Mercurial > repos > bgruening > hicexplorer_chicaggregatestatistic

comparison chicAggregateStatistic.xml @ 2:fb981b15ccef draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
author iuc
date Wed, 11 Mar 2020 16:58:07 -0400
parents 1baccff6ffb4
children d6f5e51e97ec
comparison
equal deleted inserted replaced
1:1baccff6ffb4 2:fb981b15ccef
9 #import re 9 #import re
10 mkdir interactionFiles && 10 mkdir interactionFiles &&
11 mkdir targetFolder && 11 mkdir targetFolder &&
12 mkdir aggregatedFilesFolder && 12 mkdir aggregatedFilesFolder &&
13 13
14 14
15 #for $file in $interactionFiles: 15 #for $file in $interactionFiles:
16 #set identifier = @ESCAPE_IDENTIFIER_FILE@ 16 #set identifier = @ESCAPE_IDENTIFIER_FILE@
17 ln -s '$file' 'interactionFiles/$identifier' && 17 ln -s '$file' 'interactionFiles/$identifier' &&
18 #end for 18 #end for
19 19
37 --targetFileFolder targetFolder 37 --targetFileFolder targetFolder
38 --targetFile $batchmode_conditional.targetFilesOrderFile 38 --targetFile $batchmode_conditional.targetFilesOrderFile
39 --batchMode 39 --batchMode
40 --writeFileNamesToFile aggregatedFilesBatch.txt 40 --writeFileNamesToFile aggregatedFilesBatch.txt
41 #end if 41 #end if
42 42
43 --outputFolder aggregatedFilesFolder 43 --outputFolder aggregatedFilesFolder
44 -suffix aggregated.bed 44 -suffix aggregated.txt
45 --threads @THREADS@ 45 --threads @THREADS@
46 46
47 ]]></command> 47 ]]></command>
48 <inputs> 48 <inputs>
49 <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/> 49 <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/>
53 <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode"> 53 <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode">
54 <option value="optionBatchmode">Batch processing</option> 54 <option value="optionBatchmode">Batch processing</option>
55 <option value="optionSinglemode" selected="True">Single file processing</option> 55 <option value="optionSinglemode" selected="True">Single file processing</option>
56 </param> 56 </param>
57 <when value="optionBatchmode"> 57 <when value="optionBatchmode">
58 <param name='interactionFilesOrderFile' type="data" format="tabular" label="Interaction file order"/> 58 <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order"/>
59 <param name='targetFilesOrderFile' type="data" format="tabular" label="Target file order"/> 59 <param name='targetFilesOrderFile' type="data" format="txt" label="Target file order"/>
60 60
61 </when> 61 </when>
62 <when value="optionSinglemode"> 62 <when value="optionSinglemode">
63 </when> 63 </when>
64 </conditional> 64 </conditional>
71 <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter> 71 <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter>
72 </data> 72 </data>
73 </outputs> 73 </outputs>
74 <tests> 74 <tests>
75 <test> 75 <test>
76 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed"/> 76 <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"/>
77 <param name="targetFiles" value="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.bed,cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed,cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed"/> 77 <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"/>
78 78
79 <conditional name="batchmode_conditional"> 79 <conditional name="batchmode_conditional">
80 <param name="batchmode_selector" value='optionBatchmode'/> 80 <param name="batchmode_selector" value='optionBatchmode'/>
81 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/> 81 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/>
82 <param name="targetFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_target_list.txt'/> 82 <param name="targetFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_target_list.txt'/>
83 </conditional> 83 </conditional>
84 84
85 <output_collection name="aggregatedFilesCollection" type="list" count="6"> 85 <output_collection name="aggregatedFilesCollection" type="list" count="6">
86 <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed" file="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed" ftype="interval" lines_diff="4"/> 86 <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"/>
87 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed" file="cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed" ftype="interval" lines_diff="4"/> 87 <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"/>
88 88
89 <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed" file="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed" ftype="interval" lines_diff="4"/> 89 <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"/>
90 <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed" file="cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed" ftype="interval" lines_diff="4"/> 90 <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"/>
91 91
92 <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed" file="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed" ftype="interval" lines_diff="4"/> 92 <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"/>
93 <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed" file="cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed" ftype="interval" lines_diff="4"/> 93 <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"/>
94 </output_collection> 94 </output_collection>
95 95
96 <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" compare="sim_size" delta='40000'/> 96 <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" compare="sim_size" delta='40000'/>
97 </test> 97 </test>
98 <test> 98 <test>
99 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed"/> 99 <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"/>
100 <param name="targetFiles" value="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed"/> 100 <param name="targetFiles" value="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt"/>
101 101
102 <conditional name="batchmode_conditional"> 102 <conditional name="batchmode_conditional">
103 <param name="batchmode_selector" value='optionSinglemode'/> 103 <param name="batchmode_selector" value='optionSinglemode'/>
104 </conditional> 104 </conditional>
105 105
106 <output_collection name="aggregatedFilesCollection" type="list" count="2"> 106 <output_collection name="aggregatedFilesCollection" type="list" count="2">
107 <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed" file="cHi-C/chicAggregateStatistic/regular_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed" ftype="interval" lines_diff="4"/> 107 <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"/>
108 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed" file="cHi-C/chicAggregateStatistic/regular_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed" ftype="interval" lines_diff="4"/> 108 <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"/>
109 </output_collection> 109 </output_collection>
110 </test> 110 </test>
111 </tests> 111 </tests>
112 <help><![CDATA[ 112 <help><![CDATA[
113 113