Mercurial > repos > bgruening > hicexplorer_hiccorrectmatrix

annotate hicCorrectMatrix.xml @ 13:a33c2124979f draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2307743fd10f0babde52eec30289fe1682236287
author iuc
date Sat, 09 Jun 2018 15:02:36 -0400
parents 27975871546b
children bccd04d7e35d
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1 <tool id="hicexplorer_hiccorrectmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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2 <description>run Imakaev's iterative correction over a Hi-C contact 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 detect_errors="exit_code"><![CDATA[
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9
0
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10 hicCorrectMatrix
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11 $mode.mode_selector
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12 --matrix '$matrix_h5_cooler'
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13
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14 ## special: --chromosomes is optional, but if given needs at least one argument
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15 #set chroms = '" "'.join([ str($var.chromosome) for $var in $chromosomes ])
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16 #if chroms
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17 --chromosomes "$chroms"
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18 #end if
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20 #if $mode.mode_selector == 'correct':
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21
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22 --iterNum $mode.iterNum
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23 --outFileName matrix.$mode.outputFormat
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25 #if $mode.filterThreshold_low and $mode.filterThreshold_large:
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26 --filterThreshold $mode.filterThreshold_low $mode.filterThreshold_large
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27 #end if
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28
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29 #if $mode.inflationCutoff:
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30 --inflationCutoff $mode.inflationCutoff
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31 #end if
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32
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33 #if $mode.transCutoff:
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34 --transCutoff $mode.transCutoff
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35 #end if
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36
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37 #if $mode.sequencedCountCutoff:
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38 --sequencedCountCutoff $mode.sequencedCountCutoff
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39 #end if
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40
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41 $mode.skipDiagonal
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42 $mode.perchr
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43
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44 #elif $mode.mode_selector == 'merge_failed':
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45 --plotName diagnostic_plot.png
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46 --outMatrixFile corrected_matrix.npz.h5
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47 #if $mode.xMax:
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48 --xMax $mode.xMax
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49 #end if
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50 #if $mode.filterThreshold_low and $mode.filterThreshold_large:
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51 --filterThreshold '$mode.filterThreshold_low' '$mode.filterThreshold_large'
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52 #end if
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53 #else:
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54 --plotName diagnostic_plot.png
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55 #if $mode.xMax:
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56 --xMax $mode.xMax
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57 #end if
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58 #end if
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59 #if $mode.mode_selector == 'correct':
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60 && mv matrix.$mode.outputFormat matrix
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61 #end if
0
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62 ]]>
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63 </command>
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64 <inputs>
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65 <expand macro='matrix_h5_cooler_macro' />
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66 <conditional name="mode">
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67 <param name="mode_selector" type="select" label="Mode">
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68 <option value="diagnostic_plot">Diagnostic plot</option>
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69 <option value="correct">Correct matrix</option>
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70 </param>
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71 <when value="diagnostic_plot">
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72 <expand macro="xMax" />
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73 </when>
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74 <when value="correct">
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75 <param argument="--iterNum" name="iterNum" type="integer" optional="true" value="500"
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76 label="Number of iterations" />
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77
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78 <param argument="--inflationCutoff" name="inflationCutoff" type="float" optional="true"
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79 label="Inflation cutoff" value=""
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80 help="Value corresponding to the maximum number of times a bin can be scaled up during the iterative correction.
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81 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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82
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83 <param argument="--transCutoff" name="transCutoff" type="float" optional="true"
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84 label="Trans region cutoff" value=""
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85 help="Clip high counts in the top -transcut trans regions (i.e. between chromosomes). A usual value is 0.05."/>
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86
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87 <param argument="--sequencedCountCutoff" name="sequencedCountCutoff" optional="true" type="float"
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88 label="Sequenced count cutoff"
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89 help="Each bin receives a value indicating the fraction that is covered by reads.
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90 A cutoff of 0.5 will discard all those bins that have less than half of the bin covered."/>
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91
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92 <param argument="--skipDiagonal" name="skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" checked="false"
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93 label="Skip diagonal counts"/>
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94
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95 <param argument="--perchr" name="perchr" type="boolean" truevalue="--perchr" falsevalue="" checked="false"
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96 label="Normalize each chromosome separately" />
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97 <expand macro="filterThreshold" />
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98 <param name='outputFormat' type='select' label="Output file format">
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99 <option value='h5'>HiCExplorer format</option>
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100 <option value="cool">cool</option>
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101 </param>
0
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102 </when>
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103 </conditional>
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104
3
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105 <repeat name="chromosomes" min="0"
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106 title="Include chromosomes" help="List of chromosomes to be included in the iterative correction.
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107 The order of the given chromosomes will be kept for the resulting corrected matrix">
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108 <param name="chromosome" type="text" value="" label='chromosome (one per field)'>
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109 <validator type="empty_field" />
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110 </param>
0
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111 </repeat>
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112
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113 </inputs>
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114 <outputs>
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115 <data name="outFileName" from_work_dir="matrix" format="h5">
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116 <change_format>
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117 <when input="mode.outputFormat" value="cool" format="cool" />
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118 </change_format>
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119 <filter>mode['mode_selector'] == "correct"</filter>
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120
0
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121 </data>
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122
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123
0
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124 <data name="diagnostic_plot" from_work_dir="diagnostic_plot.png" format="png">
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125 <filter>mode['mode_selector'] == "diagnostic_plot"</filter>
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126 </data>
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127 </outputs>
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128 <tests>
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129 <test>
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130 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
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131
0
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132 <param name="mode_selector" value="correct"/>
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133 <repeat name="chromosomes">
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134 <param name="chromosome" value="chrUextra"/>
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135 </repeat>
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136 <repeat name="chromosomes">
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137 <param name="chromosome" value="chr3LHet"/>
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138 </repeat>
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139 <param name='outputFormat' value='h5'/>
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140 <param name='filterThreshold_low' value='-2.0' />
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141 <param name='filterThreshold_large' value='4' />
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142 <output name="outFileName" file="hicCorrectMatrix_result1.npz.h5" ftype="h5" compare="sim_size"/>
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143 </test>
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144 <test>
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145 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
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146 <param name="mode_selector" value="diagnostic_plot"/>
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147 <repeat name="chromosomes">
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148 <param name="chromosome" value="chrUextra"/>
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149 </repeat>
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150 <repeat name="chromosomes">
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151 <param name="chromosome" value="chr3LHet"/>
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152 </repeat>
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153 <output name="diagnostic_plot" file="diagnostic_plot.png" ftype="png" compare="sim_size"/>
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154 </test>
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155 </tests>
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156 <help><![CDATA[
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157
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158 Hi-C contact matrix correction
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159 ==============================
0
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160
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161 **hicCorrectMatrix** runs Imakaev's iterative correction, described in `Imakaev et al. (2012)`_, over a Hi-C matrix. For the matrix correction to be efficient,
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162 it is important to remove the unassembled scaffolds (e.g. `NT_`), mitochondrial DNA and Y chromosome and keep only full length
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163 chromosomes, as scaffolds create problems with matrix correction. Therefore we use the chromosome names (1-19, X, Y) here.
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164
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165 **Important**: Use ‘chr1 chr2 chr3 etc.’ if your genome index uses chromosome names with the ‘chr’ prefix.
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166
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167 Also, for the method to work correctly, bins with zero reads assigned to them should be removed as they can not be corrected. Also, bins with low number of reads should be removed, otherwise, during the correction step, the counts associated with those bins will be amplified (usually, zero and low coverage bins tend contain repetitive regions). Bins with extremely high number of reads can also be removed from the correction as they may represent copy number variations.
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168
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169 To aid in the identification of bins with low and high read coverage, the ``diagnostic plot`` function of **hicCorrectMatrix** must be used.
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170
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171 Indeed, **hicCorrectMatrix** works in two steps:
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172
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173 - **Diagnostic plot**: First a histogram containing the sum of contact per bin (row sum) is produced. This plot needs to be inspected to decide the best threshold for removing bins with lower number of reads.
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175 - **Correct**: The second step removes the bins outside of the defined thresholds and perfroms the iterative correction.
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177 _________________
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179 Usage
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180 -----
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181
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182 This tool must be used on uncorrected matrices at restriction enzyme resolution or with merged bins (``hicMergeMatrixBins``).
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183
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184 _________________
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186 Output
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187 ------
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188
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189 Diagnostic plot
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190 _______________
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192
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193 The goal of the diagnostic plot is to help the user decide on a cutoff threshold that will ignore Hi-C matrix
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194 bins with few reads assigned to them. The plot is a histogram of the total number of Hi-C reads per matrix bin.
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195 A secondary scale based on the mean absolute deviation score, is shown on top of the figure.
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196 This secondary scale aims to offer 'normalized' values that are comparable across samples
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197 independently of the sequencing depth and the fraction of usable Hi-C reads. In all samples that we have studied,
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198 the histogram follows a bimodal distribution where the first peak is for bins with zero reads which usually occur
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199 at repetitive regions. Other low scoring bins tend to be close to repetitive regions.
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200 Also, low scoring bins can be caused by absence of a restriction site in the bin or because the restriction
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201 site is present but the restriction enzyme did not cut. The valley between the two peaks in the
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202 histogram is set by default as cutoff threshold.
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203 However, it is important to revise this as in some cases the selected value could not be correct.
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206 .. image:: $PATH_TO_IMAGES/diagnostic_plot.png
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207 :width: 50%
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208
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209 On the example plot above, a user can then use the lower threshold defined by the Median Absolute Deviation (MAD) method (black bold bar), or define its own threshold based on the contacts distribution.
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211 Correct
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212 _______
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214 Run the iterative correction and outputs the corrected matrix. This matrix can then be used with all downstream analysis tools such as ``hicPlotMatrix``, ``hicPlotTADs``, ``hicPlotViewpoint``, ``hicAggregateContacts`` for **visualization of Hi-C data**, ``hicCorrelate``, ``hicPlotDistVsCounts``, ``hicTransform``, ``hicFindTADs``, ``hicPCA`` **for data and scores computation on Hi-C data**.
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216 It is noteworthy that ``hicSumMatrices`` and ``hicMergeMatrixBins`` **must be performed on uncorrected matrices**.
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218 _________________
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220 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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222 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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223 .. _`Imakaev et al. (2012)`: https://doi.org/10.1038/nmeth.2148
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224 ]]></help>
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225 <expand macro="citations" />
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226 </tool>