Mercurial > repos > bgruening > hicexplorer_chicsignificantinteractions

annotate chicSignificantInteractions.xml @ 4:38fa8a72ece6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
author iuc
date Fri, 14 Aug 2020 05:59:38 -0400
parents 7668fac6cc3a
children 6001400eed99
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38fa8a72ece6 "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_chicsignificantinteractions" name="@BINARY@" version="@WRAPPER_VERSION@.1">
0
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2 <description>computes viewpoints with the given reference points and a background model</description>
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3 <macros>
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4 <token name="@BINARY@">chicSignificantInteractions</token>
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5 <import>macros.xml</import>
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6 </macros>
2f279a01f3ff "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[
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9 #import re
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2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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11 mkdir interactionFiles &&
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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12 mkdir targetFolder &&
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13 mkdir significantFilesFolder &&
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14
4
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
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15 #if $tar_input_conditional.tar_input_selector == 'tar_input':
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16 ln -s '$tar_input_conditional.interactionFiles' viewpoints.tar &&
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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17 tar -C interactionFiles -xvf viewpoints.tar &&
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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18 #else:
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19 #for $file in $tar_input_conditional.interactionFiles:
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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20 #set identifier = @ESCAPE_IDENTIFIER_FILE@
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21
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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22 ln -s '$file' 'interactionFiles/$identifier' &&
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23 #end for
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24 #end if
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25
0
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26 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
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27 #set $interactonfileslist = ' '.join([ '\'interactionFiles/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ])
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28 #end if
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29 @BINARY@
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30 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
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31 --interactionFile $interactonfileslist
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32 --computeSampleNumber $batchmode_conditional.computeSampleNumber
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33
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34 #else:
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35 --interactionFile $batchmode_conditional.interactionFilesOrderFile
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36 --interactionFileFolder interactionFiles
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37 --batchMode
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38 --targetFileList targetListFile.txt
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39 --writeFileNamesToFile significantFiles.txt
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40 --computeSampleNumber $batchmode_conditional.computeSampleNumber
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41 #end if
2
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42
0
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43 --pValue $pvalue
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44
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45 #if $filter_conditional.filter_selector == 'optionXfold':
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46 --xFoldBackground $filter_conditional.xfold
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47 #else:
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48 --loosePValue $filter_conditional.loosePvalue
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49
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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50 #end if
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51 --backgroundModelFile '$backgroundModelFile'
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52 --resolution $resolution
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53 --peakInteractionsThreshold $peakInteractionsThreshold
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54 --range $rangeUpstream $rangeDownstream
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55 --targetFolder targetFolder
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56 --outputFolder significantFilesFolder
3
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57 $truncateZeroPvalues
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58 --fixateRange $fixateRange
2
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59 -suffix significant_interactions.txt
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60 --threads @THREADS@
4
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61
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62 #if $tar:
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63 && cd targetFolder
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64 && tar -cvf ../targetFolder.tar *
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65 && cd ..
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66 && rm -rf targetFolder
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67
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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68 && cd significantFilesFolder
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69 && tar -cvf ../significantFilesFolder.tar *
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70 && cd ..
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71 && rm -rf significantFilesFolder
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72
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73 #end if
0
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74 ]]></command>
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75 <inputs>
4
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76 <conditional name="tar_input_conditional">
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77 <param name="tar_input_selector" type="select" label="Compute files individually or in batch mode">
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78 <option value="tar_input">Tar file</option>
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79 <option value="interval_input" selected="True">Interval files</option>
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80 </param>
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81 <when value="tar_input">
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82 <param name='interactionFiles' type="data" format="tar" label="Interaction files" multiple="false"/>
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83 </when>
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84 <when value="interval_input">
0
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85 <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/>
4
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86 </when>
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87 </conditional>
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88
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89
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90
0
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91 <conditional name="batchmode_conditional">
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92 <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode">
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93 <option value="optionBatchmode">Batch processing</option>
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94 <option value="optionSinglemode" selected="True">Single file processing</option>
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95 </param>
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96 <when value="optionBatchmode">
2
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97 <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order"/>
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98 <param name='computeSampleNumber' type="integer" value='2' label="Create one target file for n consecutive files."/>
0
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99 </when>
2
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100 <when value="optionSinglemode">
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101 <param name='computeSampleNumber' type="integer" value='2' label="Create one target file for n consecutive files."/>
0
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102 </when>
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103 </conditional>
2
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104 <param name='pvalue' type="float" value='0.05' label="P-value of interaction to be accepted as significant"/>
0
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105 <conditional name="filter_conditional">
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106 <param name="filter_selector" type="select" label="List of chromosomes or a BED file containg regions">
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107 <option value="optionXfold">x-fold over mean background</option>
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108 <option value="optionLoosePvalue" selected="True">Loose p-value (NB background)</option>
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109 </param>
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110 <when value="optionXfold">
2
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111 <param name='xfold' type="float" value='2.0' label="X-fold over mean background to be accepted." help='Filter x-fold over background. Used to merge neighboring bins with a broader peak but
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112 less significant interactions to one peak with high significance. Used only for pValue option.'/>
0
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113 </when>
2
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114 <when value="optionLoosePvalue">
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115 <param name='loosePvalue' type="float" value='0.3' label="Loose p-value" help='loose p-value threshold value to filter target regions in a first round.
0
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116 Used to merge neighboring bins with a broader peak but less significant interactions to one peak with high significance.
2
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117 Used only for pValue option.'/>
0
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118 </when>
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119 </conditional>
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120 <param argument="--backgroundModelFile" type="data" format='tabular'
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121 label="Background model"
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122 help="The background file computed by chicViewpointBackgroundModel" />
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123 <param argument="--peakInteractionsThreshold" type="integer" value="5" label="Minimum interactions" help='The minimum number of interactions a detected peaks needs to have to be considered.'/>
0
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124 <param argument="--resolution" type="integer" value="1000" label="Bin resolution of the used 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.
2
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125 This value is used to merge neighboring bins.'/>
0
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126 <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.' />
2
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127 <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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128 <param argument="--fixateRange" type="integer" value="500000" label="Clip background distance" help='Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.'/>
3
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129 <param name='truncateZeroPvalues' type='boolean' truevalue='--truncateZeroPvalues' falsevalue="" checked="false" label="Truncate zeros by setting them to one."
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130 help="Sets all p-values which are equal to zero to one. This has the effect that the associated positions are not part of the significance decision."/>
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131 <param name='tar' type='boolean' checked="false" truevalue='True' label="tar output to one file"
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132 help="The output is tarred to one file and not written to a collection. Set this option if the number of files is large."/>
0
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133 </inputs>
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134 <outputs>
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135 <collection name="significantFilesCollection" type="list" label="Significant files">
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136 <discover_datasets pattern="__name__" format="interval" directory="significantFilesFolder" />
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137 </collection>
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138 <collection name="targetFilesCollection" type="list" label="Target files">
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139 <discover_datasets pattern="__name__" format="interval" directory="targetFolder" />
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140 </collection>
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141 <data name="significantFileNames" from_work_dir="significantFiles.txt" format="txt" label="${tool.name} significant file names">
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142 <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter>
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143 </data>
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144 <data name="targetFileNames" from_work_dir="targetListFile.txt" format="txt" label="${tool.name} target file names">
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145 <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter>
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146 </data>
4
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147 <data name="targetFolderTar" from_work_dir="targetFolder.tar" format="tar" label="Target files tar">
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148 <filter>tar</filter>
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149 </data>
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150 <data name="significantFilesFolderTar" from_work_dir="significantFilesFolder.tar" format="tar" label="Significant files tar">
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151 <filter>tar</filter>
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152 </data>
0
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153 </outputs>
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154 <tests>
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155 <test>
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156 <conditional name="tar_input_conditional">
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157 <param name="tar_input_selector" value='interval_input'/>
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158 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt"/>
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159 </conditional>
0
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160 <conditional name="batchmode_conditional">
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161 <param name="batchmode_selector" value='optionBatchmode'/>
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162 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/>
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163 <param name="computeSampleNumber" value='2'/>
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164 </conditional>
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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165 <param name="pvalue" value='0.2'/>
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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166
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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167 <conditional name="filter_conditional">
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
168 <param name="filter_selector" value='optionLoosePvalue'/>
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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169 <param name="loosePvalue" value='0.5'/>
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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170 </conditional>
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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171
2
3df84bb4486c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents: 1
diff changeset
172 <param name="backgroundModelFile" value="cHi-C/background.txt"/>
0
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
173 <param name="rangeUpstream" value="200000"/>
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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diff changeset
174 <param name="rangeDownstream" value="200000"/>
2
3df84bb4486c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents: 1
diff changeset
175
0
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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diff changeset
176 <output_collection name="significantFilesCollection" type="list" count="6">
3
7668fac6cc3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
parents: 2
diff changeset
177 <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt" ftype="interval" lines_diff="4"/>
7668fac6cc3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
parents: 2
diff changeset
178 <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" ftype="interval" lines_diff="4"/>
7668fac6cc3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
parents: 2
diff changeset
179 <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt" ftype="interval" lines_diff="4"/>
0
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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180
3
7668fac6cc3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
parents: 2
diff changeset
181 <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt" ftype="interval" lines_diff="4"/>
7668fac6cc3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
parents: 2
diff changeset
182 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" ftype="interval" lines_diff="4"/>
7668fac6cc3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
parents: 2
diff changeset
183 <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt" ftype="interval" lines_diff="4"/>
0
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
184 </output_collection>
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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185
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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diff changeset
186 <output_collection name="targetFilesCollection" type="list" count="3">
2
3df84bb4486c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents: 1
diff changeset
187 <element name="FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt" file="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt" ftype="interval" lines_diff="4"/>
3df84bb4486c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents: 1
diff changeset
188 <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" file="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" ftype="interval" lines_diff="4"/>
3df84bb4486c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents: 1
diff changeset
189 <element name="FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt" file="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt" ftype="interval" lines_diff="4"/>
0
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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diff changeset
190 </output_collection>
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
191 <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" compare="sim_size" delta='40000'/>
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
192 <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" compare="sim_size" delta='40000'/>
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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diff changeset
193 </test>
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
194 <test>
4
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 3
diff changeset
195 <conditional name="tar_input_conditional">
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 3
diff changeset
196 <param name="tar_input_selector" value='interval_input'/>
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 3
diff changeset
197 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt"/>
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 3
diff changeset
198 </conditional>
0
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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diff changeset
199 <conditional name="batchmode_conditional">
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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diff changeset
200 <param name="batchmode_selector" value='optionSinglemode'/>
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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diff changeset
201 <param name="computeSampleNumber" value="1"/>
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
202 </conditional>
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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diff changeset
203 <param name="pvalue" value='0.2'/>
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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diff changeset
204
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
205 <conditional name="filter_conditional">
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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diff changeset
206 <param name="filter_selector" value='optionXfold'/>
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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diff changeset
207 <param name="xfold" value='1.5'/>
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
208 </conditional>
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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diff changeset
209
2
3df84bb4486c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents: 1
diff changeset
210 <param name="backgroundModelFile" value="cHi-C/background.txt"/>
0
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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diff changeset
211 <param name="rangeUpstream" value="200000"/>
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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diff changeset
212 <param name="rangeDownstream" value="200000"/>
2
3df84bb4486c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents: 1
diff changeset
213
0
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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diff changeset
214 <output_collection name="significantFilesCollection" type="list" count="2">
2
3df84bb4486c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents: 1
diff changeset
215 <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt" ftype="interval" lines_diff="4"/>
3df84bb4486c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents: 1
diff changeset
216 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt" ftype="interval" lines_diff="4"/>
0
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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diff changeset
217 </output_collection>
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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diff changeset
218
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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diff changeset
219 <output_collection name="targetFilesCollection" type="list" count="2">
2
3df84bb4486c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents: 1
diff changeset
220 <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt" file="cHi-C/chicSignificantInteractions/output_3_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt" ftype="interval" lines_diff="4"/>
3df84bb4486c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents: 1
diff changeset
221 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" file="cHi-C/chicSignificantInteractions/output_3_target/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" ftype="interval" lines_diff="4"/>
0
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
222 </output_collection>
4
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 3
diff changeset
223 </test>
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 3
diff changeset
224
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 3
diff changeset
225 <test>
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 3
diff changeset
226 <conditional name="tar_input_conditional">
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 3
diff changeset
227 <param name="tar_input_selector" value='interval_input'/>
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 3
diff changeset
228 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt"/>
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 3
diff changeset
229 </conditional>
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 3
diff changeset
230 <conditional name="batchmode_conditional">
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 3
diff changeset
231 <param name="batchmode_selector" value='optionBatchmode'/>
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 3
diff changeset
232 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/>
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 3
diff changeset
233 <param name="computeSampleNumber" value='2'/>
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 3
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234 </conditional>
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235 <param name="pvalue" value='0.2'/>
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236
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237 <conditional name="filter_conditional">
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238 <param name="filter_selector" value='optionLoosePvalue'/>
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239 <param name="loosePvalue" value='0.5'/>
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240 </conditional>
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241
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242 <param name="backgroundModelFile" value="cHi-C/background.txt"/>
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243 <param name="rangeUpstream" value="200000"/>
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244 <param name="rangeDownstream" value="200000"/>
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245
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246 <param name='tar' value='True'/>
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247
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248 <output name="targetFolderTar" file="cHi-C/chicSignificantInteractions/targetFolder.tar" ftype='tar' compare="sim_size" delta='40000' />
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249 <output name="significantFilesFolderTar" file="cHi-C/chicSignificantInteractions/significantFilesFolder.tar" ftype='tar' compare="sim_size" delta='40000' />
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250
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251 <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" compare="sim_size" delta='40000'/>
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252 <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" compare="sim_size" delta='40000'/>
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253 </test>
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254
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255 <test>
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256 <conditional name="tar_input_conditional">
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257 <param name="tar_input_selector" value='tar_input'/>
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258 <param name="interactionFiles" value="cHi-C/chicViewpoint/viewpoints.tar"/>
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259 </conditional>
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260 <conditional name="batchmode_conditional">
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261 <param name="batchmode_selector" value='optionBatchmode'/>
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262 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/>
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263 <param name="computeSampleNumber" value='2'/>
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264 </conditional>
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265 <param name="pvalue" value='0.2'/>
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266
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267 <conditional name="filter_conditional">
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268 <param name="filter_selector" value='optionLoosePvalue'/>
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269 <param name="loosePvalue" value='0.5'/>
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270 </conditional>
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271
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272 <param name="backgroundModelFile" value="cHi-C/background.txt"/>
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273 <param name="rangeUpstream" value="200000"/>
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274 <param name="rangeDownstream" value="200000"/>
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275
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276 <param name='tar' value='True'/>
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277
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278 <output name="targetFolderTar" file="cHi-C/chicSignificantInteractions/targetFolder.tar" ftype='tar' compare="sim_size" delta='40000' />
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279 <output name="significantFilesFolderTar" file="cHi-C/chicSignificantInteractions/significantFilesFolder.tar" ftype='tar' compare="sim_size" delta='40000' />
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280
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281 <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" compare="sim_size" delta='40000'/>
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282 <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" compare="sim_size" delta='40000'/>
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283 </test>
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284
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285 </tests>
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286 <help><![CDATA[
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287
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288 Significant interaction detection
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289 =================================
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290
2
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291 Significant interactions are detected by this tool for each viewpoint based on the background model. chicSignificantInteractions outputs for each viewpoint a file containing all recorded significant interactions and
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292 a target file. The target file is especially useful in the batch mode context, as it merges for two consecutive listed control and treatment viewpoint the significant interactions which can then be used
0
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293 to test for a differential interaction scheme.
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294
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295 chicSignificantInteractions supports two modes to detect significant interactions, either by an x-fold over the average background or a loose p-value. In both cases neighboring significant peaks are merged together and an additional
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296 p-value based on the sum of interactions for this neighborhood is computed. Only interactions with a higher p-value as specified by the threshold `--pValue` are accepted as a significant interaction.
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297
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298 For more information about HiCExplorer please consider our documentation on readthedocs.io_
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299
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300 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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301 ]]></help>
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302 <expand macro="citations" />
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303 </tool>