Mercurial > repos > bgruening > hicexplorer_hicplotmatrix

annotate hicPlotMatrix.xml @ 21:b63363075c2e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
author iuc
date Wed, 18 Oct 2023 11:11:47 +0000
parents 9939786dd9c9
children 12d51d7be66f
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7babd8a46fe0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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1 <tool id="hicexplorer_hicplotmatrix" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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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
8
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 $pca = '--bigwig pca.bw'
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b63363075c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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13 #elif str($pca_conditional.pca_type) == 'no_file':
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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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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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18 --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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20 #if $title and $title is not None:
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21 --title '$title'
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22 #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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24 #if $scoreName and $scoreName is not None:
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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25 --scoreName '$scoreName'
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26 #end if
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27
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28 --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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30 $perChromosome
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31 $clearMaskedBins
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a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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33 ## special: --chromosomeOrder is optional, but if given needs at least one argument
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34 #set chroms = ' '.join([ '\'' + str($var.chromosome) + '\'' for $var in $chromosomeOrder ])
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35 #if chroms:
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36 --chromosomeOrder $chroms
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37 #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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39 #if $region:
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40 --region '$region'
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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41 #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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43 #if $region2:
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44 --region2 '$region2'
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45 #end if
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46 $log1p
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47 $log
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48
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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49 #if $colormap:
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50 --colorMap $colormap
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51 #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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53 #if $vMin:
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54 --vMin $vMin
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55 #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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57 #if $vMax:
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58 --vMax $vMax
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59 #end if
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61 #if str($pca_conditional.pca_type) == 'bigwig':
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62 #if $pca_conditional.vMinBigwig:
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63 --vMinBigwig $pca_conditional.vMinBigwig
b553d14a7845 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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64 #end if
b553d14a7845 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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65 #if $pca_conditional.vMaxBigwig:
b553d14a7845 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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66 --vMaxBigwig $pca_conditional.vMaxBigwig
b553d14a7845 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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67 #end if
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68 $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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70 #if $pca_conditional.scaleFactorBigwig:
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71 --scaleFactorBigwig $pca_conditional.scaleFactorBigwig
b553d14a7845 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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72 #end if
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73 $pca_conditional.bigwigAdditionalVerticalAxis
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74 #end if
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75 $pca
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76 #if $dpi:
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77 --dpi $dpi
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78 #end if
b553d14a7845 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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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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80 #if $fontSize:
b553d14a7845 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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81 --fontSize $fontSize
b553d14a7845 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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82 #end if
b553d14a7845 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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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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84 #if $rotationX:
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85 --rotationX $rotationX
b553d14a7845 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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86 #end if
b553d14a7845 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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87
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88 #if $rotationY:
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89 --rotationY $rotationY
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90 #end if
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91
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92 #if $increaseFigureWidth:
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93 --increaseFigureWidth $increaseFigureWidth
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94 #end if
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95
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96 #if $increaseFigureHeight:
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97 --increaseFigureHeight $increaseFigureHeight
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98 #end if
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99
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100 #if str($loop_conditional.loop_selector) == 'yes':
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101 --loops $loop_conditional.loops
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102 --loopLargeRegionsOperation $loop_conditional.loops_large_selector
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103 #end if
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104
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105 #if $tads:
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106 --tads '$tads'
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107 #end if
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108 && mv plot.$image_file_format plot
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109 ]]>
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110 </command>
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111 <inputs>
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112 <expand macro="matrix_h5_cooler_macro" />
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113
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114 <param argument="--title" type="text" optional="true" label="Plot title">
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115 <validator type="expression" message="Only alphanumeric characters and a space are allowed.">value.isalnum()</validator>
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116 </param>
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117 <param argument="--scoreName" type="text" optional="true" label="Score name" help="The label for the heatmap legend.">
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118 <validator type="expression" message="Only alphanumeric characters and a space are allowed.">value.isalnum()</validator>
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119 </param>
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120 <param argument="--perChromosome" type="boolean" truevalue="--perChromosome" falsevalue="" checked="false" label="Plot per chromosome" 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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121 <param argument="--clearMaskedBins" type="boolean" truevalue="--clearMaskedBins" falsevalue="" checked="false" label="Remove masked bins from the matrix" />
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122
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123 <repeat name="chromosomeOrder" min="0" title="Chromosomes to include (and order to plot in):" help="This option overrides --region and --region2">
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124 <param name="chromosome" type="text">
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125 <validator type="empty_field" />
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126 </param>
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127 </repeat>
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128
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129 <param argument="--region" type="text" optional="True" label="Plot only this region" 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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130 <validator type="expression" message="Only alphanumeric characters, the colon or a dash are allowed.">value.replace(':', '').replace('-', '').isalnum()</validator>
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131 </param>
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132 <param argument="--region2" type="text" optional="True" label="Region two to plot" 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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133 <validator type="expression" message="Only alphanumeric characters, the colon or a dash are allowed.">value.replace(':', '').replace('-', '').isalnum()</validator>
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134 </param>
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135 <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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136 <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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137 <param argument="--fontSize" type="integer" optional="true" label="Font size" help="Fontsize in the plot for x and y axis." />
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138 <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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139 <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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140 <param argument="--increaseFigureWidth" type="float" value="0.5" optional="true" label="Increase figure width size" help="Plotting additional bigwig tracks can cause compression in x or y direction of the heatmap. Set this factor to a value unequal to 0 to correct this." />
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141 <param argument="--increaseFigureHeight" type="float" value="0.5" optional="true" label="Increase figure height size" help="Plotting additional bigwig tracks can cause compression in x or y direction of the heatmap. Set this factor to a value unequal to 0 to correct this." />
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142 <expand macro="colormap" />
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143
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144 <param argument="--vMin" type="float" optional="true" label="vMin" help="Minimum value of the plotted score." />
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145 <param argument="--vMax" type="float" optional="true" label="vMax" help="Maximum value of the plotted score." />
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146
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147 <conditional name="pca_conditional">
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148 <param name="pca_type" label="Datatype of eigenvector file" type="select">
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149 <option value="no_file" selected="true">No file</option>
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150 <option value="bigwig">bigwig</option>
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151 </param>
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152 <when value="no_file" />
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153 <when value="bigwig">
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154 <param name="pca_bigwig" type="data" format="bigwig" label="Eigenvector file" />
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155 <param argument="--vMinBigwig" type="float" optional="true" label="vMinBigwig" help="Minimum value of the plotted bigwig score." />
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156 <param argument="--vMaxBigwig" type="float" optional="true" label="vMaxBigwig" help="Maximum value of the plotted bigwig score." />
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157 <param name="flipBigwigSign" type="boolean" optional="true" truevalue="--flipBigwigSign" falsevalue="" label="Flip the sign of the bigwig values" />
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158 <param argument="--scaleFactorBigwig" type="float" optional="true" label="Scale factor for bigwig" help="Scale the bigwig values by a factor." />
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159 <param name="bigwigAdditionalVerticalAxis" type="boolean" optional="true" truevalue="--bigwigAdditionalVerticalAxis" falsevalue="" label="Plot an additional vertical axis." />
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160 </when>
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161 </conditional>
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162 <conditional name="loop_conditional">
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163 <param name="loop_selector" type="select" label="Plot loops">
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164 <option value="yes">Yes</option>
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165 <option value="no" selected="True">No</option>
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166 </param>
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167 <when value="yes">
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168 <param name="loops" type="data" format="interval" optional="True" label="Add detected loops" />
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169 <param name="loops_large_selector" label="Start bin of the loop for plotting" type="select">
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170 <option value="first" selected="true">First</option>
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171 <option value="center">Center</option>
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172 <option value="last">Last</option>
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173 </param>
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174 </when>
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175 <when value="no" />
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176
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177 </conditional>
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178 <param name="loops" type="data" format="interval" optional="True" label="Add detected loops" />
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179 <param name="tads" type="data" format="interval" optional="True" label="Add detected tads" />
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180
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181 <param name="image_file_format" type="select" label="Image output format">
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182 <option value="png" selected="True">png</option>
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183 <option value="svg">svg</option>
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184 <option value="pdf">pdf</option>
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185 </param>
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186 <expand macro="dpi" />
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187 </inputs>
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188 <outputs>
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189 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Plot">
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190 <change_format>
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191 <when input="image_file_format" value="svg" format="svg" />
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192 <when input="image_file_format" value="pdf" format="pdf" />
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193 </change_format>
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194 </data>
0
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195 </outputs>
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196 <tests>
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197 <test>
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198 <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
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199 <conditional name="pca_conditional">
21
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200 <param name="pca_type" value="no_file" />
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201 </conditional>
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202 <param name="region" value="chr2L:3000000-3500000" />
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203 <param name="region2" value="chr2L:3100000-3600000" />
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204 <param name="log1p" value="True" />
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205 <param name="clearMaskedBins" value="True" />
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206 <param name="image_file_format" value="png" />
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207 <param name="dpi" value="10" />
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208
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209 <output name="outFileName" file="hicPlotMatrix/plot1.png" ftype="png" compare="sim_size" />
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210 </test>
5
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211 <test>
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212 <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
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213 <param name="region" value="chr2L:3000000-3500000" />
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214 <conditional name="pca_conditional">
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215 <param name="pca_type" value="no_file" />
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216 </conditional>
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217 <param name="image_file_format" value="pdf" />
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218 <param name="dpi" value="10" />
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219 <output name="outFileName" file="hicPlotMatrix/plot2.pdf" ftype="pdf" compare="sim_size" />
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220 </test>
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221 <test>
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222 <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
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223 <conditional name="pca_conditional">
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224 <param name="pca_type" value="bigwig" />
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225 <param name="pca_bigwig" value="hicPCA/pca1_test1.bw" />
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226 <param name="vMinBigwig" value="10" />
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227 <param name="vMaxBigwig" value="20" />
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228 <param name="scaleFactorBigwig" value="2000" />
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229 <param name="flipBigwigSign" value="True" />
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230 </conditional>
21
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231 <param name="colormap" value="hot" />
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232 <param name="region" value="chr2L:3000000-3500000" />
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233 <param name="dpi" value="10" />
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234
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235 <param name="image_file_format" value="svg" />
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236 <output name="outFileName" file="hicPlotMatrix/plot3_pca.svg" ftype="svg" compare="sim_size" />
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237 </test>
0
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238 </tests>
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239 <help><![CDATA[
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240
4
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241 Contact matrix plot
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242 =======================
0
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243
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244 **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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245 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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246
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247 _________________
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248
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249 Usage
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250 -----
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252 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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254 _________________
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255
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256 Output
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257 ------
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258
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259 **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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260
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261 .. image:: $PATH_TO_IMAGES/hicPlotMatrix.png
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262 :width: 50%
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263
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264 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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265
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266 Another example is available below using Hi-C data published by `Lieberman-Aiden <https://pubmed.ncbi.nlm.nih.gov/19815776/>`_ 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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268 .. image:: $PATH_TO_IMAGES/SRR0279XX_perChr_eigenvector1.png
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269 :width: 70 %
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270
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271 _________________
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272
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273 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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275 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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276 .. _Colormaps: https://matplotlib.org/examples/color/colormaps_reference.html
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277 ]]> </help>
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278 <expand macro="citations" />
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279 </tool>