Mercurial > repos > bgruening > hicexplorer_chicaggregatestatistic

comparison chicAggregateStatistic.xml @ 6:b53973719d7b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
author iuc
date Tue, 16 Mar 2021 15:19:00 +0000
parents d6f5e51e97ec
children 01c37e54e86e
comparison
equal deleted inserted replaced
5:989cec209ba2 6:b53973719d7b
1 <tool id="hicexplorer_chicaggregatestatistic" name="@BINARY@" version="@WRAPPER_VERSION@.1"> 1 <tool id="hicexplorer_chicaggregatestatistic" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>computes with a target file the to be tested regions for chicDifferentialTest</description> 2 <description>computes with a target file the to be tested regions for chicDifferentialTest</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">chicAggregateStatistic</token> 4 <token name="@BINARY@">chicAggregateStatistic</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
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
14 13
15 #if $tar_input_conditional.tar_input_selector == 'tar_input': 14 #if $tar_input_conditional.tar_input_selector == 'tar_input':
16 ln -s '$tar_input_conditional.interactionFiles' viewpoints.tar && 15 ln -s '$tar_input_conditional.interactionFiles' viewpoints.tar &&
17 tar -C interactionFiles -xvf viewpoints.tar && 16 tar -C interactionFiles -xvf viewpoints.tar &&
18 17
28 27
29 #for $file in $targetFiles: 28 #for $file in $targetFiles:
30 #set identifier = @ESCAPE_IDENTIFIER_FILE@ 29 #set identifier = @ESCAPE_IDENTIFIER_FILE@
31 ln -s '$file' 'targetFolder/$identifier' && 30 ln -s '$file' 'targetFolder/$identifier' &&
32 #end for 31 #end for
33
34 #end if 32 #end if
35
36 33
37 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': 34 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
38 #set $interactonfileslist = ' '.join([ 'interactionFiles/%s' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ]) 35 #set $interactonfileslist = ' '.join([ 'interactionFiles/%s' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ])
39 #set $targetfileslist = ' '.join([ 'targetFolder/%s' % @ESCAPE_IDENTIFIER_FILE@ for $file in $targetFiles ]) 36 #set $targetfileslist = ' '.join([ 'targetFolder/%s' % @ESCAPE_IDENTIFIER_FILE@ for $file in $targetFiles ])
40
41 #end if 37 #end if
42 @BINARY@ 38 @BINARY@
43 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': 39 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
44 --interactionFile $interactonfileslist 40 --interactionFile $interactonfileslist
45 --targetFile $targetfileslist 41 --targetFile $targetfileslist
61 && tar -cvf ../aggregatedFilesFolder.tar * 57 && tar -cvf ../aggregatedFilesFolder.tar *
62 && cd .. 58 && cd ..
63 && rm -rf aggregatedFilesFolder 59 && rm -rf aggregatedFilesFolder
64 #end if 60 #end if
65 61
66 ]]></command> 62 ]]> </command>
67 <inputs> 63 <inputs>
68 64
69 <conditional name="tar_input_conditional"> 65 <conditional name="tar_input_conditional">
70 <param name="tar_input_selector" type="select" label="Compute files individually or in batch mode"> 66 <param name="tar_input_selector" type="select" label="Compute files individually or in batch mode">
71 <option value="tar_input">Tar file</option> 67 <option value="tar_input">Tar file</option>
72 <option value="interval_input" selected="True">Interval files</option> 68 <option value="interval_input" selected="True">Interval files</option>
73 </param> 69 </param>
74 <when value="tar_input"> 70 <when value="tar_input">
75 <param name='interactionFiles' type="data" format="tar" label="Interaction files" multiple="false"/> 71 <param name='interactionFiles' type="data" format="tar" label="Interaction files" multiple="false" />
76 <param name='targetFiles' type="data" format="tar" label="Target files" multiple="false"/> 72 <param name='targetFiles' type="data" format="tar" label="Target files" multiple="false" />
77 </when> 73 </when>
78 <when value="interval_input"> 74 <when value="interval_input">
79 <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/> 75 <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true" />
80 <param name='targetFiles' type="data" format="interval" label="Target files" multiple="true"/> 76 <param name='targetFiles' type="data" format="interval" label="Target files" multiple="true" />
81 </when> 77 </when>
82 </conditional> 78 </conditional>
83
84 79
85 <conditional name="batchmode_conditional"> 80 <conditional name="batchmode_conditional">
86 <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode"> 81 <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode">
87 <option value="optionBatchmode">Batch processing</option> 82 <option value="optionBatchmode">Batch processing</option>
88 <option value="optionSinglemode" selected="True">Single file processing</option> 83 <option value="optionSinglemode" selected="True">Single file processing</option>
89 </param> 84 </param>
90 <when value="optionBatchmode"> 85 <when value="optionBatchmode">
91 <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order"/> 86 <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order" />
92 <param name='targetFilesOrderFile' type="data" format="txt" label="Target file order"/> 87 <param name='targetFilesOrderFile' type="data" format="txt" label="Target file order" />
93
94 </when> 88 </when>
95 <when value="optionSinglemode"> 89 <when value="optionSinglemode">
96 </when> 90 </when>
97 </conditional> 91 </conditional>
98 <param name='tar' type='boolean' checked="false" truevalue='True' label="tar output to one file" 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." />
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."/>
100
101 </inputs> 93 </inputs>
102 <outputs> 94 <outputs>
103 <collection name="aggregatedFilesCollection" type="list" label="Aggregated files"> 95 <collection name="aggregatedFilesCollection" type="list" label="Aggregated files">
104
105 <discover_datasets pattern="__name__" format='interval' directory="aggregatedFilesFolder" /> 96 <discover_datasets pattern="__name__" format='interval' directory="aggregatedFilesFolder" />
106 </collection> 97 </collection>
107 <data name="aggregatedFileNames" from_work_dir="aggregatedFilesBatch.txt" format="txt" label="${tool.name} aggregated file names"> 98 <data name="aggregatedFileNames" from_work_dir="aggregatedFilesBatch.txt" format="txt" label="${tool.name} aggregated file names">
108 <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter> 99 <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter>
109 </data> 100 </data>
111 <filter>tar</filter> 102 <filter>tar</filter>
112 </data> 103 </data>
113 </outputs> 104 </outputs>
114 <tests> 105 <tests>
115 <test> 106 <test>
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"/> 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" />
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"/> 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" />
118 109
119 <conditional name="batchmode_conditional"> 110 <conditional name="batchmode_conditional">
120 <param name="batchmode_selector" value='optionBatchmode'/> 111 <param name="batchmode_selector" value='optionBatchmode' />
121 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/> 112 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' />
122 <param name="targetFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_target_list.txt'/> 113 <param name="targetFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_target_list.txt' />
123 </conditional> 114 </conditional>
124 115
125 <output_collection name="aggregatedFilesCollection" type="list" count="6"> 116 <output_collection name="aggregatedFilesCollection" type="list" count="6">
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"/> 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" />
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"/> 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" />
128 119 <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" />
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"/> 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" />
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"/> 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" />
131 122 <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" />
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"/>
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"/>
134 </output_collection> 123 </output_collection>
135 124 <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" />
136 <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" compare="sim_size" delta='40000'/>
137 </test> 125 </test>
138 <test> 126 <test>
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"/> 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" />
140 <param name="targetFiles" value="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt"/> 128 <param name="targetFiles" value="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" />
141 129
142 <conditional name="batchmode_conditional"> 130 <conditional name="batchmode_conditional">
143 <param name="batchmode_selector" value='optionSinglemode'/> 131 <param name="batchmode_selector" value='optionSinglemode' />
144 </conditional> 132 </conditional>
145 133
146 <output_collection name="aggregatedFilesCollection" type="list" count="2"> 134 <output_collection name="aggregatedFilesCollection" type="list" count="2">
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"/> 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" />
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"/> 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" />
149 </output_collection> 137 </output_collection>
150 </test> 138 </test>
151 139
152 <test> 140 <test>
153 <conditional name="tar_input_conditional"> 141 <conditional name="tar_input_conditional">
154 <param name="tar_input_selector" value='interval_input'/> 142 <param name="tar_input_selector" value='interval_input' />
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"/> 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" />
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"/> 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" />
157 </conditional> 145 </conditional>
158 146
159 <conditional name="batchmode_conditional"> 147 <conditional name="batchmode_conditional">
160 <param name="batchmode_selector" value='optionBatchmode'/> 148 <param name="batchmode_selector" value='optionBatchmode' />
161 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/> 149 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' />
162 <param name="targetFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_target_list.txt'/> 150 <param name="targetFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_target_list.txt' />
163 </conditional> 151 </conditional>
164 152 <param name='tar' value='True' />
165 <param name='tar' value='True'/>
166
167 <output name="aggregatedFilesFolderTar" file="cHi-C/chicAggregateStatistic/batch_mode.tar" ftype='tar' compare="sim_size" delta='40000' /> 153 <output name="aggregatedFilesFolderTar" file="cHi-C/chicAggregateStatistic/batch_mode.tar" ftype='tar' compare="sim_size" delta='40000' />
168 <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" compare="sim_size" delta='40000'/> 154 <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" />
169 </test> 155 </test>
170 156
171 <test> 157 <test>
172 <conditional name="tar_input_conditional"> 158 <conditional name="tar_input_conditional">
173 <param name="tar_input_selector" value='tar_input'/> 159 <param name="tar_input_selector" value='tar_input' />
174 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1.tar"/> 160 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1.tar" />
175 <param name="targetFiles" value="cHi-C/chicSignificantInteractions/targetFolder.tar"/> 161 <param name="targetFiles" value="cHi-C/chicSignificantInteractions/targetFolder.tar" />
176 </conditional> 162 </conditional>
177 163
178 <conditional name="batchmode_conditional"> 164 <conditional name="batchmode_conditional">
179 <param name="batchmode_selector" value='optionBatchmode'/> 165 <param name="batchmode_selector" value='optionBatchmode' />
180 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/> 166 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' />
181 <param name="targetFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_target_list.txt'/> 167 <param name="targetFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_target_list.txt' />
182 </conditional> 168 </conditional>
183 169
184 <param name='tar' value='True'/> 170 <param name='tar' value='True' />
185 171
186 <output name="aggregatedFilesFolderTar" file="cHi-C/chicAggregateStatistic/batch_mode.tar" ftype='tar' compare="sim_size" delta='40000' /> 172 <output name="aggregatedFilesFolderTar" file="cHi-C/chicAggregateStatistic/batch_mode.tar" ftype='tar' compare="sim_size" delta='40000' />
187 <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" compare="sim_size" delta='40000'/> 173 <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" />
188 </test> 174 </test>
189 </tests> 175 </tests>
190 <help><![CDATA[ 176 <help><![CDATA[
191 177
192 Aggregate statistic for differential testing 178 Aggregate statistic for differential testing
197 target file for all viewpoints is accepted. 183 target file for all viewpoints is accepted.
198 184
199 For more information about HiCExplorer please consider our documentation on readthedocs.io_ 185 For more information about HiCExplorer please consider our documentation on readthedocs.io_
200 186
201 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html 187 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
202 ]]></help> 188 ]]> </help>
203 <expand macro="citations" /> 189 <expand macro="citations" />
204 </tool> 190 </tool>