Mercurial > repos > bgruening > hicexplorer_chicaggregatestatistic

comparison chicAggregateStatistic.xml @ 0:ee745fbe9f14 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
author bgruening
date Mon, 16 Dec 2019 15:35:06 -0500
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children 1baccff6ffb4
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-1:000000000000 0:ee745fbe9f14
1 <tool id="hicexplorer_chicaggregatestatistic" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>computes with a target file the to be tested regions for chicDifferentialTest</description>
3 <macros>
4 <token name="@BINARY@">chicAggregateStatistic</token>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[
9 #import re
10 mkdir interactionFiles &&
11 mkdir targetFolder &&
12 mkdir aggregatedFilesFolder &&
13
14
15 #for $file in $interactionFiles:
16 #set identifier = @ESCAPE_IDENTIFIER_FILE@
17 ln -s '$file' 'interactionFiles/$identifier' &&
18 #end for
19
20 #for $file in $targetFiles:
21 #set identifier = @ESCAPE_IDENTIFIER_FILE@
22 ln -s '$file' 'targetFolder/$identifier' &&
23 #end for
24
25 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
26 #set $interactonfileslist = ' '.join([ 'interactionFiles/%s' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ])
27 #set $targetfileslist = ' '.join([ 'targetFolder/%s' % @ESCAPE_IDENTIFIER_FILE@ for $file in $targetFiles ])
28
29 #end if
30 @BINARY@
31 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
32 --interactionFile $interactonfileslist
33 --targetFile $targetfileslist
34 #else:
35 --interactionFile $batchmode_conditional.interactionFilesOrderFile
36 --interactionFileFolder interactionFiles
37 --targetFileFolder targetFolder
38 --targetFile $batchmode_conditional.targetFilesOrderFile
39 --batchMode
40 --writeFileNamesToFile aggregatedFilesBatch.txt
41 #end if
42
43 --outputFolder aggregatedFilesFolder
44 -suffix aggregated.bed
45 --threads @THREADS@
46
47 ]]></command>
48 <inputs>
49 <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/>
50 <param name='targetFiles' type="data" format="interval" label="Target files" multiple="true"/>
51
52 <conditional name="batchmode_conditional">
53 <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode">
54 <option value="optionBatchmode">Batch processing</option>
55 <option value="optionSinglemode" selected="True">Single file processing</option>
56 </param>
57 <when value="optionBatchmode">
58 <param name='interactionFilesOrderFile' type="data" format="tabular" label="Interaction file order"/>
59 <param name='targetFilesOrderFile' type="data" format="tabular" label="Target file order"/>
60
61 </when>
62 <when value="optionSinglemode">
63 </when>
64 </conditional>
65 </inputs>
66 <outputs>
67 <collection name="aggregatedFilesCollection" type="list" label="Aggregated files">
68 <discover_datasets pattern="__name__" format='interval' directory="aggregatedFilesFolder" />
69 </collection>
70 <data name="aggregatedFileNames" from_work_dir="aggregatedFilesBatch.txt" format="txt" label="${tool.name} aggregated file names">
71 <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter>
72 </data>
73 </outputs>
74 <tests>
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"/>
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"/>
78
79 <conditional name="batchmode_conditional">
80 <param name="batchmode_selector" value='optionBatchmode'/>
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'/>
83 </conditional>
84
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"/>
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"/>
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"/>
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"/>
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"/>
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"/>
94 </output_collection>
95
96 <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" compare="sim_size" delta='40000'/>
97 </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"/>
100 <param name="targetFiles" value="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed"/>
101
102 <conditional name="batchmode_conditional">
103 <param name="batchmode_selector" value='optionSinglemode'/>
104 </conditional>
105
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"/>
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"/>
109 </output_collection>
110 </test>
111 </tests>
112 <help><![CDATA[
113
114 Aggregate statistic for differential testing
115 ============================================
116
117 chicAggregateStatistic is a preprocessing tool for chicDifferentialTest. It takes two consecutive viewpoint files and one target file and creates one
118 file containing all locations which should be tested for differential interactions. Either one target file for two consecutive viewpoint files or one
119 target file for all viewpoints is accepted.
120
121 For more information about HiCExplorer please consider our documentation on readthedocs.io_
122
123 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
124 ]]></help>
125 <expand macro="citations" />
126 </tool>