Mercurial > repos > bgruening > hicexplorer_chicaggregatestatistic

comparison chicAggregateStatistic.xml @ 8:01c37e54e86e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
author iuc
date Wed, 18 Oct 2023 13:04:27 +0000
parents b53973719d7b
children
comparison
equal deleted inserted replaced
7:1eae6fe69bbd 8:01c37e54e86e
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 #import re 9 #import re
10 mkdir interactionFiles && 10
11 mkdir targetFolder && 11 @BINARY@
12 mkdir aggregatedFilesFolder && 12
13 13 --interactionFile '$interactionFile'
14 #if $tar_input_conditional.tar_input_selector == 'tar_input': 14 --outFileName aggregatedFile.hdf5
15 ln -s '$tar_input_conditional.interactionFiles' viewpoints.tar && 15 #if $targetFormat_conditional.targetFormat_selector == 'hdf5':
16 tar -C interactionFiles -xvf viewpoints.tar && 16 --targetFile '$targetFormat_conditional.targetFileHDF'
17 17 #else:
18 #if $targetFiles: 18 --targetFile '$targetFormat_conditional.targetFileBED'
19 ln -s '$tar_input_conditional.targetFiles' targetFiles.tar &&
20 tar -C targetFolder -xvf targetFiles.tar &&
21 #end if 19 #end if
22 #else:
23 #for $file in $tar_input_conditional.interactionFiles:
24 #set identifier = @ESCAPE_IDENTIFIER_FILE@
25 ln -s '$file' 'interactionFiles/$identifier' &&
26 #end for
27
28 #for $file in $targetFiles:
29 #set identifier = @ESCAPE_IDENTIFIER_FILE@
30 ln -s '$file' 'targetFolder/$identifier' &&
31 #end for
32 #end if
33
34 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
35 #set $interactonfileslist = ' '.join([ 'interactionFiles/%s' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ])
36 #set $targetfileslist = ' '.join([ 'targetFolder/%s' % @ESCAPE_IDENTIFIER_FILE@ for $file in $targetFiles ])
37 #end if
38 @BINARY@
39 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
40 --interactionFile $interactonfileslist
41 --targetFile $targetfileslist
42 #else:
43 --interactionFile $batchmode_conditional.interactionFilesOrderFile
44 --interactionFileFolder interactionFiles
45 --targetFileFolder targetFolder
46 --targetFile $batchmode_conditional.targetFilesOrderFile
47 --batchMode
48 --writeFileNamesToFile aggregatedFilesBatch.txt
49 #end if
50
51 --outputFolder aggregatedFilesFolder
52 -suffix aggregated.txt
53 --threads @THREADS@ 20 --threads @THREADS@
54
55 #if $tar:
56 && cd aggregatedFilesFolder
57 && tar -cvf ../aggregatedFilesFolder.tar *
58 && cd ..
59 && rm -rf aggregatedFilesFolder
60 #end if
61 21
62 ]]> </command> 22 ]]> </command>
63 <inputs> 23 <inputs>
64 24
65 <conditional name="tar_input_conditional"> 25 <param name="interactionFile" type="data" format="h5" label="The interaction data file created by chicViewpoint" />
66 <param name="tar_input_selector" type="select" label="Compute files individually or in batch mode"> 26 <conditional name="targetFormat_conditional">
67 <option value="tar_input">Tar file</option> 27 <param name="targetFormat_selector" type="select" label="List of chromosomes or a BED file containg regions">
68 <option value="interval_input" selected="True">Interval files</option> 28 <option value="hdf5">Target file from chicSignificantInteractions (h5 / hdf5)</option>
29 <option value="bed" selected="True">Regions of interest (bed)</option>
69 </param> 30 </param>
70 <when value="tar_input"> 31 <when value="hdf5">
71 <param name='interactionFiles' type="data" format="tar" label="Interaction files" multiple="false" /> 32 <param name="targetFileHDF" type="data" format="h5" label="The target data file created by chicSignificantInteractions" />
72 <param name='targetFiles' type="data" format="tar" label="Target files" multiple="false" />
73 </when> 33 </when>
74 <when value="interval_input"> 34 <when value="bed">
75 <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true" /> 35 <param name="targetFileBED" type="data" format="bed" label="Regions of interest" help="BED file which stores a list of regions that are used to aggregate the data for the differntial test." />
76 <param name='targetFiles' type="data" format="interval" label="Target files" multiple="true" />
77 </when> 36 </when>
78 </conditional> 37 </conditional>
79 38 </inputs>
80 <conditional name="batchmode_conditional">
81 <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode">
82 <option value="optionBatchmode">Batch processing</option>
83 <option value="optionSinglemode" selected="True">Single file processing</option>
84 </param>
85 <when value="optionBatchmode">
86 <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order" />
87 <param name='targetFilesOrderFile' type="data" format="txt" label="Target file order" />
88 </when>
89 <when value="optionSinglemode">
90 </when>
91 </conditional>
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." />
93 </inputs>
94 <outputs> 39 <outputs>
95 <collection name="aggregatedFilesCollection" type="list" label="Aggregated files"> 40 <data name="aggregatedFile" from_work_dir="aggregatedFile.hdf5" format="h5" label="Aggregated file" />
96 <discover_datasets pattern="__name__" format='interval' directory="aggregatedFilesFolder" />
97 </collection>
98 <data name="aggregatedFileNames" from_work_dir="aggregatedFilesBatch.txt" format="txt" label="${tool.name} aggregated file names">
99 <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter>
100 </data>
101 <data name="aggregatedFilesFolderTar" from_work_dir="aggregatedFilesFolder.tar" format="tar" label="Aggregated files tar.gz">
102 <filter>tar</filter>
103 </data>
104 </outputs> 41 </outputs>
105 <tests> 42 <tests>
106 <test> 43 <test>
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" /> 44 <param name="interactionFile" value="cHi-C/chicViewpoint/two_matrices.hdf5" />
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" /> 45 <conditional name="targetFormat_conditional">
109 46 <param name="targetFormat_selector" value="hdf5" />
110 <conditional name="batchmode_conditional"> 47 <param name="targetFileHDF" value="cHi-C/chicSignificantInteractions/targetFile_dual.hdf5" />
111 <param name="batchmode_selector" value='optionBatchmode' />
112 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' />
113 <param name="targetFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_target_list.txt' />
114 </conditional> 48 </conditional>
115 49 <output name="aggregatedFile" ftype="h5">
116 <output_collection name="aggregatedFilesCollection" type="list" count="6"> 50 <assert_contents>
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" /> 51 <has_h5_attribute key="type" value="aggregate" />
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" /> 52 </assert_contents>
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" /> 53 </output>
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" />
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" />
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" />
123 </output_collection>
124 <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" />
125 </test> 54 </test>
126 <test> 55 <test>
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" /> 56 <param name="interactionFile" value="cHi-C/chicViewpoint/two_matrices.hdf5" />
128 <param name="targetFiles" value="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" />
129 57
130 <conditional name="batchmode_conditional"> 58 <conditional name="targetFormat_conditional">
131 <param name="batchmode_selector" value='optionSinglemode' /> 59 <param name="targetFormat_selector" value="bed" />
60 <param name="targetFileBED" value="cHi-C/target_list.bed" />
132 </conditional> 61 </conditional>
133 62 <output name="aggregatedFile" ftype="h5">
134 <output_collection name="aggregatedFilesCollection" type="list" count="2"> 63 <assert_contents>
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" /> 64 <has_h5_attribute key="type" value="aggregate" />
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" /> 65 </assert_contents>
137 </output_collection> 66 </output>
138 </test>
139
140 <test>
141 <conditional name="tar_input_conditional">
142 <param name="tar_input_selector" value='interval_input' />
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" />
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" />
145 </conditional>
146
147 <conditional name="batchmode_conditional">
148 <param name="batchmode_selector" value='optionBatchmode' />
149 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' />
150 <param name="targetFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_target_list.txt' />
151 </conditional>
152 <param name='tar' value='True' />
153 <output name="aggregatedFilesFolderTar" file="cHi-C/chicAggregateStatistic/batch_mode.tar" ftype='tar' compare="sim_size" delta='40000' />
154 <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" />
155 </test>
156
157 <test>
158 <conditional name="tar_input_conditional">
159 <param name="tar_input_selector" value='tar_input' />
160 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1.tar" />
161 <param name="targetFiles" value="cHi-C/chicSignificantInteractions/targetFolder.tar" />
162 </conditional>
163
164 <conditional name="batchmode_conditional">
165 <param name="batchmode_selector" value='optionBatchmode' />
166 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' />
167 <param name="targetFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_target_list.txt' />
168 </conditional>
169
170 <param name='tar' value='True' />
171
172 <output name="aggregatedFilesFolderTar" file="cHi-C/chicAggregateStatistic/batch_mode.tar" ftype='tar' compare="sim_size" delta='40000' />
173 <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" />
174 </test> 67 </test>
175 </tests> 68 </tests>
176 <help><![CDATA[ 69 <help><![CDATA[
177 70
178 Aggregate statistic for differential testing 71 Aggregate statistic for differential testing