Mercurial > repos > bgruening > hicexplorer_chicaggregatestatistic

annotate chicAggregateStatistic.xml @ 7:1eae6fe69bbd 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 19:06:29 +0000
parents b53973719d7b
children 01c37e54e86e
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b53973719d7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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1 <tool id="hicexplorer_chicaggregatestatistic" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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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13
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14 #if $tar_input_conditional.tar_input_selector == 'tar_input':
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15 ln -s '$tar_input_conditional.interactionFiles' viewpoints.tar &&
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16 tar -C interactionFiles -xvf viewpoints.tar &&
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17
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18 #if $targetFiles:
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19 ln -s '$tar_input_conditional.targetFiles' targetFiles.tar &&
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20 tar -C targetFolder -xvf targetFiles.tar &&
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21 #end if
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22 #else:
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23 #for $file in $tar_input_conditional.interactionFiles:
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24 #set identifier = @ESCAPE_IDENTIFIER_FILE@
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25 ln -s '$file' 'interactionFiles/$identifier' &&
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26 #end for
0
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27
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28 #for $file in $targetFiles:
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29 #set identifier = @ESCAPE_IDENTIFIER_FILE@
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30 ln -s '$file' 'targetFolder/$identifier' &&
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31 #end for
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32 #end if
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33
0
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34 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
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35 #set $interactonfileslist = ' '.join([ 'interactionFiles/%s' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ])
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36 #set $targetfileslist = ' '.join([ 'targetFolder/%s' % @ESCAPE_IDENTIFIER_FILE@ for $file in $targetFiles ])
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37 #end if
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38 @BINARY@
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39 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
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40 --interactionFile $interactonfileslist
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41 --targetFile $targetfileslist
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42 #else:
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43 --interactionFile $batchmode_conditional.interactionFilesOrderFile
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44 --interactionFileFolder interactionFiles
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45 --targetFileFolder targetFolder
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46 --targetFile $batchmode_conditional.targetFilesOrderFile
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47 --batchMode
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48 --writeFileNamesToFile aggregatedFilesBatch.txt
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49 #end if
2
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50
0
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51 --outputFolder aggregatedFilesFolder
2
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52 -suffix aggregated.txt
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53 --threads @THREADS@
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54
4
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55 #if $tar:
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56 && cd aggregatedFilesFolder
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57 && tar -cvf ../aggregatedFilesFolder.tar *
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58 && cd ..
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59 && rm -rf aggregatedFilesFolder
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60 #end if
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61
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62 ]]> </command>
0
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63 <inputs>
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64
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65 <conditional name="tar_input_conditional">
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66 <param name="tar_input_selector" type="select" label="Compute files individually or in batch mode">
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67 <option value="tar_input">Tar file</option>
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68 <option value="interval_input" selected="True">Interval files</option>
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69 </param>
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70 <when value="tar_input">
6
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71 <param name='interactionFiles' type="data" format="tar" label="Interaction files" multiple="false" />
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72 <param name='targetFiles' type="data" format="tar" label="Target files" multiple="false" />
4
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73 </when>
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74 <when value="interval_input">
6
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75 <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true" />
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76 <param name='targetFiles' type="data" format="interval" label="Target files" multiple="true" />
4
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77 </when>
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78 </conditional>
0
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79
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80 <conditional name="batchmode_conditional">
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81 <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode">
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82 <option value="optionBatchmode">Batch processing</option>
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83 <option value="optionSinglemode" selected="True">Single file processing</option>
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84 </param>
ee745fbe9f14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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85 <when value="optionBatchmode">
6
b53973719d7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
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86 <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order" />
b53973719d7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
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87 <param name='targetFilesOrderFile' type="data" format="txt" label="Target file order" />
0
ee745fbe9f14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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88 </when>
1
1baccff6ffb4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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89 <when value="optionSinglemode">
0
ee745fbe9f14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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90 </when>
ee745fbe9f14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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91 </conditional>
6
b53973719d7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
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92 <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
ee745fbe9f14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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93 </inputs>
ee745fbe9f14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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94 <outputs>
ee745fbe9f14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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95 <collection name="aggregatedFilesCollection" type="list" label="Aggregated files">
ee745fbe9f14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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96 <discover_datasets pattern="__name__" format='interval' directory="aggregatedFilesFolder" />
ee745fbe9f14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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97 </collection>
ee745fbe9f14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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98 <data name="aggregatedFileNames" from_work_dir="aggregatedFilesBatch.txt" format="txt" label="${tool.name} aggregated file names">
ee745fbe9f14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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99 <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter>
ee745fbe9f14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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100 </data>
4
d6f5e51e97ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 2
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101 <data name="aggregatedFilesFolderTar" from_work_dir="aggregatedFilesFolder.tar" format="tar" label="Aggregated files tar.gz">
d6f5e51e97ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
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102 <filter>tar</filter>
d6f5e51e97ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 2
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103 </data>
0
ee745fbe9f14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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104 </outputs>
ee745fbe9f14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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105 <tests>
ee745fbe9f14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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106 <test>
6
b53973719d7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
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107 <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" />
b53973719d7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
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108 <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" />
2
fb981b15ccef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents: 1
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109
0
ee745fbe9f14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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110 <conditional name="batchmode_conditional">
6
b53973719d7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
111 <param name="batchmode_selector" value='optionBatchmode' />
b53973719d7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
112 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' />
b53973719d7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
113 <param name="targetFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_target_list.txt' />
0
ee745fbe9f14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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114 </conditional>
2
fb981b15ccef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents: 1
diff changeset
115
0
ee745fbe9f14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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116 <output_collection name="aggregatedFilesCollection" type="list" count="6">
6
b53973719d7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
117 <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" />
b53973719d7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
118 <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" />
b53973719d7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
119 <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" />
b53973719d7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
120 <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" />
b53973719d7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
121 <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" />
b53973719d7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
122 <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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123 </output_collection>
6
b53973719d7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
124 <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" />
0
ee745fbe9f14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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125 </test>
ee745fbe9f14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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126 <test>
6
b53973719d7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
127 <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" />
b53973719d7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
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128 <param name="targetFiles" value="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" />
2
fb981b15ccef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents: 1
diff changeset
129
0
ee745fbe9f14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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130 <conditional name="batchmode_conditional">
6
b53973719d7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
131 <param name="batchmode_selector" value='optionSinglemode' />
0
ee745fbe9f14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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132 </conditional>
2
fb981b15ccef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents: 1
diff changeset
133
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 name="aggregatedFilesCollection" type="list" count="2">
6
b53973719d7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
135 <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" />
b53973719d7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
136 <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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137 </output_collection>
ee745fbe9f14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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138 </test>
4
d6f5e51e97ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 2
diff changeset
139
d6f5e51e97ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 2
diff changeset
140 <test>
d6f5e51e97ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 2
diff changeset
141 <conditional name="tar_input_conditional">
6
b53973719d7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
142 <param name="tar_input_selector" value='interval_input' />
b53973719d7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
143 <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" />
b53973719d7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
144 <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" />
4
d6f5e51e97ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 2
diff changeset
145 </conditional>
d6f5e51e97ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 2
diff changeset
146
d6f5e51e97ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 2
diff changeset
147 <conditional name="batchmode_conditional">
6
b53973719d7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
148 <param name="batchmode_selector" value='optionBatchmode' />
b53973719d7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
149 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' />
b53973719d7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
150 <param name="targetFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_target_list.txt' />
4
d6f5e51e97ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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151 </conditional>
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152 <param name='tar' value='True' />
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153 <output name="aggregatedFilesFolderTar" file="cHi-C/chicAggregateStatistic/batch_mode.tar" ftype='tar' compare="sim_size" delta='40000' />
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154 <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" />
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155 </test>
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156
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157 <test>
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158 <conditional name="tar_input_conditional">
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159 <param name="tar_input_selector" value='tar_input' />
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160 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1.tar" />
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161 <param name="targetFiles" value="cHi-C/chicSignificantInteractions/targetFolder.tar" />
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162 </conditional>
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163
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164 <conditional name="batchmode_conditional">
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165 <param name="batchmode_selector" value='optionBatchmode' />
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166 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' />
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167 <param name="targetFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_target_list.txt' />
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168 </conditional>
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169
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170 <param name='tar' value='True' />
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171
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172 <output name="aggregatedFilesFolderTar" file="cHi-C/chicAggregateStatistic/batch_mode.tar" ftype='tar' compare="sim_size" delta='40000' />
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173 <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" />
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174 </test>
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175 </tests>
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176 <help><![CDATA[
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177
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178 Aggregate statistic for differential testing
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179 ============================================
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180
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181 chicAggregateStatistic is a preprocessing tool for chicDifferentialTest. It takes two consecutive viewpoint files and one target file and creates one
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182 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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183 target file for all viewpoints is accepted.
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184
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185 For more information about HiCExplorer please consider our documentation on readthedocs.io_
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186
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187 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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188 ]]> </help>
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189 <expand macro="citations" />
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190 </tool>