param argument="--transCutoff" name="transCutoff" type="float" optional="true"
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87 label="Trans region cutoff" value=""
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88 help="Clip high counts in the top -transcut trans regions (i.e. between chromosomes). A usual value is 0.05."/>
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89
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90 <param argument="--sequencedCountCutoff" name="sequencedCountCutoff" optional="true" type="float"
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91 label="Sequenced count cutoff"
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92 help="Each bin receives a value indicating the fraction that is covered by reads.
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93 A cutoff of 0.5 will discard all those bins that have less than half of the bin covered."/>
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94
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95 <param argument="--skipDiagonal" name="skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" checked="false"
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96 label="Skip diagonal counts"/>
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97
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98 <param argument="--perchr" name="perchr" type="boolean" truevalue="--perchr" falsevalue="" checked="false"
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99 label="Normalize each chromosome separately" />
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100 <expand macro="filterThreshold" />
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101
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102 </when>
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103 <when value="merge_failed">
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104 <expand macro="filterThreshold" />
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105 <expand macro="xMax" />
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106 </when>
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107 </conditional>
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108
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109 <repeat name="chromosomes" min="1"
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110 title="Include chromosomes" help="List of chromosomes to be included in the iterative correction.
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111 The order of the given chromosomes will be kept for the resulting corrected matrix">
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112 <param name="chromosome" type="text" value="" />
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113 </repeat>
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114
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115 </inputs>
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116 <outputs>
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117 <data name="outFileName" from_work_dir="corrected_matrix.npz.h5" format="h5">
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118 <filter>mode['mode_selector'] == "correct" or mode['mode_selector'] == "merge_failed"</filter>
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119 </data>
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120 <data name="diagnostic_plot" from_work_dir="diagnostic_plot.png" format="png">
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121 <filter>mode['mode_selector'] == "diagnostic_plot" or mode['mode_selector'] == "merge_failed"</filter>
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122 </data>
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123 </outputs>
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124 <tests>
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125 <test>
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126 <param name="matrix" value="hicBuildMatrix_result1.npz.h5" ftype="h5"/>
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127 <param name="mode_selector" value="correct"/>
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128 <repeat name="chromosomes">
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129 <param name="chromosome" value="chrUextra"/>
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130 </repeat>
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131 <repeat name="chromosomes">
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132 <param name="chromosome" value="chr3LHet"/>
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133 </repeat>
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134 <output name="outFileName" file="hicCorrectMatrix_result1.npz.h5" ftype="h5" compare="sim_size"/>
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135 </test>
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136 <test>
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137 <param name="matrix" ftype="h5" value="hicBuildMatrix_result1.npz.h5"/>
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138 <param name="mode_selector" value="diagnostic_plot"/>
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139 <repeat name="chromosomes">
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140 <param name="chromosome" value="chrUextra"/>
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141 </repeat>
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142 <repeat name="chromosomes">
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143 <param name="chromosome" value="chr3LHet"/>
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144 </repeat>
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145 <output name="diagnostic_plot" file="diagnostic_plot.png" ftype="png" compare="sim_size"/>
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146 </test>
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147 <test>
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148 <param name="matrix" ftype="h5" value="hicBuildMatrix_result1.npz.h5"/>
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149 <param name="mode_selector" value="merge_failed"/>
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150 <repeat name="chromosomes">
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151 <param name="chromosome" value="chrUextra"/>
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152 </repeat>
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153 <repeat name="chromosomes">
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154 <param name="chromosome" value="chr3LHet"/>
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155 </repeat>
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156 <output name="diagnostic_plot" file="diagnostic_plot.png" ftype="png" compare="sim_size"/>
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157 <output name="outMatrixFile" file="merged_matrix.npz.h5" ftype="h5" compare="sim_size"/>
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158 </test>
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159 </tests>
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160 <help><![CDATA[
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161
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162 **What it does**
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163
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164 Runs Dekker's iterative correction over a hic matrix.
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165
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166
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167 correct Run the iterative correction.
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168 diagnostic_plot
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169 Plots a histogram of the coverage per bin together with the
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170 modified z-score based on the median absolute deviation
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171 method (see Boris Iglewicz and David Hoaglin 1993, Volume
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172 16: How to Detect and Handle Outliers The ASQC Basic
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173 References in Quality Control: Statistical Techniques,
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174 Edward F. Mykytka, Ph.D., Editor.
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175 merge_failed Merges together failed bins to rescue some of the
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176 information instead of discarding it. This option is mostly
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177 useful with processing small restrition fragment size bins
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181 ]]></help>
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182 <expand macro="citations" />
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183 </tool>
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184