Mercurial > repos > bgruening > hicexplorer_hicplotmatrix

annotate hicPlotMatrix.xml @ 4:fd5e51d2b558 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
author iuc
date Sat, 16 Dec 2017 16:30:53 -0500
parents 2c0069f645bc
children c3703afea1b1
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1 <tool id="hicexplorer_hicplotmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.1">
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2 <description>Plots a HiC 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 ln -s '$matrix' input_matrix.h5 &&
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11 @BINARY@
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13 --matrix input_matrix.h5
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15 #if $title and $title is not None:
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16 --title '$title'
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17 #end if
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19 #if $scoreName and $scoreName is not None:
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20 --scoreName '$scoreName'
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21 #end if
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24 --outFileName plot.$image_file_format
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26 $perChromosome
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27 $clearMaskedBins
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29 --whatToShow heatmap
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32 ## special: --chromosomeOrder is optional, but if given needs at least one argument
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33 #set chroms = '" "'.join([ str($var.chromosome) for $var in $chromosomeOrder ])
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34 #if chroms:
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35 --chromosomeOrder '$chroms'
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36 #end if
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37
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38 #if $region:
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39 --region '$region'
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40 #end if
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42 #if $region2:
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43 --region2 '$region2'
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44 #end if
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45 $log1p
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46 $log
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47
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48 #if $colormap:
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49 --colorMap $colormap
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50 #end if
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52 #if $vMin:
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53 --vMin $vMin
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54 #end if
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55
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56 #if $vMax:
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57 --vMax $vMax
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58 #end if
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59
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60 && mv plot.$image_file_format plot
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61 ]]>
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62 </command>
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63 <inputs>
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64 <param argument="--matrix" type="data" format="h5" label="Hi-C matrix to plot"/>
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65 <param argument="--title" type="text" optional="true" label="Plot title"/>
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66 <param argument="--scoreName" type="text" optional="true" label="Score name"/>
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67 <param argument="--perChromosome" type="boolean" truevalue="--perChromosome" falsevalue="" checked="false"
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68 label="Plot per chromosome"
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69 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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70 <param argument="--clearMaskedBins" type="boolean" truevalue="--clearMaskedBins" falsevalue="" checked="false"
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71 label="Remove masked bins from the matrix" />
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72
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73 <repeat name="chromosomeOrder" min="0" title="Chromosomes to include (and order to plot in):"
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74 help="This option overrides --region and --region2" >
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75 <param name="chromosome" type="text" >
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76 <validator type="empty_field" />
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77 </param>
0
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78 </repeat>
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79
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80 <param argument="--region" type="text" optional="True" label="Plot only this region"
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81 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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82 <param argument="--region2" type="text" optional="True" label="Region two to plot"
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83 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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84 <param argument="--log1p" type="boolean" truevalue="--log1p" falsevalue="" checked="false" label="Plot the log1p of the matrix values."/>
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85 <param argument="--log" type="boolean" truevalue="--log" falsevalue="" checked="false" label="Plot the log of the matrix values."/>
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86
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87 <expand macro="colormap" />
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88
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89 <param argument="--vMin" type="float" optional="true" label="vMin"/>
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90 <param argument="--vMax" type="float" optional="true" label="vMax"/>
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91 <param name="image_file_format" type="select" label="Image output format">
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92 <option value="png" selected="True">png</option>
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93 <option value="svg">svg</option>
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94 </param>
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95 </inputs>
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96 <outputs>
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97 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on ${on_string}">
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98 <change_format>
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99 <when input="image_file_format" value="svg" format="svg" />
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100 </change_format>
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101 </data>
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102 </outputs>
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103 <tests>
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104 <test>
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105 <param name="matrix" ftype="h5" value="Li_et_al_2015.h5"/>
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106 <param name="region" value="chrX:3000000-3500000"/>
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107 <param name="region2" value="chrX:3100000-3600000"/>
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108 <param name="log1p" value="True"/>
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109 <param name="clearMaskedBins" value="True"/>
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110 <!-- <param name="whatToShow_select" value="heatmap"/> -->
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111 <param name="image_file_format" value="png" />
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112 <output name="outFileName" file="master_matrix_plot.png" ftype="png" compare="sim_size"/>
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113 </test>
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114 </tests>
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115 <help><![CDATA[
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116 Contact matrix plot
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117 =======================
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118
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119 ``hicPlotMatrix`` is a visualization tool for a contact matrix. It supports to plot the whole contact matrix, one or more chromosomes, a region or two regions against each other.
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120
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121 .. Additional it can plot the result of a principal component analysis to have a better understanding of A / B compartments.
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122
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123 Input
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124 -----
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125
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126 Parameters
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127 __________
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128 - the contact matrix
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129 - A title for the plot
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130 - Score name
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131 - per chromosome
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132 - The chromosomes to include in the plot.
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133 - What to show:
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134 - The region(s) to plot. This parameter overrides 'chromosome'. If either 'chromosomes' or 'region' is given the full contact matrix is used.
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135 - log / log1p of the values: It is recommended to use log1p.
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136 - Colormaps_ for the heatmap.
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137 - vMin / vMax
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138
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139 .. - principal component: a bedgraph file
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140
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141 Output
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142 ------
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143
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144 The contact matrix plotted for chromosome 1.
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145
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146 .. image:: SRR027956.svg
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147 :width: 70%
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148
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149
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150 The contact matrix used with ``--perChr`` and the first eigenvector from the tool ``hicPCA``. For this plot a pearson correlated matrix was used which is computed by creating first an observed / expected matrix and second a pearson correlation matrix. These matricies can be computed with ``hicChangeMatrixType``. The used Hi-C data were 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>`_.
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151
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152 .. image:: $PATH_TO_IMAGES/SRR0279XX_perChr_eigenvector1.png
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153 :width: 70 %
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154
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155 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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156
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157 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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158 .. _Colormaps: https://matplotlib.org/examples/color/colormaps_reference.html
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159 ]]></help>
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160 <expand macro="citations" />
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161 </tool>
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162