Mercurial > repos > bgruening > hicexplorer_chicplotviewpoint

annotate chicPlotViewpoint.xml @ 5:46793007f090 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3e5c2f8ce3e540b0474746a33ee20b4a374dd38c"
author iuc
date Fri, 11 Dec 2020 21:20:38 +0000
parents ac7999229ac6
children 031872f8e2e0
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ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
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1 <tool id="hicexplorer_chicplotviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.1">
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2 <description>creates plots for viewpoints</description>
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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3 <macros>
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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4 <token name="@BINARY@">chicPlotViewpoint</token>
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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5 <import>macros.xml</import>
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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6 </macros>
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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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 &&
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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12 mkdir differentialFolder &&
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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13 mkdir significantFolder &&
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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14 mkdir plots &&
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
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16 #if $tar_input_conditional.tar_input_selector == 'tar_input':
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
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17 ln -s '$tar_input_conditional.interactionFiles' viewpoints.tar &&
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
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18 tar -C interactionFiles -xvf viewpoints.tar &&
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iuc
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20 #if $differentialFiles:
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21 ln -s '$tar_input_conditional.differentialFiles' differential.tar &&
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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22 tar -C differentialFolder -xvf differential.tar &&
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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23 #end if
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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24 #if $significantFiles:
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25 ln -s '$tar_input_conditional.significantFiles' significantFiles.tar &&
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
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26 tar -C significantFolder -xvf significantFiles.tar &&
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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27 #end if
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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28 #else:
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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29 #for $file in $tar_input_conditional.interactionFiles:
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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30 #set identifier = @ESCAPE_IDENTIFIER_FILE@
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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31 ln -s '$file' 'interactionFiles/$identifier' &&
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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32 #end for
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34 #for $file in $tar_input_conditional.differentialFiles:
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35 #set identifier = @ESCAPE_IDENTIFIER_FILE@
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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36 ln -s '$file' 'differentialFolder/$identifier' &&
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37 #end for
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ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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39 #for $file in $tar_input_conditional.significantFiles:
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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40 #set identifier = @ESCAPE_IDENTIFIER_FILE@
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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41 ln -s '$file' 'significantFolder/$identifier' &&
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42 #end for
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43 #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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ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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46 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
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47 #set $interactonfileslist = ' '.join([ '\'interactionFiles/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $tar_input_conditional.interactionFiles ])
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48 #set $differentialfileslist = ' '.join([ '\'differentialFolder/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $tar_input_conditional.differentialFiles ])
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49 #set $significantfileslist = ' '.join([ '\'significantFolder/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $tar_input_conditional.significantFiles ])
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50
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51 #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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53 @BINARY@
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54 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
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55 --interactionFile $interactonfileslist
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56 #if $tar_input_conditional.differentialFiles:
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57 --differentialTestResult $differentialfileslist
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58 #end if
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ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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60 #if $tar_input_conditional.significantFiles:
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61 --significantInteractions $significantfileslist
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62 #end if
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ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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64 -o out_plot.$image_file_format
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65 #else:
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66 --interactionFile $batchmode_conditional.interactionFilesOrderFile
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67 --interactionFileFolder interactionFiles
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68 #if $batchmode_conditional.differentialFilesOrderFile:
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69 --differentialTestResult $batchmode_conditional.differentialFilesOrderFile
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70 --differentialTestResultsFolder differentialFolder
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71 #end if
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72 #if $batchmode_conditional.significantInteractionFilesOrderFile:
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73 --significantInteractions $batchmode_conditional.significantInteractionFilesOrderFile
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74 --significantInteractionFileFolder significantFolder
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75 #end if
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76 --plotSampleNumber $batchmode_conditional.computeSampleNumber
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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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78 --batchMode
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79 --outputFolder plots
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80 --outputFormat $image_file_format
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83 #end if
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84
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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85 --range $rangeUpstream $rangeDownstream
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86 #if $backgroundModelFile:
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87 --backgroundModelFile $backgroundModelFile
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88 #end if
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89
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90 #if $dpi:
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91 --dpi $dpi
2
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92 #end if
0
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93
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94 #if $maxPValue:
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95 --maxPValue $maxPValue
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96 #end if
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97
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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98 #if $minPValue:
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99 --minPValue $minPValue
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100 #end if
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101
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102 --binResolution $resolution
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103 #if $colormap:
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104 --colorMapPvalue $colormap
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105 #end if
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106
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107 $pvalue
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108 #if $xFold:
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109 --xFold $xFold
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110 #end if
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111 --colorList $colorList
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112 --threads @THREADS@
3
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113 $truncateZeroPvalues
0
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114 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
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115 && mv out_plot.$image_file_format plots/out_plot.$image_file_format
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116 #end if
4
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117
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118 #if $tar:
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119 && cd plots
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120 && tar -cvf ../plots.tar *
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121 && cd ..
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122 && rm -rf plots
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123 #end if
0
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124 ]]></command>
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125 <inputs>
4
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126 <conditional name="tar_input_conditional">
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127 <param name="tar_input_selector" type="select" label="Compute files individually or in batch mode">
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128 <option value="tar_input">Tar file</option>
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129 <option value="interval_input" selected="True">Interval files</option>
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130 </param>
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131 <when value="tar_input">
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132 <param name='interactionFiles' type="data" format="tar" label="Interaction files" multiple="false"/>
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133 <param name='differentialFiles' type="data" format="tar" label="Rejected H0 files" multiple="true" optional='false'/>
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134 <param name='significantFiles' type="data" format="tar" label="Significant interaction files" multiple="true" optional='false'/>
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135 </when>
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136 <when value="interval_input">
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137 <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/>
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138 <param name='differentialFiles' type="data" format="interval" label="Rejected H0 files" multiple="true" optional='true'/>
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139 <param name='significantFiles' type="data" format="interval" label="Significant interaction files" multiple="true" optional='true'/>
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140 </when>
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141 </conditional>
2
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142
4
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143 <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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144 <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.' />
0
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145 <param argument="--backgroundModelFile" type="data" format='tabular'
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146 label="Background model"
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147 help="The background file computed by chicViewpointBackgroundModel" optional='true'/>
2
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148
0
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149 <conditional name="batchmode_conditional">
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150 <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode">
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151 <option value="optionBatchmode">Batch processing</option>
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152 <option value="optionSinglemode" selected="True">Single file processing</option>
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153 </param>
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154 <when value="optionBatchmode">
2
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155 <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order"/>
0
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156 <param name='differentialFilesOrderFile' type="data" format="txt" label="Rejected H0 file order" optional='true'/>
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157 <param name='significantInteractionFilesOrderFile' type="data" format="txt" label="Significant file order" optional='true'/>
2
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158 <param name='computeSampleNumber' type="integer" value='2' label="Plot n sample in one plot"/>
0
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159
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160 </when>
2
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161 <when value="optionSinglemode">
0
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162 </when>
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163 </conditional>
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164
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165
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166 <param argument="--maxPValue" type="float" optional="true" label="Max p-value" help="Maximum value of the plotted p-value."/>
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167 <param argument="--minPValue" type="float" optional="true" label="Min p-value" help="Minimum value of the plotted p-value."/>
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168 <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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169 <param name='pvalue' type='boolean' truevalue='--pValue' falsevalue="" checked="false" label="Plot p-values as a colorbar"/>
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170 <expand macro="colormap" />
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171
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172 <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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173
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174 <param name="image_file_format" type="select" label="Image output format">
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175 <option value="png" selected="True">png</option>
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176 <option value="svg">svg</option>
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177 <option value="pdf">pdf</option>
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178 </param>
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179 <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/>
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180 <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'/>
3
dbf82dd7bdb3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
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181 <param name='truncateZeroPvalues' type='boolean' truevalue='--truncateZeroPvalues' falsevalue="" checked="false" label="Truncate zeros by setting them to one."
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182 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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183
4
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184 <param name='tar' type='boolean' checked="false" truevalue='True' label="tar output to one file"
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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185 help="The output is tarred to one file and not written to a collection. Set this option if the number of files is large."/>
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186
0
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187 </inputs>
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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188 <outputs>
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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189 <collection name="plotsCollection" type="list" label="cHi-C viewpoint plots">
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190 <discover_datasets pattern="__name_and_ext__" directory="plots" />
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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191 </collection>
4
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192 <data name="plotsTar" from_work_dir="plots.tar" format="tar" label="cHi-C viewpoint plots tar">
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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193 <filter>tar</filter>
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194 </data>
0
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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195 </outputs>
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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196 <tests>
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197 <test>
4
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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198 <conditional name="tar_input_conditional">
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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199 <param name="tar_input_selector" value='interval_input'/>
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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200 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt"/>
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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201 <param name="differentialFiles" value="cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt,cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt,cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt"/>
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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202 <param name="significantFiles" value="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt"/>
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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203 </conditional>
0
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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204
2
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parents: 0
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205
0
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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206 <conditional name="batchmode_conditional">
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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207 <param name="batchmode_selector" value='optionBatchmode'/>
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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208 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/>
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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209 <param name="differentialFilesOrderFile" value='cHi-C/chicDifferentialTest/rejectedFilesList.txt'/>
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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210 <param name="significantInteractionFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_significant_files.txt'/>
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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211 <param name='computeSampleNumber' value='2'/>
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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212 </conditional>
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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213 <param name="pvalue" value='True'/>
3
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214 <param name="truncateZeroPvalues" value='True'/>
dbf82dd7bdb3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
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215
2
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216 <param name='backgroundModelFile' value='cHi-C/background.txt'/>
0
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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217 <param name='xFold' value='1.5'/>
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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218 <output_collection name="plotsCollection" type="list" count="3">
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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219 <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'/>
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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220 <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'/>
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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221 <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'/>
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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222 </output_collection>
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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223
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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224 </test>
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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225 <test>
4
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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226 <conditional name="tar_input_conditional">
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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227 <param name="tar_input_selector" value='interval_input'/>
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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228 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt"/>
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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229 </conditional>
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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230
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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231 <conditional name="batchmode_conditional">
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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232 <param name="batchmode_selector" value='optionSinglemode'/>
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233 </conditional>
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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234
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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235 <output_collection name="plotsCollection" type="list" count="1">
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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236 <element name="out_plot" file="cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png" ftype="png" compare='sim_size' delta='40000'/>
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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237
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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238 </output_collection>
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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239 </test>
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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240
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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241 <test>
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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242 <conditional name="tar_input_conditional">
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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243 <param name="tar_input_selector" value='interval_input'/>
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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244 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt"/>
ac7999229ac6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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245 </conditional>
2
136ebddd6ec3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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246
0
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247 <conditional name="batchmode_conditional">
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248 <param name="batchmode_selector" value='optionSinglemode'/>
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249 </conditional>
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250
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251 <output_collection name="plotsCollection" type="list" count="1">
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252 <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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253
ae8bf5420df2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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254 </output_collection>
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255 </test>
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256
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257 <test>
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258 <conditional name="tar_input_conditional">
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259 <param name="tar_input_selector" value='interval_input'/>
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260 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt"/>
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261 <param name="differentialFiles" value="cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt,cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt,cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt"/>
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262 <param name="significantFiles" value="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt"/>
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263 </conditional>
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264
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265 <conditional name="batchmode_conditional">
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266 <param name="batchmode_selector" value='optionBatchmode'/>
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267 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/>
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268 <param name="differentialFilesOrderFile" value='cHi-C/chicDifferentialTest/rejectedFilesList.txt'/>
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269 <param name="significantInteractionFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_significant_files.txt'/>
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270 <param name='computeSampleNumber' value='2'/>
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271 </conditional>
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272 <param name="pvalue" value='True'/>
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273 <param name="truncateZeroPvalues" value='True'/>
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274
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275 <param name='backgroundModelFile' value='cHi-C/background.txt'/>
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276 <param name='xFold' value='1.5'/>
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277 <param name='tar' value='True'/>
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278 <output name="plotsTar" file="cHi-C/chicPlotViewpoint/batchMode/plots.tar" ftype='tar' compare="sim_size" delta='40000' />
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279 </test>
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280
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281 <test>
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282 <conditional name="tar_input_conditional">
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283 <param name="tar_input_selector" value='tar_input'/>
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284 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1.tar"/>
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285 <param name="differentialFiles" value="cHi-C/chicDifferentialTest/batch_mode_fisher_outfile.tar"/>
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286 <param name="significantFiles" value="cHi-C/chicSignificantInteractions/significantFilesFolder.tar"/>
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287 </conditional>
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288
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289 <conditional name="batchmode_conditional">
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290 <param name="batchmode_selector" value='optionBatchmode'/>
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291 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/>
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292 <param name="differentialFilesOrderFile" value='cHi-C/chicDifferentialTest/rejectedFilesList.txt'/>
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293 <param name="significantInteractionFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_significant_files.txt'/>
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294 <param name='computeSampleNumber' value='2'/>
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295 </conditional>
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296 <param name="pvalue" value='True'/>
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297 <param name="truncateZeroPvalues" value='True'/>
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298
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299 <param name='backgroundModelFile' value='cHi-C/background.txt'/>
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300 <param name='xFold' value='1.5'/>
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301 <param name='tar' value='True'/>
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302 <output name="plotsTar" file="cHi-C/chicPlotViewpoint/batchMode/plots.tar" ftype='tar' compare="sim_size" delta='40000' />
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303 </test>
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304 </tests>
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305 <help><![CDATA[
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306
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307 Plot of viewpoints
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308 ==================
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309
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310 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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311
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312 An example usage is:
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313
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314 `$ chicPlotViewpoint --interactionFile viewpoint1.txt viewpoint2.txt --range 500000 500000 --backgroundModelFile background_model.txt --pValue --outFileName viewpoint1_2.png --dpi 300`
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315
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316
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317 In batch mode the list of file names and the folders containing the files need to be given:
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318
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319 `$ chicPlotViewpoint --interactionFile viewpoint_names.txt -interactionFileFolder viewpointFilesFolder --differentialTestResult rejected_H0.txt --differentialTestResultsFolder differentialFolder --range 500000 500000 --backgroundModelFile background_model.txt --pValue --outputFolder plotsFOlder --dpi 300 --threads 20`
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320
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321
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322 For more information about HiCExplorer please consider our documentation on readthedocs.io_
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323
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324 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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325 ]]></help>
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326 <expand macro="citations" />
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327 </tool>