Mercurial > repos > bgruening > hicexplorer_hicplotmatrix
annotate hicPlotMatrix.xml @ 12:492c1c966a22 draft
"planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 91a0182476a7fc26be7bef1677790518c4e88348-dirty"
author | bgruening |
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date | Mon, 16 Dec 2019 10:34:05 -0500 |
parents | 653c6fead9f9 |
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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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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 $pca = '' |
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15 #end if |
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16 |
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17 @BINARY@ |
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18 |
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19 --matrix '$matrix_h5_cooler' |
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20 |
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21 #if $title and $title is not None: |
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22 --title '$title' |
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23 #end if |
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24 |
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25 #if $scoreName and $scoreName is not None: |
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26 --scoreName '$scoreName' |
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27 #end if |
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28 |
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29 --outFileName plot.$image_file_format |
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30 |
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31 $perChromosome |
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32 $clearMaskedBins |
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33 |
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34 ## special: --chromosomeOrder is optional, but if given needs at least one argument |
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35 #set chroms = '" "'.join([ str($var.chromosome) for $var in $chromosomeOrder ]) |
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36 #if chroms: |
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37 --chromosomeOrder "$chroms" |
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38 #end if |
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39 |
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40 #if $region: |
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41 --region '$region' |
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42 #end if |
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43 |
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44 #if $region2: |
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45 --region2 '$region2' |
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46 #end if |
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47 $log1p |
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48 $log |
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49 |
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50 #if $colormap: |
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51 --colorMap $colormap |
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52 #end if |
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53 |
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54 #if $vMin: |
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55 --vMin $vMin |
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56 #end if |
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57 |
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58 #if $vMax: |
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59 --vMax $vMax |
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60 #end if |
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61 |
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62 $pca |
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63 |
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64 && mv plot.$image_file_format plot |
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65 ]]> |
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66 </command> |
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67 <inputs> |
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68 <expand macro='matrix_h5_cooler_macro' /> |
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69 |
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70 <param argument="--title" type="text" optional="true" label="Plot title"/> |
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71 <param argument="--scoreName" type="text" optional="true" label="Score name" help="The label for the heatmap legend."/> |
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72 <param argument="--perChromosome" type="boolean" truevalue="--perChromosome" falsevalue="" checked="false" |
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73 label="Plot per chromosome" |
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74 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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75 <param argument="--clearMaskedBins" type="boolean" truevalue="--clearMaskedBins" falsevalue="" checked="false" |
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76 label="Remove masked bins from the matrix" /> |
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77 |
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78 <repeat name="chromosomeOrder" min="0" title="Chromosomes to include (and order to plot in):" |
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79 help="This option overrides --region and --region2" > |
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80 <param name="chromosome" type="text" > |
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81 <validator type="empty_field" /> |
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82 </param> |
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83 </repeat> |
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84 |
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85 <param argument="--region" type="text" optional="True" label="Plot only this region" |
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86 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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87 <param argument="--region2" type="text" optional="True" label="Region two to plot" |
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88 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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89 <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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90 <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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91 |
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92 <expand macro="colormap" /> |
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93 |
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94 <param argument="--vMin" type="float" optional="true" label="vMin" help="Minimum value of the plotted score."/> |
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95 <param argument="--vMax" type="float" optional="true" label="vMax" help="Maximum value of the plotted score."/> |
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96 |
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97 <conditional name="pca_conditional"> |
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98 <param name='pca_type' label='Datatype of eigenvector file' type='select'> |
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99 <option value='' selected="true"></option> |
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100 <option value='bigwig'>bigwig</option> |
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101 </param> |
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102 <when value='' /> |
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103 <when value='bigwig'> |
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104 <param name='pca_bigwig' type="data" format="bigwig" |
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105 label="Eigenvector file"/> |
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106 </when> |
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107 </conditional> |
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108 <param name="image_file_format" type="select" label="Image output format"> |
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109 <option value="png" selected="True">png</option> |
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110 <option value="svg">svg</option> |
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111 </param> |
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112 </inputs> |
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113 <outputs> |
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114 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Plot"> |
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115 <change_format> |
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116 <when input="image_file_format" value="svg" format="svg" /> |
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117 </change_format> |
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118 </data> |
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119 </outputs> |
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120 <tests> |
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121 <test> |
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122 <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/> |
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123 <conditional name="pca_conditional"> |
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124 <param name="pca_type" value=''/> |
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125 </conditional> |
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126 <param name="region" value="chrX:3000000-3500000"/> |
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127 <param name="region2" value="chrX:3100000-3600000"/> |
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128 <param name="log1p" value="True"/> |
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129 <param name="clearMaskedBins" value="True"/> |
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130 <param name="image_file_format" value="png" /> |
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131 <output name="outFileName" file="master_matrix_plot.png" ftype="png" compare="sim_size"/> |
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132 </test> |
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133 <test> |
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134 <param name="matrix_h5_cooler" value="Li_et_al_2015.cool"/> |
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135 <conditional name="pca_conditional"> |
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136 <param name="pca_type" value=''/> |
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137 </conditional> |
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138 <param name="region" value="X:3000000-3500000"/> |
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139 <param name="image_file_format" value="png" /> |
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140 <output name="outFileName" file="Li_chrX30-35_cool.png" ftype="png" compare="sim_size"/> |
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141 </test> |
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142 <test> |
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143 <param name="matrix_h5_cooler" value="pearson_small_50kb.cool"/> |
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144 <param name="perChromosome" value="True"/> |
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145 <conditional name="pca_conditional"> |
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146 <param name="pca_type" value='bigwig'/> |
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147 <param name="pca_bigwig" value="pca1.bw"/> |
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148 </conditional> |
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149 <param name='colormap' value='hot'/> |
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150 <param name="image_file_format" value="svg" /> |
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151 <output name="outFileName" file="small_matrix_50kb_pearson_pca1_plot.svg" ftype="svg" compare="sim_size" delta='35000'/> |
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152 </test> |
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153 <test> |
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154 <param name="matrix_h5_cooler" value="pearson_small_50kb.h5"/> |
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155 <param name="perChromosome" value="True"/> |
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156 <conditional name="pca_conditional"> |
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157 <param name="pca_type" value='bigwig'/> |
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158 <param name="pca_bigwig" value="pca1.bw"/> |
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159 </conditional> |
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160 <param name='colormap' value='hot'/> |
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161 |
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162 <param name="image_file_format" value="svg" /> |
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163 <output name="outFileName" file="small_matrix_50kb_pearson_pca1_plot.svg" ftype="svg" compare="sim_size" delta='35000'/> |
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164 </test> |
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165 </tests> |
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166 <help><![CDATA[ |
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167 Contact matrix plot |
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168 ======================= |
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169 |
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170 **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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171 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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172 |
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173 _________________ |
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174 |
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175 Usage |
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176 ----- |
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177 |
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178 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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179 |
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180 _________________ |
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181 |
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182 Output |
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183 ------ |
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184 |
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185 **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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186 |
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187 .. image:: $PATH_TO_IMAGES/hicPlotMatrix.png |
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188 :width: 50% |
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189 |
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190 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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191 |
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192 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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193 |
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194 .. image:: $PATH_TO_IMAGES/SRR0279XX_perChr_eigenvector1.png |
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195 :width: 70 % |
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196 |
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197 _________________ |
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198 |
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199 | For more information about HiCExplorer please consider our documentation on readthedocs.io_ |
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200 |
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201 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html |
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202 .. _Colormaps: https://matplotlib.org/examples/color/colormaps_reference.html |
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203 ]]></help> |
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204 <expand macro="citations" /> |
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205 </tool> |