Mercurial > repos > bgruening > hicexplorer_chicplotviewpoint

annotate chicPlotViewpoint.xml @ 10:b9ab56aecd18 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 79133bc3739fbcc6c2055d589679aae312161d03
author iuc
date Mon, 04 Nov 2024 23:23:26 +0000
parents f47ac4a0b337
children
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1 <tool id="hicexplorer_chicplotviewpoint" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>creates plots for viewpoints</description>
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3 <macros>
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4 <token name="@BINARY@">chicPlotViewpoint</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 #import re
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10
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11 @BINARY@
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13 --interactionFile '$interactionFile'
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14 #if $differentialFile:
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15 --differentialTestResult '$differentialFile'
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16 #end if
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18 #if $significantInteractionFile:
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19 --significantInteractions '$significantInteractionFile'
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20 $plotSignificantInteractions
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21 #end if
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23 --range $rangeUpstream $rangeDownstream
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24 #if $backgroundModelFile:
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25 --backgroundModelFile '$backgroundModelFile'
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26 #end if
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28 --combinationMode $combinationMode_conditional.combinationMode_selector
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30 #if $combinationMode_conditional.combinationMode_selector == 'oneGene':
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31 --combinationName $combinationMode_conditional.geneName
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32 #end if
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34 #if $dpi:
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35 --dpi $dpi
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36 #end if
0
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38 #if $maxPValue:
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39 --maxPValue $maxPValue
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40 #end if
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42 #if $minPValue:
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43 --minPValue $minPValue
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44 #end if
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45
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46
0
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47 #if $colormap:
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48 --colorMapPvalue $colormap
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49 #end if
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50
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51 $pvalue
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52 #if $xFold:
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53 --xFold $xFold
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54 #end if
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55 --colorList $colorList
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56 --threads @THREADS@
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57 $truncateZeroPvalues
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59 -o plots.tar.gz
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60
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61 ]]> </command>
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62 <inputs>
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63
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64 <param name="interactionFile" type="data" format="h5" label="Interaction file order" />
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65 <param name="differentialFile" type="data" format="h5" label="Rejected H0 file order" optional="true" />
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66 <param name="significantInteractionFile" type="data" format="h5" label="Significant file order" optional="true" />
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67 <param argument="--plotSignificantInteractions" type="boolean" truevalue="--plotSignificantInteractions" falsevalue="" checked="false" label="Plot significant interactions" help="Select if the significant regions should be highlighted in the plot. If not set, the significant file data is used only to update the p-values." />
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68
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69 <param name="rangeUpstream" type="integer" value="100000" label="Upstream range" help="Defines the region upstream of a reference point which should be considered in the analysis." />
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70 <param name="rangeDownstream" type="integer" value="100000" label="Downstream range" help="Defines the region upstream of a reference point which should be considered in the analysis." />
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71 <param argument="--backgroundModelFile" type="data" format="tabular" label="Background model" help="The background file computed by chicViewpointBackgroundModel" optional="true" />
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72 <conditional name="combinationMode_conditional">
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73 <param name="combinationMode_selector" type="select" label="Combination mode for the plots">
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74 <option value="dual">Dual</option>
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75 <option value="single" selected="True">Single</option>
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76 <option value="allGenes" >All genes</option>
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77 <option value="oneGene" >One gene</option>
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78 </param>
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79 <when value="dual" >
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80 </when>
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81 <when value="single" >
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82 </when>
8
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83 <when value="allGenes" >
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84 </when>
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85 <when value="oneGene" >
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86 <param name="geneName" type="text" value="" label="Gene name" help="Gene name that should be plotted." />
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87 </when>
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88 </conditional>
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89
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90 <param argument="--maxPValue" type="float" optional="true" label="Max p-value" help="Maximum value of the plotted p-value." />
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91 <param argument="--minPValue" type="float" optional="true" label="Min p-value" help="Minimum value of the plotted p-value." />
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92 <param name="pvalue" type="boolean" truevalue="--pValue" falsevalue="" checked="false" label="Plot p-values as a colorbar" />
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93 <expand macro="colormap" />
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94
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95 <param name="xFold" type="float" value="" optional="true" label="X-fold mean background" help="Plot x-fold region for the mean background." />
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96
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97 <param name="image_file_format" type="select" label="Image output format">
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98 <option value="png" selected="True">png</option>
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99 <option value="svg">svg</option>
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100 <option value="pdf">pdf</option>
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101 </param>
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102 <param name="dpi" type="integer" optional="true" label="DPI for image" help="Change the default resolution of the plot." />
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103 <param name="colorList" type="text" value="g b c m y k" optional="true" label="Color list" help="Colorlist for the viewpoint lines. For all available colors please check matplotlib documentation: https://matplotlib.org/stable/gallery/color/named_colors.html">
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104 <validator type="expression" message="Only alphabetic characters and the colon are allowed.">value.replace(' ', '').replace(':', '').isalpha()</validator>
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105 </param>
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106 <param argument="--truncateZeroPvalues" type="boolean" truevalue="--truncateZeroPvalues" falsevalue="" checked="false" label="Truncate zeros by setting them to one." help="Sets all p-values which are equal to zero to one. This has the effect that the associated positions are not disturbing the presenation of small p-values." />
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107 </inputs>
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108 <outputs>
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109 <data name="plotsTar" from_work_dir="plots.tar.gz" format="tar.gz" label="cHi-C viewpoint plots" />
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110 </outputs>
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111 <tests>
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112 <test>
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113 <param name="interactionFile" value="cHi-C/chicViewpoint/two_matrices.hdf5" />
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114 <param name="differentialFile" value="cHi-C/chicDifferentialTest/differential.hdf5" />
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115 <param name="significantInteractionFile" value="cHi-C/chicSignificantInteractions/significantInteractions_dual.hdf5" />
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116 <conditional name="combinationMode_conditional">
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117 <param name="combinationMode_selector" value="dual" />
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118 </conditional>
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119 <param name="pvalue" value="True" />
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120 <param name="truncateZeroPvalues" value="True" />
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121
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122 <param name="backgroundModelFile" value="cHi-C/background.txt" />
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123 <param name="xFold" value="1.5" />
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124 <output name="plotsTar" file="cHi-C/plots.tar.gz" ftype="tar.gz" compare="sim_size" />
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125
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126 </test>
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127 </tests>
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128 <help><![CDATA[
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129
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130 Plot of viewpoints
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131 ==================
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132
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133 chicPlotViewpoint plots one or many viewpoints with the average background model and the computed p-value per sample. Moreover it can highlight differential interactions of two samples and/or significant regions.
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134
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135 An example usage is:
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136
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137 `$ chicPlotViewpoint --interactionFile interactions.hdf5 --range 500000 500000 --backgroundModelFile background_model.txt --pValue --outFileName viewpoint1_2.tar.gz --dpi 300`
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138
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139
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140 For more information about HiCExplorer please consider our documentation on readthedocs.io_
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141
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142 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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143 ]]> </help>
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144 <expand macro="citations" />
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145 </tool>