Mercurial > repos > bgruening > hicexplorer_chicplotviewpoint

comparison chicPlotViewpoint.xml @ 7:274976af50cb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
author iuc
date Mon, 01 Jul 2024 18:53:41 +0000
parents 06eeb469a2fb
children
comparison
equal deleted inserted replaced
6:c0180ac1f7c9 7:274976af50cb
1 <tool id="hicexplorer_chicplotviewpoint" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="hicexplorer_chicplotviewpoint" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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>
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 10
11 mkdir interactionFiles && 11 @BINARY@
12 mkdir differentialFolder && 12
13 mkdir significantFolder && 13 --interactionFile '$interactionFile'
14 mkdir plots && 14 #if $differentialFile:
15 --differentialTestResult '$differentialFile'
16 #end if
15 17
16 #if $tar_input_conditional.tar_input_selector == 'tar_input': 18 #if $significantInteractionFile:
17 ln -s '$tar_input_conditional.interactionFiles' viewpoints.tar && 19 --significantInteractions '$significantInteractionFile'
18 tar -C interactionFiles -xvf viewpoints.tar && 20 $plotSignificantInteractions
19
20 #if $differentialFiles:
21 ln -s '$tar_input_conditional.differentialFiles' differential.tar &&
22 tar -C differentialFolder -xvf differential.tar &&
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 $tar_input_conditional.interactionFiles:
30 #set identifier = @ESCAPE_IDENTIFIER_FILE@
31 ln -s '$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' &&
42 #end for
43 #end if
44
45 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
46 #set $interactonfileslist = ' '.join([ '\'interactionFiles/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $tar_input_conditional.interactionFiles ])
47 #set $differentialfileslist = ' '.join([ '\'differentialFolder/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $tar_input_conditional.differentialFiles ])
48 #set $significantfileslist = ' '.join([ '\'significantFolder/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $tar_input_conditional.significantFiles ])
49 #end if
50
51 @BINARY@
52 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
53 --interactionFile $interactonfileslist
54 #if $tar_input_conditional.differentialFiles:
55 --differentialTestResult $differentialfileslist
56 #end if
57
58 #if $tar_input_conditional.significantFiles:
59 --significantInteractions $significantfileslist
60 #end if
61
62 -o out_plot.$image_file_format
63 #else:
64 --interactionFile $batchmode_conditional.interactionFilesOrderFile
65 --interactionFileFolder interactionFiles
66 #if $batchmode_conditional.differentialFilesOrderFile:
67 --differentialTestResult $batchmode_conditional.differentialFilesOrderFile
68 --differentialTestResultsFolder differentialFolder
69 #end if
70 #if $batchmode_conditional.significantInteractionFilesOrderFile:
71 --significantInteractions $batchmode_conditional.significantInteractionFilesOrderFile
72 --significantInteractionFileFolder significantFolder
73 #end if
74 --plotSampleNumber $batchmode_conditional.computeSampleNumber
75
76 --batchMode
77 --outputFolder plots
78 --outputFormat $image_file_format
79 #end if 21 #end if
80 22
81 --range $rangeUpstream $rangeDownstream 23 --range $rangeUpstream $rangeDownstream
82 #if $backgroundModelFile: 24 #if $backgroundModelFile:
83 --backgroundModelFile '$backgroundModelFile' 25 --backgroundModelFile '$backgroundModelFile'
26 #end if
27
28 --combinationMode $combinationMode_conditional.combinationMode_selector
29
30 #if $combinationMode_conditional.combinationMode_selector == 'oneGene':
31 --combinationName $combinationMode_conditional.geneName
84 #end if 32 #end if
85 33
86 #if $dpi: 34 #if $dpi:
87 --dpi $dpi 35 --dpi $dpi
88 #end if 36 #end if
93 41
94 #if $minPValue: 42 #if $minPValue:
95 --minPValue $minPValue 43 --minPValue $minPValue
96 #end if 44 #end if
97 45
98 --binResolution $resolution 46
99 #if $colormap: 47 #if $colormap:
100 --colorMapPvalue $colormap 48 --colorMapPvalue $colormap
101 #end if 49 #end if
102 50
103 $pvalue 51 $pvalue
105 --xFold $xFold 53 --xFold $xFold
106 #end if 54 #end if
107 --colorList $colorList 55 --colorList $colorList
108 --threads @THREADS@ 56 --threads @THREADS@
109 $truncateZeroPvalues 57 $truncateZeroPvalues
110 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': 58
111 && mv out_plot.$image_file_format plots/out_plot.$image_file_format 59 -o plots.tar.gz
112 #end if 60
113
114 #if $tar:
115 && cd plots
116 && tar -cvf ../plots.tar *
117 && cd ..
118 && rm -rf plots
119 #end if
120 ]]> </command> 61 ]]> </command>
121 <inputs> 62 <inputs>
122 <conditional name="tar_input_conditional"> 63
123 <param name="tar_input_selector" type="select" label="Compute files individually or in batch mode"> 64 <param name="interactionFile" type="data" format="h5" label="Interaction file order" />
124 <option value="tar_input">Tar file</option> 65 <param name="differentialFile" type="data" format="h5" label="Rejected H0 file order" optional="true" />
125 <option value="interval_input" selected="True">Interval files</option> 66 <param name="significantInteractionFile" type="data" format="h5" label="Significant file order" optional="true" />
67 <param argument="--plotSignificantInteractions" type="boolean" truevalue="--plotSignificantInteractions" falsevalue="" checked="false" label="Plot significant interactions" help="Select if the significant regions should be highlighted in the plot. If not set, the significant file data is used only to update the p-values." />
68
69 <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." />
70 <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." />
71 <param argument="--backgroundModelFile" type="data" format="tabular" label="Background model" help="The background file computed by chicViewpointBackgroundModel" optional="true" />
72 <conditional name="combinationMode_conditional">
73 <param name="combinationMode_selector" type="select" label="Combination mode for the plots">
74 <option value="dual">Dual</option>
75 <option value="single" selected="True">Single</option>
76 <option value="allGenes" >All genes</option>
77 <option value="oneGene" >One gene</option>
126 </param> 78 </param>
127 <when value="tar_input"> 79 <when value="dual" >
128 <param name='interactionFiles' type="data" format="tar" label="Interaction files" multiple="false" />
129 <param name='differentialFiles' type="data" format="tar" label="Rejected H0 files" multiple="true" optional='false' />
130 <param name='significantFiles' type="data" format="tar" label="Significant interaction files" multiple="true" optional='false' />
131 </when> 80 </when>
132 <when value="interval_input"> 81 <when value="single" >
133 <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true" /> 82 </when>
134 <param name='differentialFiles' type="data" format="interval" label="Rejected H0 files" multiple="true" optional='true' /> 83 <when value="allGenes" >
135 <param name='significantFiles' type="data" format="interval" label="Significant interaction files" multiple="true" optional='true' /> 84 </when>
85 <when value="oneGene" >
86 <param name="geneName" type="text" value="" label="Gene name" help="Gene name that should be plotted." />
136 </when> 87 </when>
137 </conditional> 88 </conditional>
138 89
139 <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.' />
140 <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.' />
141 <param argument="--backgroundModelFile" type="data" format='tabular' label="Background model" help="The background file computed by chicViewpointBackgroundModel" optional='true' />
142
143 <conditional name="batchmode_conditional">
144 <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode">
145 <option value="optionBatchmode">Batch processing</option>
146 <option value="optionSinglemode" selected="True">Single file processing</option>
147 </param>
148 <when value="optionBatchmode">
149 <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order" />
150 <param name='differentialFilesOrderFile' type="data" format="txt" label="Rejected H0 file order" optional='true' />
151 <param name='significantInteractionFilesOrderFile' type="data" format="txt" label="Significant file order" optional='true' />
152 <param name='computeSampleNumber' type="integer" value='2' label="Plot n sample in one plot" />
153 </when>
154 <when value="optionSinglemode">
155 </when>
156 </conditional>
157
158 <param argument="--maxPValue" type="float" optional="true" label="Max p-value" help="Maximum value of the plotted p-value." /> 90 <param argument="--maxPValue" type="float" optional="true" label="Max p-value" help="Maximum value of the plotted p-value." />
159 <param argument="--minPValue" type="float" optional="true" label="Min p-value" help="Minimum value of the plotted p-value." /> 91 <param argument="--minPValue" type="float" optional="true" label="Min p-value" help="Minimum value of the plotted p-value." />
160 <param name='resolution' type='integer' value='1000' min="1" optional='true' label='Resolution of cHi-C data' help='Resolution of the bin in genomic units. Values are usually e.g. 1000 for a 1kb, 5000 for a 5kb or 10000 for a 10kb resolution.' /> 92 <param name="pvalue" type="boolean" truevalue="--pValue" falsevalue="" checked="false" label="Plot p-values as a colorbar" />
161 <param name='pvalue' type='boolean' truevalue='--pValue' falsevalue="" checked="false" label="Plot p-values as a colorbar" />
162 <expand macro="colormap" /> 93 <expand macro="colormap" />
163 94
164 <param name='xFold' type='float' value='' optional='true' label='X-fold mean background' help='Plot x-fold region for the mean background.' /> 95 <param name="xFold" type="float" value="" optional="true" label="X-fold mean background" help="Plot x-fold region for the mean background." />
165 96
166 <param name="image_file_format" type="select" label="Image output format"> 97 <param name="image_file_format" type="select" label="Image output format">
167 <option value="png" selected="True">png</option> 98 <option value="png" selected="True">png</option>
168 <option value="svg">svg</option> 99 <option value="svg">svg</option>
169 <option value="pdf">pdf</option> 100 <option value="pdf">pdf</option>
170 </param> 101 </param>
171 <param name='dpi' type='integer' optional='true' label='DPI for image' help='Change the default resolution of the plot.' /> 102 <param name="dpi" type="integer" optional="true" label="DPI for image" help="Change the default resolution of the plot." />
172 <param name='colorList' type='text' value='g b c m y k' optional='true' label='Color list' help='Colorlist for the viewpoint lines. For all available colors please check matplotlib documentation: https://matplotlib.org/stable/gallery/color/named_colors.html'> 103 <param name="colorList" type="text" value="g b c m y k" optional="true" label="Color list" help="Colorlist for the viewpoint lines. For all available colors please check matplotlib documentation: https://matplotlib.org/stable/gallery/color/named_colors.html">
173 <validator type="expression" message="Only alphabetic characters and the colon are allowed.">value.replace(' ', '').replace(':', '').isalpha()</validator> 104 <validator type="expression" message="Only alphabetic characters and the colon are allowed.">value.replace(' ', '').replace(':', '').isalpha()</validator>
174 </param> 105 </param>
175 <param argument='--truncateZeroPvalues' type='boolean' truevalue='--truncateZeroPvalues' falsevalue="" checked="false" label="Truncate zeros by setting them to one." 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." /> 106 <param argument="--truncateZeroPvalues" type="boolean" truevalue="--truncateZeroPvalues" falsevalue="" checked="false" label="Truncate zeros by setting them to one." 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." />
176 <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." />
177 </inputs> 107 </inputs>
178 <outputs> 108 <outputs>
179 <collection name="plotsCollection" type="list" label="cHi-C viewpoint plots"> 109 <data name="plotsTar" from_work_dir="plots.tar.gz" format="tar.gz" label="cHi-C viewpoint plots" />
180 <discover_datasets pattern="__name_and_ext__" directory="plots" />
181 </collection>
182 <data name="plotsTar" from_work_dir="plots.tar" format="tar" label="cHi-C viewpoint plots tar">
183 <filter>tar</filter>
184 </data>
185 </outputs> 110 </outputs>
186 <tests> 111 <tests>
187 <test> 112 <test>
188 <conditional name="tar_input_conditional"> 113 <param name="interactionFile" value="cHi-C/chicViewpoint/two_matrices.hdf5" />
189 <param name="tar_input_selector" value='interval_input' /> 114 <param name="differentialFile" value="cHi-C/chicDifferentialTest/differential.hdf5" />
190 <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" /> 115 <param name="significantInteractionFile" value="cHi-C/chicSignificantInteractions/significantInteractions_dual.hdf5" />
191 <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" /> 116 <conditional name="combinationMode_conditional">
192 <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" /> 117 <param name="combinationMode_selector" value="dual" />
193 </conditional> 118 </conditional>
194 <conditional name="batchmode_conditional"> 119 <param name="pvalue" value="True" />
195 <param name="batchmode_selector" value='optionBatchmode' /> 120 <param name="truncateZeroPvalues" value="True" />
196 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' />
197 <param name="differentialFilesOrderFile" value='cHi-C/chicDifferentialTest/rejectedFilesList.txt' />
198 <param name="significantInteractionFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_significant_files.txt' />
199 <param name='computeSampleNumber' value='2' />
200 </conditional>
201 <param name="pvalue" value='True' />
202 <param name="truncateZeroPvalues" value='True' />
203 121
204 <param name='backgroundModelFile' value='cHi-C/background.txt' /> 122 <param name="backgroundModelFile" value="cHi-C/background.txt" />
205 <param name='xFold' value='1.5' /> 123 <param name="xFold" value="1.5" />
206 <output_collection name="plotsCollection" type="list" count="3"> 124 <output name="plotsTar" file="cHi-C/plots.tar.gz" ftype="tar.gz" compare="sim_size" />
207 <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' /> 125
208 <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' />
209 <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' />
210 </output_collection>
211 </test>
212 <test>
213 <conditional name="tar_input_conditional">
214 <param name="tar_input_selector" value='interval_input' />
215 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt" />
216 </conditional>
217
218 <conditional name="batchmode_conditional">
219 <param name="batchmode_selector" value='optionSinglemode' />
220 </conditional>
221
222 <output_collection name="plotsCollection" type="list" count="1">
223 <element name="out_plot" file="cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png" ftype="png" compare='sim_size' />
224 </output_collection>
225 </test>
226
227 <test>
228 <conditional name="tar_input_conditional">
229 <param name="tar_input_selector" value='interval_input' />
230 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt" />
231 </conditional>
232
233 <conditional name="batchmode_conditional">
234 <param name="batchmode_selector" value='optionSinglemode' />
235 </conditional>
236
237 <output_collection name="plotsCollection" type="list" count="1">
238 <element name="out_plot" file="cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png" ftype="png" compare='sim_size' />
239 </output_collection>
240 </test>
241
242 <test>
243 <conditional name="tar_input_conditional">
244 <param name="tar_input_selector" value='interval_input' />
245 <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" />
246 <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" />
247 <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" />
248 </conditional>
249
250 <conditional name="batchmode_conditional">
251 <param name="batchmode_selector" value='optionBatchmode' />
252 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' />
253 <param name="differentialFilesOrderFile" value='cHi-C/chicDifferentialTest/rejectedFilesList.txt' />
254 <param name="significantInteractionFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_significant_files.txt' />
255 <param name='computeSampleNumber' value='2' />
256 </conditional>
257 <param name="pvalue" value='True' />
258 <param name="truncateZeroPvalues" value='True' />
259
260 <param name='backgroundModelFile' value='cHi-C/background.txt' />
261 <param name='xFold' value='1.5' />
262 <param name='tar' value='True' />
263 <output name="plotsTar" file="cHi-C/chicPlotViewpoint/batchMode/plots.tar" ftype='tar' compare="sim_size" delta='40000' />
264 </test>
265
266 <test>
267 <conditional name="tar_input_conditional">
268 <param name="tar_input_selector" value='tar_input' />
269 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1.tar" />
270 <param name="differentialFiles" value="cHi-C/chicDifferentialTest/batch_mode_fisher_outfile.tar" />
271 <param name="significantFiles" value="cHi-C/chicSignificantInteractions/significantFilesFolder.tar" />
272 </conditional>
273
274 <conditional name="batchmode_conditional">
275 <param name="batchmode_selector" value='optionBatchmode' />
276 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' />
277 <param name="differentialFilesOrderFile" value='cHi-C/chicDifferentialTest/rejectedFilesList.txt' />
278 <param name="significantInteractionFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_significant_files.txt' />
279 <param name='computeSampleNumber' value='2' />
280 </conditional>
281 <param name="pvalue" value='True' />
282 <param name="truncateZeroPvalues" value='True' />
283
284 <param name='backgroundModelFile' value='cHi-C/background.txt' />
285 <param name='xFold' value='1.5' />
286 <param name='tar' value='True' />
287 <output name="plotsTar" file="cHi-C/chicPlotViewpoint/batchMode/plots.tar" ftype='tar' compare="sim_size" delta='40000' />
288 </test> 126 </test>
289 </tests> 127 </tests>
290 <help><![CDATA[ 128 <help><![CDATA[
291 129
292 Plot of viewpoints 130 Plot of viewpoints
294 132
295 chicPlotViewpoint plots one or many viewpoints with the average background model and the computed p-value per sample. Moreover it can highlight differential interactions of two samples and/or significant regions. 133 chicPlotViewpoint plots one or many viewpoints with the average background model and the computed p-value per sample. Moreover it can highlight differential interactions of two samples and/or significant regions.
296 134
297 An example usage is: 135 An example usage is:
298 136
299 `$ chicPlotViewpoint --interactionFile viewpoint1.txt viewpoint2.txt --range 500000 500000 --backgroundModelFile background_model.txt --pValue --outFileName viewpoint1_2.png --dpi 300` 137 `$ chicPlotViewpoint --interactionFile interactions.hdf5 --range 500000 500000 --backgroundModelFile background_model.txt --pValue --outFileName viewpoint1_2.tar.gz --dpi 300`
300
301
302 In batch mode the list of file names and the folders containing the files need to be given:
303
304 `$ chicPlotViewpoint --interactionFile viewpoint_names.txt -interactionFileFolder viewpointFilesFolder --differentialTestResult rejected_H0.txt --differentialTestResultsFolder differentialFolder --range 500000 500000 --backgroundModelFile background_model.txt --pValue --outputFolder plotsFOlder --dpi 300 --threads 20`
305 138
306 139
307 For more information about HiCExplorer please consider our documentation on readthedocs.io_ 140 For more information about HiCExplorer please consider our documentation on readthedocs.io_
308 141
309 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html 142 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html