Mercurial > repos > bgruening > hicexplorer_hicplotmatrix

annotate hicPlotMatrix.xml @ 17:79acdf9d5e1d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
author iuc
date Fri, 14 Aug 2020 06:08:55 -0400
parents b553d14a7845
children 7babd8a46fe0
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c3703afea1b1 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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1 <tool id="hicexplorer_hicplotmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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2 <description>plot a Hi-C contact matrix heatmap</description>
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3 <macros>
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4 <token name="@BINARY@">hicPlotMatrix</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
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d398f5373c70 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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10 #if str($pca_conditional.pca_type) == 'bigwig':
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11 ln -s '$pca_conditional.pca_bigwig' pca.bw &&
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12 #set $pca = '--bigwig pca.bw'
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13 #elif str($pca_conditional.pca_type) == '':
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14 #set $pca = ''
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15 #end if
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16 ln -s $matrix_h5_cooler matrix.$matrix_h5_cooler.ext &&
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17 @BINARY@
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b553d14a7845 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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20 --matrix 'matrix.$matrix_h5_cooler.ext'
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a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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22 #if $title and $title is not None:
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23 --title '$title'
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24 #end if
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a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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26 #if $scoreName and $scoreName is not None:
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27 --scoreName '$scoreName'
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28 #end if
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30 --outFileName plot.$image_file_format
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a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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32 $perChromosome
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33 $clearMaskedBins
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a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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35 ## special: --chromosomeOrder is optional, but if given needs at least one argument
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36 #set chroms = ' '.join([ '\'' + str($var.chromosome) + '\'' for $var in $chromosomeOrder ])
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37 #if chroms:
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38 --chromosomeOrder $chroms
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39 #end if
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a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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41 #if $region:
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42 --region '$region'
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43 #end if
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a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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45 #if $region2:
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46 --region2 '$region2'
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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47 #end if
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48 $log1p
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49 $log
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a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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51 #if $colormap:
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52 --colorMap $colormap
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53 #end if
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a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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55 #if $vMin:
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56 --vMin $vMin
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57 #end if
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a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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59 #if $vMax:
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60 --vMax $vMax
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61 #end if
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62
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63 #if str($pca_conditional.pca_type) == 'bigwig':
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64 #if $pca_conditional.vMinBigwig:
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65 --vMinBigwig $pca_conditional.vMinBigwig
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66 #end if
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67 #if $pca_conditional.vMaxBigwig:
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68 --vMaxBigwig $pca_conditional.vMaxBigwig
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69 #end if
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70 $pca_conditional.flipBigwigSign
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b553d14a7845 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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72 #if $pca_conditional.scaleFactorBigwig:
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73 --scaleFactorBigwig $pca_conditional.scaleFactorBigwig
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74 #end if
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75 $pca_conditional.bigwigAdditionalVerticalAxis
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76 #end if
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77 $pca
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78 #if $dpi:
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79 --dpi $dpi
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80 #end if
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b553d14a7845 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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82 #if $fontSize:
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83 --fontSize $fontSize
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84 #end if
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b553d14a7845 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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86 #if $rotationX:
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87 --rotationX $rotationX
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88 #end if
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89
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90 #if $rotationY:
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91 --rotationY $rotationY
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92 #end if
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93
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94 #if $loops:
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95 --loops '$loops'
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96 #end if
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97 && mv plot.$image_file_format plot
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98 ]]>
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99 </command>
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100 <inputs>
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101 <expand macro='matrix_h5_cooler_macro' />
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102
0
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103 <param argument="--title" type="text" optional="true" label="Plot title"/>
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104 <param argument="--scoreName" type="text" optional="true" label="Score name" help="The label for the heatmap legend."/>
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105 <param argument="--perChromosome" type="boolean" truevalue="--perChromosome" falsevalue="" checked="false"
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106 label="Plot per chromosome"
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107 help="Instead of plotting the whole matrix each chromosome is plotted next to the other. This parameter is not compatible with --region" />
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108 <param argument="--clearMaskedBins" type="boolean" truevalue="--clearMaskedBins" falsevalue="" checked="false"
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109 label="Remove masked bins from the matrix" />
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110
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111 <repeat name="chromosomeOrder" min="0" title="Chromosomes to include (and order to plot in):"
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112 help="This option overrides --region and --region2" >
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113 <param name="chromosome" type="text" >
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114 <validator type="empty_field" />
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115 </param>
0
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116 </repeat>
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117
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118 <param argument="--region" type="text" optional="True" label="Plot only this region"
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119 help="The format is chr:start-end The plotted region contains the main diagonal and is symmetric unless --region2 is given"/>
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120 <param argument="--region2" type="text" optional="True" label="Region two to plot"
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121 help="If given then only the region defined by --region and --region2 is plotted. The format is the same as --region"/>
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122 <param argument="--log1p" type="boolean" truevalue="--log1p" falsevalue="" checked="false" label="Plot the log1p of the matrix values (log(Hi-C contacts+1)). This option is recommended."/>
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123 <param argument="--log" type="boolean" truevalue="--log" falsevalue="" checked="false" label="Plot the log of the matrix values. (log(Hi-C contacts))"/>
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124 <param argument="--fontSize" type="integer" optional="true" label="Font size" help="Fontsize in the plot for x and y axis."/>
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125 <param argument="--rotationX" type="integer" optional="true" label="Rotate x-labels by degree" help="Rotation in degrees for the labels of x-axis."/>
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126 <param argument="--rotationY" type="integer" optional="true" label="Rotate y-labels by degree" help="Rotation in degrees for the labels of y-axis."/>
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127
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128 <expand macro="colormap" />
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129
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130 <param argument="--vMin" type="float" optional="true" label="vMin" help="Minimum value of the plotted score."/>
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131 <param argument="--vMax" type="float" optional="true" label="vMax" help="Maximum value of the plotted score."/>
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132
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133 <conditional name="pca_conditional">
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134 <param name='pca_type' label='Datatype of eigenvector file' type='select'>
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135 <option value='' selected="true"></option>
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136 <option value='bigwig'>bigwig</option>
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137 </param>
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138 <when value='' />
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139 <when value='bigwig'>
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140 <param name='pca_bigwig' type="data" format="bigwig"
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141 label="Eigenvector file"/>
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142 <param argument="--vMinBigwig" type="float" optional="true" label="vMinBigwig" help="Minimum value of the plotted bigwig score."/>
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143 <param argument="--vMaxBigwig" type="float" optional="true" label="vMaxBigwig" help="Maximum value of the plotted bigwig score."/>
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144 <param name='flipBigwigSign' type='boolean' optional="true" truevalue='--flipBigwigSign' falsevalue='' label='Flip the sign of the bigwig values' />
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145 <param argument="--scaleFactorBigwig" type="float" optional="true" label="Scale factor for bigwig" help="Scale the bigwig values by a factor."/>
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146 <param name='bigwigAdditionalVerticalAxis' type='boolean' optional="true" truevalue='--bigwigAdditionalVerticalAxis' falsevalue='' label='Plot an additional vertical axis.' />
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147
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148
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149 </when>
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150 </conditional>
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151 <param name='loops' type="data" format="interval" optional='True' label="Add detected loops"/>
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152 <param name="image_file_format" type="select" label="Image output format">
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153 <option value="png" selected="True">png</option>
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154 <option value="svg">svg</option>
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155 <option value="pdf">pdf</option>
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156
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157 </param>
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158 <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/>
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159 </inputs>
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160 <outputs>
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161 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Plot">
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162 <change_format>
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163 <when input="image_file_format" value="svg" format="svg" />
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164 <when input="image_file_format" value="pdf" format="pdf" />
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165 </change_format>
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166 </data>
0
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167 </outputs>
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168 <tests>
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169 <test>
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170 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
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171 <conditional name="pca_conditional">
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172 <param name="pca_type" value=''/>
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173 </conditional>
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174 <param name="region" value="chr2L:3000000-3500000"/>
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175 <param name="region2" value="chr2L:3100000-3600000"/>
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176 <param name="log1p" value="True"/>
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177 <param name="clearMaskedBins" value="True"/>
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178 <param name="image_file_format" value="png" />
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179 <param name="dpi" value="10" />
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180
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181 <output name="outFileName" file="hicPlotMatrix/plot1.png" ftype="png" compare="sim_size"/>
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182 </test>
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183 <test>
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184 <param name="matrix_h5_cooler" value="small_test_matrix.cool"/>
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185 <param name="region" value="chr2L:3000000-3500000"/>
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186
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187 <conditional name="pca_conditional">
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188 <param name="pca_type" value=''/>
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189 </conditional>
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190 <param name="image_file_format" value="pdf" />
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191 <param name="dpi" value="10" />
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192
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193 <output name="outFileName" file="hicPlotMatrix/plot2.pdf" ftype="pdf" compare="sim_size"/>
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194 </test>
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195 <test>
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196 <param name="matrix_h5_cooler" value="small_test_matrix.cool"/>
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197 <conditional name="pca_conditional">
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198 <param name="pca_type" value='bigwig'/>
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199 <param name="pca_bigwig" value="hicPCA/pca1_test1.bw"/>
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200 <param name='vMinBigwig' value='10'/>
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201 <param name='vMaxBigwig' value='20'/>
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202 <param name='scaleFactorBigwig' value='2000'/>
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203 <param name='flipBigwigSign' value='True'/>
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204 </conditional>
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205 <param name='colormap' value='hot'/>
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206 <param name="region" value="chr2L:3000000-3500000"/>
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207 <param name="dpi" value="10" />
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208
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209 <param name="image_file_format" value="svg" />
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210 <output name="outFileName" file="hicPlotMatrix/plot3_pca.svg" ftype="svg" compare="sim_size" delta="35000"/>
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211 </test>
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212
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213 </tests>
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214 <help><![CDATA[
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215 Contact matrix plot
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216 =======================
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217
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218 **hicPlotMatrix** is a visualization tool for Hi-C contact matrices. It supports to plot genome-wide contact matrices, one or multiple chromosomes, a region or two regions against each other.
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219 Additionally it can plot the result of a principal component analysis obtained by ``hicPCA`` to have a better understanding of A / B compartments.
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220
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221 _________________
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222
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223 Usage
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224 -----
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225
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226 This tool can be used on any h5 or cool Hi-C contact matrix. It is noteworthy that for comparisons of 2 matrices or more, they must all have the same or similar number of contacts.
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227
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228 _________________
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229
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230 Output
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231 ------
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232
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233 **hicPlotMatrix** outputs a heatmap of a contact matrix in either png or svg format, below is an example of such a plot:
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234
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235 .. image:: $PATH_TO_IMAGES/hicPlotMatrix.png
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236 :width: 50%
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237
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238 Contact matrix of *Drosophila melanogaster* embryos visualized using **hicPlotMatrix**. Hi-C matrix bins were merged to a 25 kb bin size using ``hicMergeMatrixBins`` and the matrix has then been corrected using ``hicCorrectMatrix`` before plotting.
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239
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240 Another example is available below using Hi-C data published by `Lieberman-Aiden <https://doi.org/10.1126/science.1181369>`_ in 2009, (`GSE18199 <https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18199>`_). A Hi-C contact matrix has been plotted with the ``--perChr`` option and the first eigenvector (pca1) computed by ``hicPCA``. For this plot a pearson correlated matrix was used, which is computed by first creating an observed / expected matrix and then a pearson correlation matrix with ``hicTransform``.
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241
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242 .. image:: $PATH_TO_IMAGES/SRR0279XX_perChr_eigenvector1.png
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243 :width: 70 %
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244
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245 _________________
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246
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247 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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248
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249 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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250 .. _Colormaps: https://matplotlib.org/examples/color/colormaps_reference.html
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251 ]]></help>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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252 <expand macro="citations" />
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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253 </tool>