Mercurial > repos > bgruening > hicexplorer_chicsignificantinteractions

annotate chicSignificantInteractions.xml @ 7:6ef732512682 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa140a9f660eab2459e21b0b637b129d7de24c02
author iuc
date Tue, 10 Jan 2023 18:50:07 +0000
parents 6001400eed99
children 640e0e45518a
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6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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1 <tool id="hicexplorer_chicsignificantinteractions" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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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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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 &&
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17 tar -C interactionFiles -xvf viewpoints.tar &&
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18 #else:
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19 #for $file in $tar_input_conditional.interactionFiles:
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20 #set identifier = @ESCAPE_IDENTIFIER_FILE@
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21 ln -s '$file' 'interactionFiles/$identifier' &&
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22 #end for
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23 #end if
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24
0
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25 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
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26 #set $interactonfileslist = ' '.join([ '\'interactionFiles/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ])
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27 #end if
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28 @BINARY@
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29 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
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30 --interactionFile $interactonfileslist
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31 --computeSampleNumber $batchmode_conditional.computeSampleNumber
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32 #else:
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33 --interactionFile '$batchmode_conditional.interactionFilesOrderFile'
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34 --interactionFileFolder interactionFiles
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35 --batchMode
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36 --targetFileList targetListFile.txt
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37 --writeFileNamesToFile significantFiles.txt
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38 --computeSampleNumber $batchmode_conditional.computeSampleNumber
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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39 #end if
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40
0
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41 --pValue $pvalue
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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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43 #if $filter_conditional.filter_selector == 'optionXfold':
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44 --xFoldBackground $filter_conditional.xfold
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45 #else:
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46 --loosePValue $filter_conditional.loosePvalue
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47
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48 #end if
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49 --backgroundModelFile '$backgroundModelFile'
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50 --resolution $resolution
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51 --peakInteractionsThreshold $peakInteractionsThreshold
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52 --range $rangeUpstream $rangeDownstream
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53 --targetFolder targetFolder
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54 --outputFolder significantFilesFolder
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55 $truncateZeroPvalues
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56 --fixateRange $fixateRange
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57 -suffix significant_interactions.txt
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58 --threads @THREADS@
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59
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60 #if $tar:
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61 && cd targetFolder
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62 && tar -cvf ../targetFolder.tar *
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63 && cd ..
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64 && rm -rf targetFolder
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65
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66 && cd significantFilesFolder
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67 && tar -cvf ../significantFilesFolder.tar *
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68 && cd ..
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69 && rm -rf significantFilesFolder
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70
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71 #end if
6
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72 ]]> </command>
0
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73 <inputs>
4
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74 <conditional name="tar_input_conditional">
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75 <param name="tar_input_selector" type="select" label="Compute files individually or in batch mode">
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76 <option value="tar_input">Tar file</option>
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77 <option value="interval_input" selected="True">Interval files</option>
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78 </param>
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79 <when value="tar_input">
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80 <param name='interactionFiles' type="data" format="tar" label="Interaction files" multiple="false" />
4
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81 </when>
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82 <when value="interval_input">
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83 <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true" />
4
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84 </when>
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85 </conditional>
0
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86 <conditional name="batchmode_conditional">
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87 <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode">
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88 <option value="optionBatchmode">Batch processing</option>
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89 <option value="optionSinglemode" selected="True">Single file processing</option>
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90 </param>
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91 <when value="optionBatchmode">
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92 <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order" />
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93 <param name='computeSampleNumber' type="integer" value='2' label="Create one target file for n consecutive files." />
0
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94 </when>
2
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95 <when value="optionSinglemode">
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96 <param name='computeSampleNumber' type="integer" value='2' label="Create one target file for n consecutive files." />
0
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97 </when>
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98 </conditional>
6
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99 <param name='pvalue' type="float" value='0.05' label="P-value of interaction to be accepted as significant" />
0
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100 <conditional name="filter_conditional">
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101 <param name="filter_selector" type="select" label="List of chromosomes or a BED file containg regions">
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102 <option value="optionXfold">x-fold over mean background</option>
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103 <option value="optionLoosePvalue" selected="True">Loose p-value (NB background)</option>
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104 </param>
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105 <when value="optionXfold">
2
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106 <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
6
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107 less significant interactions to one peak with high significance. Used only for pValue option.' />
0
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108 </when>
2
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109 <when value="optionLoosePvalue">
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110 <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.
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111 Used to merge neighboring bins with a broader peak but less significant interactions to one peak with high significance.
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112 Used only for pValue option.' />
0
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113 </when>
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114 </conditional>
6
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115 <param argument="--backgroundModelFile" type="data" format='tabular' label="Background model" help="The background file computed by chicViewpointBackgroundModel" />
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116 <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.' />
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117 <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.
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118 This value is used to merge neighboring bins.' />
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119 <param name="rangeUpstream" type="integer" value="500000" label="Upstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' />
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120 <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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121 <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.' />
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122 <param name='truncateZeroPvalues' type='boolean' truevalue='--truncateZeroPvalues' falsevalue="" checked="false" label="Truncate zeros by setting them to one." help="Sets all p-values which are equal to zero to one. This has the effect that the associated positions are not part of the significance decision." />
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123 <param name='tar' type='boolean' checked="false" truevalue='True' label="tar output to one file" 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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124 </inputs>
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125 <outputs>
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126 <collection name="significantFilesCollection" type="list" label="Significant files">
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127 <discover_datasets pattern="__name__" format="interval" directory="significantFilesFolder" />
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128 </collection>
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129 <collection name="targetFilesCollection" type="list" label="Target files">
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130 <discover_datasets pattern="__name__" format="interval" directory="targetFolder" />
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131 </collection>
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132 <data name="significantFileNames" from_work_dir="significantFiles.txt" format="txt" label="${tool.name} significant file names">
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133 <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter>
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134 </data>
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135 <data name="targetFileNames" from_work_dir="targetListFile.txt" format="txt" label="${tool.name} target file names">
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136 <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter>
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137 </data>
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138 <data name="targetFolderTar" from_work_dir="targetFolder.tar" format="tar" label="Target files tar">
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139 <filter>tar</filter>
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140 </data>
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141 <data name="significantFilesFolderTar" from_work_dir="significantFilesFolder.tar" format="tar" label="Significant files tar">
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142 <filter>tar</filter>
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143 </data>
0
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144 </outputs>
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145 <tests>
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146 <test>
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147 <conditional name="tar_input_conditional">
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148 <param name="tar_input_selector" value='interval_input' />
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149 <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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150 </conditional>
0
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151 <conditional name="batchmode_conditional">
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152 <param name="batchmode_selector" value='optionBatchmode' />
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153 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' />
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154 <param name="computeSampleNumber" value='2' />
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155 </conditional>
6
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156 <param name="pvalue" value='0.2' />
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157
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158 <conditional name="filter_conditional">
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159 <param name="filter_selector" value='optionLoosePvalue' />
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160 <param name="loosePvalue" value='0.5' />
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161 </conditional>
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162
6
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diff changeset
163 <param name="backgroundModelFile" value="cHi-C/background.txt" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
164 <param name="rangeUpstream" value="200000" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
165 <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
166
0
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
167 <output_collection name="significantFilesCollection" type="list" count="6">
6
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
168 <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt" ftype="interval">
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
169 <assert_contents>
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
170 <has_text text="4480000" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
171 <has_text text="chr1" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
172 <has_text text="Sox17" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
173 <has_text text="810.0" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
174 <has_text text="interactions" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
175 </assert_contents>
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
176 </element>
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
177 <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" ftype="interval">
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
178 <assert_contents>
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
179 <has_text text="14274000" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
180 <has_text text="chr1" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
181 <has_text text="Eya1" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
182 <has_text text="interactions" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
183 </assert_contents>
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
184 </element>
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
185 <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" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
186 <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt" ftype="interval">
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
187 <assert_contents>
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
188 <has_text text="4480000" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
189 <has_text text="chr1" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
190 <has_text text="Sox17" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
191 <has_text text="interactions" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
192 <has_text text="93000" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
193 <has_text text="978.0" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
194 </assert_contents>
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
195 </element>
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
196 <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" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
197 <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt" ftype="interval">
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
198 <assert_contents>
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
199 <has_text text="19077000" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
200 <has_text text="chr1" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
201 <has_text text="Tfap2d" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
202 <has_text text="interactions" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
203 <has_text text="-15000" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
204 </assert_contents>
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
205 </element>
0
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
206 </output_collection>
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
207 <output_collection name="targetFilesCollection" type="list" count="3">
6
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
208 <element name="FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt" ftype="interval">
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
209 <assert_contents>
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
210 <has_text text="4555000" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
211 <has_text text="chr1" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
212 <has_text text="p-value" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
213 <has_text text="interactions" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
214 </assert_contents>
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
215 </element>
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
216 <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" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
217 <element name="FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt" ftype="interval">
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
218 <assert_contents>
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
219 <has_text text="19143000" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
220 <has_text text="chr1" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
221 <has_text text="p-value" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
222 <has_text text="19150000" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
223 </assert_contents>
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
224 </element>
0
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
225 </output_collection>
6
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
226 <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
227 <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" />
0
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
228 </test>
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
229 <test>
4
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="tar_input_conditional">
6
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
231 <param name="tar_input_selector" value='interval_input' />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
232 <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" />
4
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 3
diff changeset
233 </conditional>
0
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
234 <conditional name="batchmode_conditional">
6
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
235 <param name="batchmode_selector" value='optionSinglemode' />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
236 <param name="computeSampleNumber" value="1" />
0
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
237 </conditional>
6
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
238 <param name="pvalue" value='0.2' />
0
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
239
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
240 <conditional name="filter_conditional">
6
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
241 <param name="filter_selector" value='optionXfold' />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
242 <param name="xfold" value='1.5' />
0
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
243 </conditional>
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
244
6
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
245 <param name="backgroundModelFile" value="cHi-C/background.txt" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
246 <param name="rangeUpstream" value="200000" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
247 <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
248
0
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
249 <output_collection name="significantFilesCollection" type="list" count="2">
6
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
250 <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" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
251 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" ftype="interval">
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
252 <assert_contents>
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
253 <has_text text="14295000" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
254 <has_text text="chr1" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
255 <has_text text="Eya1" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
256 <has_text text="interactions" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
257 </assert_contents>
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
258 </element>
0
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
259 </output_collection>
2f279a01f3ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
260 <output_collection name="targetFilesCollection" type="list" count="2">
6
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
261 <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" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
262 <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"
bgruening
parents:
diff changeset
263 </output_collection>
6
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
264 </test>
4
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 3
diff changeset
265
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 3
diff changeset
266 <test>
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 3
diff changeset
267 <conditional name="tar_input_conditional">
6
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
268 <param name="tar_input_selector" value='interval_input' />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
269 <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" />
4
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 3
diff changeset
270 </conditional>
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 3
diff changeset
271 <conditional name="batchmode_conditional">
6
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
272 <param name="batchmode_selector" value='optionBatchmode' />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
273 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
274 <param name="computeSampleNumber" value='2' />
4
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 3
diff changeset
275 </conditional>
6
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
276 <param name="pvalue" value='0.2' />
4
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 3
diff changeset
277
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 3
diff changeset
278 <conditional name="filter_conditional">
6
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
279 <param name="filter_selector" value='optionLoosePvalue' />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
280 <param name="loosePvalue" value='0.5' />
4
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 3
diff changeset
281 </conditional>
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 3
diff changeset
282
6
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
283 <param name="backgroundModelFile" value="cHi-C/background.txt" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
284 <param name="rangeUpstream" value="200000" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
285 <param name="rangeDownstream" value="200000" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
286
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
287 <param name='tar' value='True' />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
288
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
289 <output name="targetFolderTar" file="cHi-C/chicSignificantInteractions/targetFolder.tar" ftype='tar' compare="sim_size" delta='40000' />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
290 <output name="significantFilesFolderTar" file="cHi-C/chicSignificantInteractions/significantFilesFolder.tar" ftype='tar' compare="sim_size" delta='40000' />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
291 <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
292 <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
293 </test>
4
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 3
diff changeset
294
6
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
295 <test>
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
296 <conditional name="tar_input_conditional">
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
297 <param name="tar_input_selector" value='tar_input' />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
298 <param name="interactionFiles" value="cHi-C/chicViewpoint/viewpoints.tar" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
299 </conditional>
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
300 <conditional name="batchmode_conditional">
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
301 <param name="batchmode_selector" value='optionBatchmode' />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
302 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
303 <param name="computeSampleNumber" value='2' />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
304 </conditional>
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
305 <param name="pvalue" value='0.2' />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
306
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
307 <conditional name="filter_conditional">
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
308 <param name="filter_selector" value='optionLoosePvalue' />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
309 <param name="loosePvalue" value='0.5' />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
310 </conditional>
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
311
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
312 <param name="backgroundModelFile" value="cHi-C/background.txt" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
313 <param name="rangeUpstream" value="200000" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
314 <param name="rangeDownstream" value="200000" />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
315
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
316 <param name='tar' value='True' />
4
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 3
diff changeset
317
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 3
diff changeset
318 <output name="targetFolderTar" file="cHi-C/chicSignificantInteractions/targetFolder.tar" ftype='tar' compare="sim_size" delta='40000' />
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 3
diff changeset
319 <output name="significantFilesFolderTar" file="cHi-C/chicSignificantInteractions/significantFilesFolder.tar" ftype='tar' compare="sim_size" delta='40000' />
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 3
diff changeset
320
6
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
321 <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" compare="sim_size" delta='40000' />
6001400eed99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
322 <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" compare="sim_size" delta='40000' />
4
38fa8a72ece6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 3
diff changeset
323 </test>
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324 </tests>
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325 <help><![CDATA[
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326
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327 Significant interaction detection
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328 =================================
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329
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330 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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331 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
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332 to test for a differential interaction scheme.
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333
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334 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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335 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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336
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337 For more information about HiCExplorer please consider our documentation on readthedocs.io_
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338
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339 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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340 ]]> </help>
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341 <expand macro="citations" />
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342 </tool>