Mercurial > repos > bgruening > hicexplorer_chicplotviewpoint

comparison chicPlotViewpoint.xml @ 3:fb7e8fb553b6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
author iuc
date Fri, 14 Aug 2020 09:19:50 +0000
parents df064edbd7fc
children 06eeb469a2fb
comparison
equal deleted inserted replaced
2:df064edbd7fc 3:fb7e8fb553b6
1 <tool id="hicexplorer_chicplotviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_chicplotviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.1">
2 <description>creates plots for viewpoints</description> 2 <description>creates plots for viewpoints</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">chicPlotViewpoint</token> 4 <token name="@BINARY@">chicPlotViewpoint</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
11 mkdir interactionFiles && 11 mkdir interactionFiles &&
12 mkdir differentialFolder && 12 mkdir differentialFolder &&
13 mkdir significantFolder && 13 mkdir significantFolder &&
14 mkdir plots && 14 mkdir plots &&
15 15
16 16 #if $tar_input_conditional.tar_input_selector == 'tar_input':
17 #for $file in $interactionFiles: 17 ln -s '$tar_input_conditional.interactionFiles' viewpoints.tar &&
18 #set identifier = @ESCAPE_IDENTIFIER_FILE@ 18 tar -C interactionFiles -xvf viewpoints.tar &&
19 ln -s '$file' 'interactionFiles/$identifier' && 19
20 #end for 20 #if $differentialFiles:
21 21 ln -s '$tar_input_conditional.differentialFiles' differential.tar &&
22 #if $differentialFiles: 22 tar -C differentialFolder -xvf differential.tar &&
23 #for $file in $differentialFiles: 23 #end if
24 #if $significantFiles:
25 ln -s '$tar_input_conditional.significantFiles' significantFiles.tar &&
26 tar -C significantFolder -xvf significantFiles.tar &&
27 #end if
28 #else:
29 #for $file in $tar_input_conditional.interactionFiles:
24 #set identifier = @ESCAPE_IDENTIFIER_FILE@ 30 #set identifier = @ESCAPE_IDENTIFIER_FILE@
25 ln -s '$file' 'differentialFolder/$identifier' && 31 ln -s '$file' 'interactionFiles/$identifier' &&
32 #end for
33
34 #for $file in $tar_input_conditional.differentialFiles:
35 #set identifier = @ESCAPE_IDENTIFIER_FILE@
36 ln -s '$file' 'differentialFolder/$identifier' &&
37 #end for
38
39 #for $file in $tar_input_conditional.significantFiles:
40 #set identifier = @ESCAPE_IDENTIFIER_FILE@
41 ln -s '$file' 'significantFolder/$identifier' &&
26 #end for 42 #end for
27 #end if 43 #end if
28 44
29 #if $significantFiles:
30 #for $file in $significantFiles:
31 #set identifier = @ESCAPE_IDENTIFIER_FILE@
32 ln -s '$file' 'significantFolder/$identifier' &&
33 #end for
34 #end if
35 45
36 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': 46 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
37 #set $interactonfileslist = ' '.join([ '\'interactionFiles/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ]) 47 #set $interactonfileslist = ' '.join([ '\'interactionFiles/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $tar_input_conditional.interactionFiles ])
38 #set $differentialfileslist = ' '.join([ '\'differentialFolder/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $differentialFiles ]) 48 #set $differentialfileslist = ' '.join([ '\'differentialFolder/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $tar_input_conditional.differentialFiles ])
39 #set $significantfileslist = ' '.join([ '\'significantFolder/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $significantFiles ]) 49 #set $significantfileslist = ' '.join([ '\'significantFolder/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $tar_input_conditional.significantFiles ])
40 50
41 #end if 51 #end if
42 52
43 @BINARY@ 53 @BINARY@
44 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': 54 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
45 --interactionFile $interactonfileslist 55 --interactionFile $interactonfileslist
46 #if $differentialFiles: 56 #if $tar_input_conditional.differentialFiles:
47 --differentialTestResult $differentialfileslist 57 --differentialTestResult $differentialfileslist
48 #end if 58 #end if
49 59
50 #if $significantFiles: 60 #if $tar_input_conditional.significantFiles:
51 --significantInteractions $significantfileslist 61 --significantInteractions $significantfileslist
52 #end if 62 #end if
53 63
54 -o out_plot.$image_file_format 64 -o out_plot.$image_file_format
55 #else: 65 #else:
102 --threads @THREADS@ 112 --threads @THREADS@
103 $truncateZeroPvalues 113 $truncateZeroPvalues
104 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': 114 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
105 && mv out_plot.$image_file_format plots/out_plot.$image_file_format 115 && mv out_plot.$image_file_format plots/out_plot.$image_file_format
106 #end if 116 #end if
117
118 #if $tar:
119 && cd plots
120 && tar -cvf ../plots.tar *
121 && cd ..
122 && rm -rf plots
123 #end if
107 ]]></command> 124 ]]></command>
108 <inputs> 125 <inputs>
109 <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/> 126 <conditional name="tar_input_conditional">
110 <param name='differentialFiles' type="data" format="interval" label="Rejected H0 files" multiple="true" optional='true'/> 127 <param name="tar_input_selector" type="select" label="Compute files individually or in batch mode">
111 <param name='significantFiles' type="data" format="interval" label="Significant interaction files" multiple="true" optional='true'/> 128 <option value="tar_input">Tar file</option>
112 129 <option value="interval_input" selected="True">Interval files</option>
113 <param name="rangeUpstream" type="integer" value="500000" label="Upstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' /> 130 </param>
114 <param name="rangeDownstream" type="integer" value="500000" label="Downstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' /> 131 <when value="tar_input">
132 <param name='interactionFiles' type="data" format="tar" label="Interaction files" multiple="false"/>
133 <param name='differentialFiles' type="data" format="tar" label="Rejected H0 files" multiple="true" optional='false'/>
134 <param name='significantFiles' type="data" format="tar" label="Significant interaction files" multiple="true" optional='false'/>
135 </when>
136 <when value="interval_input">
137 <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/>
138 <param name='differentialFiles' type="data" format="interval" label="Rejected H0 files" multiple="true" optional='true'/>
139 <param name='significantFiles' type="data" format="interval" label="Significant interaction files" multiple="true" optional='true'/>
140 </when>
141 </conditional>
142
143 <param name="rangeUpstream" type="integer" value="100000" label="Upstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' />
144 <param name="rangeDownstream" type="integer" value="100000" label="Downstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' />
115 <param argument="--backgroundModelFile" type="data" format='tabular' 145 <param argument="--backgroundModelFile" type="data" format='tabular'
116 label="Background model" 146 label="Background model"
117 help="The background file computed by chicViewpointBackgroundModel" optional='true'/> 147 help="The background file computed by chicViewpointBackgroundModel" optional='true'/>
118 148
119 <conditional name="batchmode_conditional"> 149 <conditional name="batchmode_conditional">
149 <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/> 179 <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/>
150 <param name='colorList' type='text' value='g b c m y k' label='Color list' help='Colorlist for the viewpoint lines. For all available colors please check matplotlib documentation: https://matplotlib.org/3.1.0/gallery/color/named_colors.html' optional='true'/> 180 <param name='colorList' type='text' value='g b c m y k' label='Color list' help='Colorlist for the viewpoint lines. For all available colors please check matplotlib documentation: https://matplotlib.org/3.1.0/gallery/color/named_colors.html' optional='true'/>
151 <param name='truncateZeroPvalues' type='boolean' truevalue='--truncateZeroPvalues' falsevalue="" checked="false" label="Truncate zeros by setting them to one." 181 <param name='truncateZeroPvalues' type='boolean' truevalue='--truncateZeroPvalues' falsevalue="" checked="false" label="Truncate zeros by setting them to one."
152 help="Sets all p-values which are equal to zero to one. This has the effect that the associated positions are not disturbing the presenation of small p-values."/> 182 help="Sets all p-values which are equal to zero to one. This has the effect that the associated positions are not disturbing the presenation of small p-values."/>
153 183
154 184 <param name='tar' type='boolean' checked="false" truevalue='True' label="tar output to one file"
185 help="The output is tarred to one file and not written to a collection. Set this option if the number of files is large."/>
186
155 </inputs> 187 </inputs>
156 <outputs> 188 <outputs>
157 <collection name="plotsCollection" type="list" label="cHi-C viewpoint plots"> 189 <collection name="plotsCollection" type="list" label="cHi-C viewpoint plots">
158 <discover_datasets pattern="__name_and_ext__" directory="plots" /> 190 <discover_datasets pattern="__name_and_ext__" directory="plots" />
159 </collection> 191 </collection>
160 192 <data name="plotsTar" from_work_dir="plots.tar" format="tar" label="cHi-C viewpoint plots tar">
193 <filter>tar</filter>
194 </data>
161 </outputs> 195 </outputs>
162 <tests> 196 <tests>
163 <test> 197 <test>
164 <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_4487435_4487435_Sox17.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_19093103_19093103_Tfap2d.txt"/> 198 <conditional name="tar_input_conditional">
165 <param name="differentialFiles" value="cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt,cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt,cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt"/> 199 <param name="tar_input_selector" value='interval_input'/>
166 <param name="significantFiles" value="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt"/> 200 <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_4487435_4487435_Sox17.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_19093103_19093103_Tfap2d.txt"/>
201 <param name="differentialFiles" value="cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt,cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt,cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt"/>
202 <param name="significantFiles" value="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt"/>
203 </conditional>
167 204
168 205
169 <conditional name="batchmode_conditional"> 206 <conditional name="batchmode_conditional">
170 <param name="batchmode_selector" value='optionBatchmode'/> 207 <param name="batchmode_selector" value='optionBatchmode'/>
171 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/> 208 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/>
174 <param name='computeSampleNumber' value='2'/> 211 <param name='computeSampleNumber' value='2'/>
175 </conditional> 212 </conditional>
176 <param name="pvalue" value='True'/> 213 <param name="pvalue" value='True'/>
177 <param name="truncateZeroPvalues" value='True'/> 214 <param name="truncateZeroPvalues" value='True'/>
178 215
179 <!-- <param name="alpha" value='0.5'/> -->
180 <param name='backgroundModelFile' value='cHi-C/background.txt'/> 216 <param name='backgroundModelFile' value='cHi-C/background.txt'/>
181 <param name='xFold' value='1.5'/> 217 <param name='xFold' value='1.5'/>
182 <output_collection name="plotsCollection" type="list" count="3"> 218 <output_collection name="plotsCollection" type="list" count="3">
183 <element name="Eya1_FL-E13-5_MB-E10-5_chr1_chr1_14300280" file="cHi-C/chicPlotViewpoint/batchMode/two/Eya1_FL-E13-5_MB-E10-5_chr1_chr1_14300280.png" ftype="png" compare='sim_size' delta='40000'/> 219 <element name="Eya1_FL-E13-5_MB-E10-5_chr1_chr1_14300280" file="cHi-C/chicPlotViewpoint/batchMode/two/Eya1_FL-E13-5_MB-E10-5_chr1_chr1_14300280.png" ftype="png" compare='sim_size' delta='40000'/>
184 <element name="Sox17_FL-E13-5_MB-E10-5_chr1_chr1_4487435" file="cHi-C/chicPlotViewpoint/batchMode/two/Sox17_FL-E13-5_MB-E10-5_chr1_chr1_4487435.png" ftype="png" compare='sim_size' delta='40000'/> 220 <element name="Sox17_FL-E13-5_MB-E10-5_chr1_chr1_4487435" file="cHi-C/chicPlotViewpoint/batchMode/two/Sox17_FL-E13-5_MB-E10-5_chr1_chr1_4487435.png" ftype="png" compare='sim_size' delta='40000'/>
185 <element name="Tfap2d_FL-E13-5_MB-E10-5_chr1_chr1_19093103" file="cHi-C/chicPlotViewpoint/batchMode/two/Tfap2d_FL-E13-5_MB-E10-5_chr1_chr1_19093103.png" ftype="png" compare='sim_size' delta='40000'/> 221 <element name="Tfap2d_FL-E13-5_MB-E10-5_chr1_chr1_19093103" file="cHi-C/chicPlotViewpoint/batchMode/two/Tfap2d_FL-E13-5_MB-E10-5_chr1_chr1_19093103.png" ftype="png" compare='sim_size' delta='40000'/>
186 </output_collection> 222 </output_collection>
187 223
188 </test> 224 </test>
189 <test> 225 <test>
190 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt"/> 226 <conditional name="tar_input_conditional">
227 <param name="tar_input_selector" value='interval_input'/>
228 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt"/>
229 </conditional>
191 230
192 <conditional name="batchmode_conditional"> 231 <conditional name="batchmode_conditional">
193 <param name="batchmode_selector" value='optionSinglemode'/> 232 <param name="batchmode_selector" value='optionSinglemode'/>
194 </conditional> 233 </conditional>
195 234
198 237
199 </output_collection> 238 </output_collection>
200 </test> 239 </test>
201 240
202 <test> 241 <test>
203 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt"/> 242 <conditional name="tar_input_conditional">
243 <param name="tar_input_selector" value='interval_input'/>
244 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt"/>
245 </conditional>
204 246
205 <conditional name="batchmode_conditional"> 247 <conditional name="batchmode_conditional">
206 <param name="batchmode_selector" value='optionSinglemode'/> 248 <param name="batchmode_selector" value='optionSinglemode'/>
207 </conditional> 249 </conditional>
208 250
209 <output_collection name="plotsCollection" type="list" count="1"> 251 <output_collection name="plotsCollection" type="list" count="1">
210 <element name="out_plot" file="cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png" ftype="png" compare='sim_size' delta='40000'/> 252 <element name="out_plot" file="cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png" ftype="png" compare='sim_size' delta='40000'/>
211 253
212 </output_collection> 254 </output_collection>
255 </test>
256
257 <test>
258 <conditional name="tar_input_conditional">
259 <param name="tar_input_selector" value='interval_input'/>
260 <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_4487435_4487435_Sox17.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_19093103_19093103_Tfap2d.txt"/>
261 <param name="differentialFiles" value="cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt,cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt,cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt"/>
262 <param name="significantFiles" value="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt"/>
263 </conditional>
264
265 <conditional name="batchmode_conditional">
266 <param name="batchmode_selector" value='optionBatchmode'/>
267 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/>
268 <param name="differentialFilesOrderFile" value='cHi-C/chicDifferentialTest/rejectedFilesList.txt'/>
269 <param name="significantInteractionFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_significant_files.txt'/>
270 <param name='computeSampleNumber' value='2'/>
271 </conditional>
272 <param name="pvalue" value='True'/>
273 <param name="truncateZeroPvalues" value='True'/>
274
275 <param name='backgroundModelFile' value='cHi-C/background.txt'/>
276 <param name='xFold' value='1.5'/>
277 <param name='tar' value='True'/>
278 <output name="plotsTar" file="cHi-C/chicPlotViewpoint/batchMode/plots.tar" ftype='tar' compare="sim_size" delta='40000' />
279 </test>
280
281 <test>
282 <conditional name="tar_input_conditional">
283 <param name="tar_input_selector" value='tar_input'/>
284 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1.tar"/>
285 <param name="differentialFiles" value="cHi-C/chicDifferentialTest/batch_mode_fisher_outfile.tar"/>
286 <param name="significantFiles" value="cHi-C/chicSignificantInteractions/significantFilesFolder.tar"/>
287 </conditional>
288
289 <conditional name="batchmode_conditional">
290 <param name="batchmode_selector" value='optionBatchmode'/>
291 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/>
292 <param name="differentialFilesOrderFile" value='cHi-C/chicDifferentialTest/rejectedFilesList.txt'/>
293 <param name="significantInteractionFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_significant_files.txt'/>
294 <param name='computeSampleNumber' value='2'/>
295 </conditional>
296 <param name="pvalue" value='True'/>
297 <param name="truncateZeroPvalues" value='True'/>
298
299 <param name='backgroundModelFile' value='cHi-C/background.txt'/>
300 <param name='xFold' value='1.5'/>
301 <param name='tar' value='True'/>
302 <output name="plotsTar" file="cHi-C/chicPlotViewpoint/batchMode/plots.tar" ftype='tar' compare="sim_size" delta='40000' />
213 </test> 303 </test>
214 </tests> 304 </tests>
215 <help><![CDATA[ 305 <help><![CDATA[
216 306
217 Plot of viewpoints 307 Plot of viewpoints