Mercurial > repos > bgruening > hicexplorer_chicplotviewpoint

comparison chicPlotViewpoint.xml @ 6:031872f8e2e0 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 14:50:31 +0000
parents ac7999229ac6
children 013e53ccc7ac
comparison
equal deleted inserted replaced
5:46793007f090 6:031872f8e2e0
1 <tool id="hicexplorer_chicplotviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.1"> 1 <tool id="hicexplorer_chicplotviewpoint" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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>
40 #set identifier = @ESCAPE_IDENTIFIER_FILE@ 40 #set identifier = @ESCAPE_IDENTIFIER_FILE@
41 ln -s '$file' 'significantFolder/$identifier' && 41 ln -s '$file' 'significantFolder/$identifier' &&
42 #end for 42 #end for
43 #end if 43 #end if
44 44
45
46 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': 45 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
47 #set $interactonfileslist = ' '.join([ '\'interactionFiles/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $tar_input_conditional.interactionFiles ]) 46 #set $interactonfileslist = ' '.join([ '\'interactionFiles/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $tar_input_conditional.interactionFiles ])
48 #set $differentialfileslist = ' '.join([ '\'differentialFolder/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $tar_input_conditional.differentialFiles ]) 47 #set $differentialfileslist = ' '.join([ '\'differentialFolder/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $tar_input_conditional.differentialFiles ])
49 #set $significantfileslist = ' '.join([ '\'significantFolder/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $tar_input_conditional.significantFiles ]) 48 #set $significantfileslist = ' '.join([ '\'significantFolder/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $tar_input_conditional.significantFiles ])
50
51 #end if 49 #end if
52 50
53 @BINARY@ 51 @BINARY@
54 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': 52 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
55 --interactionFile $interactonfileslist 53 --interactionFile $interactonfileslist
76 --plotSampleNumber $batchmode_conditional.computeSampleNumber 74 --plotSampleNumber $batchmode_conditional.computeSampleNumber
77 75
78 --batchMode 76 --batchMode
79 --outputFolder plots 77 --outputFolder plots
80 --outputFormat $image_file_format 78 --outputFormat $image_file_format
81
82
83 #end if 79 #end if
84 80
85 --range $rangeUpstream $rangeDownstream 81 --range $rangeUpstream $rangeDownstream
86 #if $backgroundModelFile: 82 #if $backgroundModelFile:
87 --backgroundModelFile $backgroundModelFile 83 --backgroundModelFile '$backgroundModelFile'
88 #end if 84 #end if
89 85
90 #if $dpi: 86 #if $dpi:
91 --dpi $dpi 87 --dpi $dpi
92 #end if 88 #end if
119 && cd plots 115 && cd plots
120 && tar -cvf ../plots.tar * 116 && tar -cvf ../plots.tar *
121 && cd .. 117 && cd ..
122 && rm -rf plots 118 && rm -rf plots
123 #end if 119 #end if
124 ]]></command> 120 ]]> </command>
125 <inputs> 121 <inputs>
126 <conditional name="tar_input_conditional"> 122 <conditional name="tar_input_conditional">
127 <param name="tar_input_selector" type="select" label="Compute files individually or in batch mode"> 123 <param name="tar_input_selector" type="select" label="Compute files individually or in batch mode">
128 <option value="tar_input">Tar file</option> 124 <option value="tar_input">Tar file</option>
129 <option value="interval_input" selected="True">Interval files</option> 125 <option value="interval_input" selected="True">Interval files</option>
130 </param> 126 </param>
131 <when value="tar_input"> 127 <when value="tar_input">
132 <param name='interactionFiles' type="data" format="tar" label="Interaction files" multiple="false"/> 128 <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'/> 129 <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'/> 130 <param name='significantFiles' type="data" format="tar" label="Significant interaction files" multiple="true" optional='false' />
135 </when> 131 </when>
136 <when value="interval_input"> 132 <when value="interval_input">
137 <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/> 133 <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'/> 134 <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'/> 135 <param name='significantFiles' type="data" format="interval" label="Significant interaction files" multiple="true" optional='true' />
140 </when> 136 </when>
141 </conditional> 137 </conditional>
142 138
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.' /> 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.' />
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.' /> 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.' />
145 <param argument="--backgroundModelFile" type="data" format='tabular' 141 <param argument="--backgroundModelFile" type="data" format='tabular' label="Background model" help="The background file computed by chicViewpointBackgroundModel" optional='true' />
146 label="Background model"
147 help="The background file computed by chicViewpointBackgroundModel" optional='true'/>
148 142
149 <conditional name="batchmode_conditional"> 143 <conditional name="batchmode_conditional">
150 <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode"> 144 <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode">
151 <option value="optionBatchmode">Batch processing</option> 145 <option value="optionBatchmode">Batch processing</option>
152 <option value="optionSinglemode" selected="True">Single file processing</option> 146 <option value="optionSinglemode" selected="True">Single file processing</option>
153 </param> 147 </param>
154 <when value="optionBatchmode"> 148 <when value="optionBatchmode">
155 <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order"/> 149 <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order" />
156 <param name='differentialFilesOrderFile' type="data" format="txt" label="Rejected H0 file order" optional='true'/> 150 <param name='differentialFilesOrderFile' type="data" format="txt" label="Rejected H0 file order" optional='true' />
157 <param name='significantInteractionFilesOrderFile' type="data" format="txt" label="Significant file order" optional='true'/> 151 <param name='significantInteractionFilesOrderFile' type="data" format="txt" label="Significant file order" optional='true' />
158 <param name='computeSampleNumber' type="integer" value='2' label="Plot n sample in one plot"/> 152 <param name='computeSampleNumber' type="integer" value='2' label="Plot n sample in one plot" />
159
160 </when> 153 </when>
161 <when value="optionSinglemode"> 154 <when value="optionSinglemode">
162 </when> 155 </when>
163 </conditional> 156 </conditional>
164 157
165 158 <param argument="--maxPValue" type="float" optional="true" label="Max p-value" help="Maximum value of the plotted p-value." />
166 <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." />
167 <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.' />
168 <param name='resolution' type='integer' value='1000' 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.' optional='true'/> 161 <param name='pvalue' type='boolean' truevalue='--pValue' falsevalue="" checked="false" label="Plot p-values as a colorbar" />
169 <param name='pvalue' type='boolean' truevalue='--pValue' falsevalue="" checked="false" label="Plot p-values as a colorbar"/>
170 <expand macro="colormap" /> 162 <expand macro="colormap" />
171 163
172 <param name='xFold' type='float' value='' label='X-fold mean background' help='Plot x-fold region for the mean background.' optional='true'/> 164 <param name='xFold' type='float' value='' optional='true' label='X-fold mean background' help='Plot x-fold region for the mean background.' />
173 165
174 <param name="image_file_format" type="select" label="Image output format"> 166 <param name="image_file_format" type="select" label="Image output format">
175 <option value="png" selected="True">png</option> 167 <option value="png" selected="True">png</option>
176 <option value="svg">svg</option> 168 <option value="svg">svg</option>
177 <option value="pdf">pdf</option> 169 <option value="pdf">pdf</option>
178 </param> 170 </param>
179 <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/> 171 <param name='dpi' type='integer' optional='true' label='DPI for image' help='Change the default resolution of the plot.' />
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'/> 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'>
181 <param name='truncateZeroPvalues' type='boolean' truevalue='--truncateZeroPvalues' falsevalue="" checked="false" label="Truncate zeros by setting them to one." 173 <validator type="expression" message="Only alphabetic characters and the colon are allowed.">value.replace(' ', '').replace(':', '').isalpha()</validator>
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."/> 174 </param>
183 175 <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." />
184 <param name='tar' type='boolean' checked="false" truevalue='True' label="tar output to one file" 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." />
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
187 </inputs> 177 </inputs>
188 <outputs> 178 <outputs>
189 <collection name="plotsCollection" type="list" label="cHi-C viewpoint plots"> 179 <collection name="plotsCollection" type="list" label="cHi-C viewpoint plots">
190 <discover_datasets pattern="__name_and_ext__" directory="plots" /> 180 <discover_datasets pattern="__name_and_ext__" directory="plots" />
191 </collection> 181 </collection>
194 </data> 184 </data>
195 </outputs> 185 </outputs>
196 <tests> 186 <tests>
197 <test> 187 <test>
198 <conditional name="tar_input_conditional"> 188 <conditional name="tar_input_conditional">
199 <param name="tar_input_selector" value='interval_input'/> 189 <param name="tar_input_selector" value='interval_input' />
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"/> 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" />
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"/> 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" />
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"/> 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" />
203 </conditional> 193 </conditional>
204 194 <conditional name="batchmode_conditional">
205 195 <param name="batchmode_selector" value='optionBatchmode' />
206 <conditional name="batchmode_conditional"> 196 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' />
207 <param name="batchmode_selector" value='optionBatchmode'/> 197 <param name="differentialFilesOrderFile" value='cHi-C/chicDifferentialTest/rejectedFilesList.txt' />
208 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/> 198 <param name="significantInteractionFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_significant_files.txt' />
209 <param name="differentialFilesOrderFile" value='cHi-C/chicDifferentialTest/rejectedFilesList.txt'/> 199 <param name='computeSampleNumber' value='2' />
210 <param name="significantInteractionFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_significant_files.txt'/> 200 </conditional>
211 <param name='computeSampleNumber' value='2'/> 201 <param name="pvalue" value='True' />
212 </conditional> 202 <param name="truncateZeroPvalues" value='True' />
213 <param name="pvalue" value='True'/> 203
214 <param name="truncateZeroPvalues" value='True'/> 204 <param name='backgroundModelFile' value='cHi-C/background.txt' />
215 205 <param name='xFold' value='1.5' />
216 <param name='backgroundModelFile' value='cHi-C/background.txt'/>
217 <param name='xFold' value='1.5'/>
218 <output_collection name="plotsCollection" type="list" count="3"> 206 <output_collection name="plotsCollection" type="list" count="3">
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'/> 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' />
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'/> 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' />
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'/> 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' />
222 </output_collection> 210 </output_collection>
223 211 </test>
224 </test> 212 <test>
225 <test> 213 <conditional name="tar_input_conditional">
226 <conditional name="tar_input_conditional"> 214 <param name="tar_input_selector" value='interval_input' />
227 <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" />
228 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt"/> 216 </conditional>
229 </conditional> 217
230 218 <conditional name="batchmode_conditional">
231 <conditional name="batchmode_conditional"> 219 <param name="batchmode_selector" value='optionSinglemode' />
232 <param name="batchmode_selector" value='optionSinglemode'/>
233 </conditional> 220 </conditional>
234 221
235 <output_collection name="plotsCollection" type="list" count="1"> 222 <output_collection name="plotsCollection" type="list" count="1">
236 <element name="out_plot" file="cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png" ftype="png" compare='sim_size' delta='40000'/> 223 <element name="out_plot" file="cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png" ftype="png" compare='sim_size' />
237
238 </output_collection> 224 </output_collection>
239 </test> 225 </test>
240 226
241 <test> 227 <test>
242 <conditional name="tar_input_conditional"> 228 <conditional name="tar_input_conditional">
243 <param name="tar_input_selector" value='interval_input'/> 229 <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"/> 230 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt" />
245 </conditional> 231 </conditional>
246 232
247 <conditional name="batchmode_conditional"> 233 <conditional name="batchmode_conditional">
248 <param name="batchmode_selector" value='optionSinglemode'/> 234 <param name="batchmode_selector" value='optionSinglemode' />
249 </conditional> 235 </conditional>
250 236
251 <output_collection name="plotsCollection" type="list" count="1"> 237 <output_collection name="plotsCollection" type="list" count="1">
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'/> 238 <element name="out_plot" file="cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png" ftype="png" compare='sim_size' />
253
254 </output_collection> 239 </output_collection>
255 </test> 240 </test>
256 241
257 <test> 242 <test>
258 <conditional name="tar_input_conditional"> 243 <conditional name="tar_input_conditional">
259 <param name="tar_input_selector" value='interval_input'/> 244 <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"/> 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" />
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"/> 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" />
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"/> 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" />
263 </conditional> 248 </conditional>
264 249
265 <conditional name="batchmode_conditional"> 250 <conditional name="batchmode_conditional">
266 <param name="batchmode_selector" value='optionBatchmode'/> 251 <param name="batchmode_selector" value='optionBatchmode' />
267 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/> 252 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' />
268 <param name="differentialFilesOrderFile" value='cHi-C/chicDifferentialTest/rejectedFilesList.txt'/> 253 <param name="differentialFilesOrderFile" value='cHi-C/chicDifferentialTest/rejectedFilesList.txt' />
269 <param name="significantInteractionFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_significant_files.txt'/> 254 <param name="significantInteractionFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_significant_files.txt' />
270 <param name='computeSampleNumber' value='2'/> 255 <param name='computeSampleNumber' value='2' />
271 </conditional> 256 </conditional>
272 <param name="pvalue" value='True'/> 257 <param name="pvalue" value='True' />
273 <param name="truncateZeroPvalues" value='True'/> 258 <param name="truncateZeroPvalues" value='True' />
274 259
275 <param name='backgroundModelFile' value='cHi-C/background.txt'/> 260 <param name='backgroundModelFile' value='cHi-C/background.txt' />
276 <param name='xFold' value='1.5'/> 261 <param name='xFold' value='1.5' />
277 <param name='tar' value='True'/> 262 <param name='tar' value='True' />
278 <output name="plotsTar" file="cHi-C/chicPlotViewpoint/batchMode/plots.tar" ftype='tar' compare="sim_size" delta='40000' /> 263 <output name="plotsTar" file="cHi-C/chicPlotViewpoint/batchMode/plots.tar" ftype='tar' compare="sim_size" delta='40000' />
279 </test> 264 </test>
280 265
281 <test> 266 <test>
282 <conditional name="tar_input_conditional"> 267 <conditional name="tar_input_conditional">
283 <param name="tar_input_selector" value='tar_input'/> 268 <param name="tar_input_selector" value='tar_input' />
284 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1.tar"/> 269 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1.tar" />
285 <param name="differentialFiles" value="cHi-C/chicDifferentialTest/batch_mode_fisher_outfile.tar"/> 270 <param name="differentialFiles" value="cHi-C/chicDifferentialTest/batch_mode_fisher_outfile.tar" />
286 <param name="significantFiles" value="cHi-C/chicSignificantInteractions/significantFilesFolder.tar"/> 271 <param name="significantFiles" value="cHi-C/chicSignificantInteractions/significantFilesFolder.tar" />
287 </conditional> 272 </conditional>
288 273
289 <conditional name="batchmode_conditional"> 274 <conditional name="batchmode_conditional">
290 <param name="batchmode_selector" value='optionBatchmode'/> 275 <param name="batchmode_selector" value='optionBatchmode' />
291 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/> 276 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' />
292 <param name="differentialFilesOrderFile" value='cHi-C/chicDifferentialTest/rejectedFilesList.txt'/> 277 <param name="differentialFilesOrderFile" value='cHi-C/chicDifferentialTest/rejectedFilesList.txt' />
293 <param name="significantInteractionFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_significant_files.txt'/> 278 <param name="significantInteractionFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_significant_files.txt' />
294 <param name='computeSampleNumber' value='2'/> 279 <param name='computeSampleNumber' value='2' />
295 </conditional> 280 </conditional>
296 <param name="pvalue" value='True'/> 281 <param name="pvalue" value='True' />
297 <param name="truncateZeroPvalues" value='True'/> 282 <param name="truncateZeroPvalues" value='True' />
298 283
299 <param name='backgroundModelFile' value='cHi-C/background.txt'/> 284 <param name='backgroundModelFile' value='cHi-C/background.txt' />
300 <param name='xFold' value='1.5'/> 285 <param name='xFold' value='1.5' />
301 <param name='tar' value='True'/> 286 <param name='tar' value='True' />
302 <output name="plotsTar" file="cHi-C/chicPlotViewpoint/batchMode/plots.tar" ftype='tar' compare="sim_size" delta='40000' /> 287 <output name="plotsTar" file="cHi-C/chicPlotViewpoint/batchMode/plots.tar" ftype='tar' compare="sim_size" delta='40000' />
303 </test> 288 </test>
304 </tests> 289 </tests>
305 <help><![CDATA[ 290 <help><![CDATA[
306 291
320 305
321 306
322 For more information about HiCExplorer please consider our documentation on readthedocs.io_ 307 For more information about HiCExplorer please consider our documentation on readthedocs.io_
323 308
324 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html 309 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
325 ]]></help> 310 ]]> </help>
326 <expand macro="citations" /> 311 <expand macro="citations" />
327 </tool> 312 </tool>