Mercurial > repos > bgruening > hicexplorer_chicplotviewpoint

annotate chicPlotViewpoint.xml @ 1:61e2d34c5b99 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
author bgruening
date Wed, 05 Feb 2020 19:55:06 -0500
parents ae8bf5420df2
children 136ebddd6ec3
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ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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1 <tool id="hicexplorer_chicplotviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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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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ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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11 mkdir interactionFiles &&
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12 mkdir differentialFolder &&
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13 mkdir significantFolder &&
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14 mkdir plots &&
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ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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17 #for $file in $interactionFiles:
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18 #set identifier = @ESCAPE_IDENTIFIER_FILE@
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19 ln -s '$file' 'interactionFiles/$identifier' &&
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20 #end for
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ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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22 #if $differentialFiles:
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23 #for $file in $differentialFiles:
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24 #set identifier = @ESCAPE_IDENTIFIER_FILE@
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25 ln -s '$file' 'differentialFolder/$identifier' &&
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26 #end for
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27 #end if
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ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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29 #if $significantFiles:
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30 #for $file in $significantFiles:
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31 #set identifier = @ESCAPE_IDENTIFIER_FILE@
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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32 ln -s '$file' 'significantFolder/$identifier' &&
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33 #end for
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34 #end if
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ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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36 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
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37 #set $interactonfileslist = ' '.join([ '\'interactionFiles/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ])
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38 #set $differentialfileslist = ' '.join([ '\'differentialFolder/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $differentialFiles ])
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39 #set $significantfileslist = ' '.join([ '\'significantFolder/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $significantFiles ])
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ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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41 #end if
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ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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43 @BINARY@
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44 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
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45 --interactionFile $interactonfileslist
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46 #if $differentialFiles:
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47 --differentialTestResult $differentialfileslist
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48 #end if
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ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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50 #if $significantFiles:
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51 --significantInteractions $significantfileslist
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52 #end if
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53
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54 -o out_plot.$image_file_format
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55 #else:
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56 --interactionFile $batchmode_conditional.interactionFilesOrderFile
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57 --interactionFileFolder interactionFiles
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58 #if $batchmode_conditional.differentialFilesOrderFile:
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59 --differentialTestResult $batchmode_conditional.differentialFilesOrderFile
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60 --differentialTestResultsFolder differentialFolder
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61 #end if
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62 #if $batchmode_conditional.significantInteractionFilesOrderFile:
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63 --significantInteractions $batchmode_conditional.significantInteractionFilesOrderFile
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64 --significantInteractionFileFolder significantFolder
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65 #end if
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66 --plotSampleNumber $batchmode_conditional.computeSampleNumber
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67
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68 --batchMode
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69 --outputFolder plots
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70 --outputFormat $image_file_format
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73 #end if
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ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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75 --range $rangeUpstream $rangeDownstream
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76 #if $backgroundModelFile:
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77 --backgroundModelFile $backgroundModelFile
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78 #end if
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ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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80 #if $dpi:
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81 --dpi $dpi
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82 #end if
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ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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84 #if $maxPValue:
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85 --maxPValue $maxPValue
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86 #end if
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88 #if $minPValue:
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89 --minPValue $minPValue
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90 #end if
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91
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92 --binResolution $resolution
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93 #if $colormap:
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94 --colorMapPvalue $colormap
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95 #end if
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96
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97 $pvalue
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98 #if $xFold:
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99 --xFold $xFold
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100 #end if
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101 --colorList $colorList
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102 --threads @THREADS@
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103
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104 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
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105 && mv out_plot.$image_file_format plots/out_plot.$image_file_format
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106 #end if
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107 ]]></command>
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108 <inputs>
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109 <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/>
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110 <param name='differentialFiles' type="data" format="interval" label="Rejected H0 files" multiple="true" optional='true'/>
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111 <param name='significantFiles' type="data" format="interval" label="Significant interaction files" multiple="true" optional='true'/>
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112
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113 <param name="rangeUpstream" type="integer" value="500000" label="Upstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' />
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114 <param name="rangeDownstream" type="integer" value="500000" label="Downstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' />
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115 <param argument="--backgroundModelFile" type="data" format='tabular'
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116 label="Background model"
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117 help="The background file computed by chicViewpointBackgroundModel" optional='true'/>
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118
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119 <conditional name="batchmode_conditional">
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120 <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode">
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121 <option value="optionBatchmode">Batch processing</option>
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122 <option value="optionSinglemode" selected="True">Single file processing</option>
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123 </param>
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124 <when value="optionBatchmode">
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125 <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order"/>
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126 <param name='differentialFilesOrderFile' type="data" format="txt" label="Rejected H0 file order" optional='true'/>
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127 <param name='significantInteractionFilesOrderFile' type="data" format="txt" label="Significant file order" optional='true'/>
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128 <param name='computeSampleNumber' type="integer" value='2' label="Plot n sample in one plot"/>
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129
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130 </when>
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131 <when value="optionSinglemode">
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132 </when>
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133 </conditional>
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134
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135
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136 <param argument="--maxPValue" type="float" optional="true" label="Max p-value" help="Maximum value of the plotted p-value."/>
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137 <param argument="--minPValue" type="float" optional="true" label="Min p-value" help="Minimum value of the plotted p-value."/>
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138 <param name='resolution' type='integer' value='1000' label='Resolution of cHi-C data' help='Resolution of the bin in genomic units. Values are usually e.g. 1000 for a 1kb, 5000 for a 5kb or 10000 for a 10kb resolution.' optional='true'/>
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139 <param name='pvalue' type='boolean' truevalue='--pValue' falsevalue="" checked="false" label="Plot p-values as a colorbar"/>
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140 <expand macro="colormap" />
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141
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142 <param name='xFold' type='float' value='' label='X-fold mean background' help='Plot x-fold region for the mean background.' optional='true'/>
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143
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144 <param name="image_file_format" type="select" label="Image output format">
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145 <option value="png" selected="True">png</option>
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146 <option value="svg">svg</option>
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147 <option value="pdf">pdf</option>
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148 </param>
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149 <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/>
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150 <param name='colorList' type='text' value='g b c m y k' label='Color list' help='Colorlist for the viewpoint lines. For all available colors please check matplotlib documentation: https://matplotlib.org/3.1.0/gallery/color/named_colors.html' optional='true'/>
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151
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152
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153 </inputs>
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154 <outputs>
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155 <collection name="plotsCollection" type="list" label="cHi-C viewpoint plots">
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156 <discover_datasets pattern="__name_and_ext__" directory="plots" />
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157 </collection>
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158
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159 </outputs>
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160 <tests>
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161 <test>
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162 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed"/>
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163 <param name="differentialFiles" value="cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.bed,cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed,cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.bed"/>
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164 <param name="significantFiles" value="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed"/>
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165
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166
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167 <conditional name="batchmode_conditional">
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168 <param name="batchmode_selector" value='optionBatchmode'/>
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169 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/>
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170 <param name="differentialFilesOrderFile" value='cHi-C/chicDifferentialTest/rejectedFilesList.txt'/>
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171 <param name="significantInteractionFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_significant_files.txt'/>
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172 <param name='computeSampleNumber' value='2'/>
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173 </conditional>
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174 <param name="pvalue" value='True'/>
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175 <param name="alpha" value='0.5'/>
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176 <param name='backgroundModelFile' value='cHi-C/background.bed'/>
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177 <param name='xFold' value='1.5'/>
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178 <output_collection name="plotsCollection" type="list" count="3">
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179 <element name="Eya1_FL-E13-5_MB-E10-5_chr1_chr1_14300280" file="cHi-C/chicPlotViewpoint/batchMode/two/Eya1_FL-E13-5_MB-E10-5_chr1_chr1_14300280.png" ftype="png" compare='sim_size' delta='40000'/>
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180 <element name="Sox17_FL-E13-5_MB-E10-5_chr1_chr1_4487435" file="cHi-C/chicPlotViewpoint/batchMode/two/Sox17_FL-E13-5_MB-E10-5_chr1_chr1_4487435.png" ftype="png" compare='sim_size' delta='40000'/>
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181 <element name="Tfap2d_FL-E13-5_MB-E10-5_chr1_chr1_19093103" file="cHi-C/chicPlotViewpoint/batchMode/two/Tfap2d_FL-E13-5_MB-E10-5_chr1_chr1_19093103.png" ftype="png" compare='sim_size' delta='40000'/>
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182 </output_collection>
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183
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184 </test>
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185 <test>
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186 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed"/>
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187
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188 <conditional name="batchmode_conditional">
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189 <param name="batchmode_selector" value='optionSinglemode'/>
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190 </conditional>
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191
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192 <output_collection name="plotsCollection" type="list" count="1">
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193 <element name="out_plot" file="cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png" ftype="png" compare='sim_size' delta='40000'/>
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194
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195 </output_collection>
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196 </test>
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197 </tests>
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198 <help><![CDATA[
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199
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200 Plot of viewpoints
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201 ==================
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202
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203 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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204
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205 An example usage is:
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206
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207 `$ chicPlotViewpoint --interactionFile viewpoint1.bed viewpoint2.bed --range 500000 500000 --backgroundModelFile background_model.bed --pValue --outFileName viewpoint1_2.png --dpi 300`
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208
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209
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210 In batch mode the list of file names and the folders containing the files need to be given:
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211
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212 `$ chicPlotViewpoint --interactionFile viewpoint_names.txt -interactionFileFolder viewpointFilesFolder --differentialTestResult rejected_H0.txt --differentialTestResultsFolder differentialFolder --range 500000 500000 --backgroundModelFile background_model.bed --pValue --outputFolder plotsFOlder --dpi 300 --threads 20`
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213
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214
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215 For more information about HiCExplorer please consider our documentation on readthedocs.io_
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216
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217 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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218 ]]></help>
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219 <expand macro="citations" />
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220 </tool>