Mercurial > repos > bgruening > hicexplorer_hiccorrectmatrix

annotate hicCorrectMatrix.xml @ 9:e1e5b2c47c00 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
author iuc
date Wed, 07 Mar 2018 02:27:16 -0500
parents 9a7d2fde825d
children 9609f9b186bb
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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 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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19
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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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24
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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'
0
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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
8
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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="Range restriction (in bp)" argument="--range">
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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="" >
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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>
8
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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>
1
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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
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141 <output name="outFileName" file="hicCorrectMatrix_result1.npz.h5" ftype="h5" compare="sim_size"/>
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142 </test>
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143 <test>
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144 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
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145 <param name="mode_selector" value="diagnostic_plot"/>
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146 <repeat name="chromosomes">
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147 <param name="chromosome" value="chrUextra"/>
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148 </repeat>
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149 <repeat name="chromosomes">
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150 <param name="chromosome" value="chr3LHet"/>
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151 </repeat>
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152 <output name="diagnostic_plot" file="diagnostic_plot.png" ftype="png" compare="sim_size"/>
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153 </test>
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154 </tests>
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155 <help><![CDATA[
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156
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157 Matrix correction
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158 ==================
0
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159
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160 ``hicCorrectMatrix`` runs Dekker's iterative correction over a Hi-C matrix (`Imakaev 2012`_.). For correcting the matrix,
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161 it is important to remove the unassembled scaffolds (e.g. `NT_`), mitochondrial DNA and Y chromosome and keep only
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162 chromosomes, as scaffolds create problems with matrix correction. Therefore
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163 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 Matrix correction works in two steps: 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. The second steps removes the low scoring bins and does the correction.
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168
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169 Input
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170 -----
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171
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172
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173 Diagnostic plot
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174 ~~~~~~~~~~~~~~~~
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175 Plots a histogram of the coverage per bin together with the
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176 modified z-score based on the median absolute deviation
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177 method.
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178
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179 See Boris Iglewicz and David Hoaglin 1993, Volume 16:
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180 How to Detect and Handle Outliers The ASQC Basic References in Quality Control: Statistical Techniques,
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181 Edward F. Mykytka, Ph.D., Editor.
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182
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183 Parameters
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184 __________
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185 - the contact matrix
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186 - Max value for the x-axis in counts per bin
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187 - include chromosomes
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188
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189
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190 Correct
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191 ~~~~~~~
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192
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193 Run the iterative correction.
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194
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195 Parameters
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196 __________
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197 - number of iterations
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198 - inflation cutoff
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199 - trans region cutoff
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200 - sequenced count cutoff
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201 - skip diagonal counts
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202 - normalize each chromosome separately
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203 - remove bins of low coverage
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204 - remove bins of large coverage
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205 - include chromosomes
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206
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207 Output
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208 ------
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209
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210 Diagnostic plot:
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211
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212 .. image:: $PATH_TO_IMAGES/diagnostic_plot.png
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213 :width: 70%
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214
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215 Correct:
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216 - the corrected contact matrix
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217
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218 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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219
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220 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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221
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222 .. _`Imakaev 2012`: http://doi.org/doi:10.1038/nmeth.2148
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223 ]]></help>
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224 <expand macro="citations" />
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225 </tool>
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226