Mercurial > repos > bgruening > hicexplorer_chicaggregatestatistic

annotate chicAggregateStatistic.xml @ 4:d6f5e51e97ec 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 06:19:12 -0400
parents fb981b15ccef
children b53973719d7b
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d6f5e51e97ec "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_chicaggregatestatistic" name="@BINARY@" version="@WRAPPER_VERSION@.1">
0
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2 <description>computes with a target file the to be tested regions for chicDifferentialTest</description>
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3 <macros>
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4 <token name="@BINARY@">chicAggregateStatistic</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 #import re
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10 mkdir interactionFiles &&
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11 mkdir targetFolder &&
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12 mkdir aggregatedFilesFolder &&
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2
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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 &&
d6f5e51e97ec "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 &&
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19 #if $targetFiles:
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20 ln -s '$tar_input_conditional.targetFiles' targetFiles.tar &&
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21 tar -C targetFolder -xvf targetFiles.tar &&
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22 #end if
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23 #else:
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24 #for $file in $tar_input_conditional.interactionFiles:
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25 #set identifier = @ESCAPE_IDENTIFIER_FILE@
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26 ln -s '$file' 'interactionFiles/$identifier' &&
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27 #end for
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29 #for $file in $targetFiles:
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30 #set identifier = @ESCAPE_IDENTIFIER_FILE@
d6f5e51e97ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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31 ln -s '$file' 'targetFolder/$identifier' &&
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32 #end for
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34 #end if
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35
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37 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
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38 #set $interactonfileslist = ' '.join([ 'interactionFiles/%s' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ])
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39 #set $targetfileslist = ' '.join([ 'targetFolder/%s' % @ESCAPE_IDENTIFIER_FILE@ for $file in $targetFiles ])
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41 #end if
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42 @BINARY@
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43 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
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44 --interactionFile $interactonfileslist
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45 --targetFile $targetfileslist
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46 #else:
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47 --interactionFile $batchmode_conditional.interactionFilesOrderFile
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48 --interactionFileFolder interactionFiles
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49 --targetFileFolder targetFolder
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50 --targetFile $batchmode_conditional.targetFilesOrderFile
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51 --batchMode
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52 --writeFileNamesToFile aggregatedFilesBatch.txt
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53 #end if
2
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54
0
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55 --outputFolder aggregatedFilesFolder
2
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56 -suffix aggregated.txt
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57 --threads @THREADS@
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58
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59 #if $tar:
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60 && cd aggregatedFilesFolder
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61 && tar -cvf ../aggregatedFilesFolder.tar *
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62 && cd ..
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63 && rm -rf aggregatedFilesFolder
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64 #end if
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65
0
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66 ]]></command>
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67 <inputs>
4
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68
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69 <conditional name="tar_input_conditional">
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70 <param name="tar_input_selector" type="select" label="Compute files individually or in batch mode">
d6f5e51e97ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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71 <option value="tar_input">Tar file</option>
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72 <option value="interval_input" selected="True">Interval files</option>
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73 </param>
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74 <when value="tar_input">
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75 <param name='interactionFiles' type="data" format="tar" label="Interaction files" multiple="false"/>
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76 <param name='targetFiles' type="data" format="tar" label="Target files" multiple="false"/>
d6f5e51e97ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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77 </when>
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78 <when value="interval_input">
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79 <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/>
d6f5e51e97ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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80 <param name='targetFiles' type="data" format="interval" label="Target files" multiple="true"/>
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81 </when>
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82 </conditional>
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83
0
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84
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85 <conditional name="batchmode_conditional">
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86 <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode">
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87 <option value="optionBatchmode">Batch processing</option>
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88 <option value="optionSinglemode" selected="True">Single file processing</option>
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89 </param>
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90 <when value="optionBatchmode">
2
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91 <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order"/>
fb981b15ccef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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92 <param name='targetFilesOrderFile' type="data" format="txt" label="Target file order"/>
0
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93
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94 </when>
1
1baccff6ffb4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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95 <when value="optionSinglemode">
0
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96 </when>
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97 </conditional>
4
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98 <param name='tar' type='boolean' checked="false" truevalue='True' label="tar output to one file"
d6f5e51e97ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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99 help="The output is tarred to one file and not written to a collection. Set this option if the number of files is large."/>
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100
0
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101 </inputs>
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102 <outputs>
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103 <collection name="aggregatedFilesCollection" type="list" label="Aggregated files">
4
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104
0
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105 <discover_datasets pattern="__name__" format='interval' directory="aggregatedFilesFolder" />
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106 </collection>
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107 <data name="aggregatedFileNames" from_work_dir="aggregatedFilesBatch.txt" format="txt" label="${tool.name} aggregated file names">
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108 <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter>
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109 </data>
4
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110 <data name="aggregatedFilesFolderTar" from_work_dir="aggregatedFilesFolder.tar" format="tar" label="Aggregated files tar.gz">
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111 <filter>tar</filter>
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112 </data>
0
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113 </outputs>
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114 <tests>
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115 <test>
2
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116 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt"/>
fb981b15ccef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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117 <param name="targetFiles" value="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt,cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt,cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt"/>
fb981b15ccef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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118
0
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119 <conditional name="batchmode_conditional">
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120 <param name="batchmode_selector" value='optionBatchmode'/>
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121 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/>
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122 <param name="targetFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_target_list.txt'/>
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123 </conditional>
2
fb981b15ccef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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124
0
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125 <output_collection name="aggregatedFilesCollection" type="list" count="6">
2
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126 <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" ftype="interval" lines_diff="4"/>
fb981b15ccef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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127 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" ftype="interval" lines_diff="4"/>
0
ee745fbe9f14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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128
2
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129 <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt" ftype="interval" lines_diff="4"/>
fb981b15ccef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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130 <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt" ftype="interval" lines_diff="4"/>
fb981b15ccef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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131
fb981b15ccef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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132 <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt" ftype="interval" lines_diff="4"/>
fb981b15ccef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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133 <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt" ftype="interval" lines_diff="4"/>
0
ee745fbe9f14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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134 </output_collection>
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135
ee745fbe9f14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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136 <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" compare="sim_size" delta='40000'/>
ee745fbe9f14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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137 </test>
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138 <test>
2
fb981b15ccef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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139 <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"/>
fb981b15ccef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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140 <param name="targetFiles" value="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt"/>
fb981b15ccef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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141
0
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142 <conditional name="batchmode_conditional">
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143 <param name="batchmode_selector" value='optionSinglemode'/>
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144 </conditional>
2
fb981b15ccef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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145
0
ee745fbe9f14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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146 <output_collection name="aggregatedFilesCollection" type="list" count="2">
2
fb981b15ccef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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147 <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" file="cHi-C/chicAggregateStatistic/regular_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" ftype="interval" lines_diff="4"/>
fb981b15ccef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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148 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" file="cHi-C/chicAggregateStatistic/regular_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" ftype="interval" lines_diff="4"/>
0
ee745fbe9f14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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149 </output_collection>
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150 </test>
4
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151
d6f5e51e97ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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152 <test>
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153 <conditional name="tar_input_conditional">
d6f5e51e97ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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154 <param name="tar_input_selector" value='interval_input'/>
d6f5e51e97ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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155 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt"/>
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156 <param name="targetFiles" value="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt,cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt,cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt"/>
d6f5e51e97ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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157 </conditional>
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158
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159 <conditional name="batchmode_conditional">
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160 <param name="batchmode_selector" value='optionBatchmode'/>
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161 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/>
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162 <param name="targetFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_target_list.txt'/>
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163 </conditional>
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164
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165 <param name='tar' value='True'/>
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166
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167 <output name="aggregatedFilesFolderTar" file="cHi-C/chicAggregateStatistic/batch_mode.tar" ftype='tar' compare="sim_size" delta='40000' />
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168 <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" compare="sim_size" delta='40000'/>
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169 </test>
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170
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171 <test>
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172 <conditional name="tar_input_conditional">
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173 <param name="tar_input_selector" value='tar_input'/>
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174 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1.tar"/>
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175 <param name="targetFiles" value="cHi-C/chicSignificantInteractions/targetFolder.tar"/>
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176 </conditional>
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177
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178 <conditional name="batchmode_conditional">
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179 <param name="batchmode_selector" value='optionBatchmode'/>
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180 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/>
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181 <param name="targetFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_target_list.txt'/>
d6f5e51e97ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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182 </conditional>
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183
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184 <param name='tar' value='True'/>
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185
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186 <output name="aggregatedFilesFolderTar" file="cHi-C/chicAggregateStatistic/batch_mode.tar" ftype='tar' compare="sim_size" delta='40000' />
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187 <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" compare="sim_size" delta='40000'/>
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188 </test>
0
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189 </tests>
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190 <help><![CDATA[
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191
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192 Aggregate statistic for differential testing
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193 ============================================
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194
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195 chicAggregateStatistic is a preprocessing tool for chicDifferentialTest. It takes two consecutive viewpoint files and one target file and creates one
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196 file containing all locations which should be tested for differential interactions. Either one target file for two consecutive viewpoint files or one
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197 target file for all viewpoints is accepted.
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198
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199 For more information about HiCExplorer please consider our documentation on readthedocs.io_
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200
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201 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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202 ]]></help>
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203 <expand macro="citations" />
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204 </tool>