Mercurial > repos > bgruening > hicexplorer_chicplotviewpoint

comparison chicPlotViewpoint.xml @ 3:dbf82dd7bdb3 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
author iuc
date Tue, 24 Mar 2020 14:12:09 -0400
parents 136ebddd6ec3
children ac7999229ac6
comparison
equal deleted inserted replaced
2:136ebddd6ec3 3:dbf82dd7bdb3
98 #if $xFold: 98 #if $xFold:
99 --xFold $xFold 99 --xFold $xFold
100 #end if 100 #end if
101 --colorList $colorList 101 --colorList $colorList
102 --threads @THREADS@ 102 --threads @THREADS@
103 103 $truncateZeroPvalues
104 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': 104 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
105 && mv out_plot.$image_file_format plots/out_plot.$image_file_format 105 && mv out_plot.$image_file_format plots/out_plot.$image_file_format
106 #end if 106 #end if
107 ]]></command> 107 ]]></command>
108 <inputs> 108 <inputs>
146 <option value="svg">svg</option> 146 <option value="svg">svg</option>
147 <option value="pdf">pdf</option> 147 <option value="pdf">pdf</option>
148 </param> 148 </param>
149 <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/> 149 <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'/> 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'/>
151 151 <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."/>
153
152 154
153 </inputs> 155 </inputs>
154 <outputs> 156 <outputs>
155 <collection name="plotsCollection" type="list" label="cHi-C viewpoint plots"> 157 <collection name="plotsCollection" type="list" label="cHi-C viewpoint plots">
156 <discover_datasets pattern="__name_and_ext__" directory="plots" /> 158 <discover_datasets pattern="__name_and_ext__" directory="plots" />
159 </outputs> 161 </outputs>
160 <tests> 162 <tests>
161 <test> 163 <test>
162 <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"/> 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"/>
163 <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"/> 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"/>
164 <param name="significantFiles" value="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt"/> 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"/>
165 167
166 168
167 <conditional name="batchmode_conditional"> 169 <conditional name="batchmode_conditional">
168 <param name="batchmode_selector" value='optionBatchmode'/> 170 <param name="batchmode_selector" value='optionBatchmode'/>
169 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/> 171 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/>
170 <param name="differentialFilesOrderFile" value='cHi-C/chicDifferentialTest/rejectedFilesList.txt'/> 172 <param name="differentialFilesOrderFile" value='cHi-C/chicDifferentialTest/rejectedFilesList.txt'/>
171 <param name="significantInteractionFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_significant_files.txt'/> 173 <param name="significantInteractionFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_significant_files.txt'/>
172 <param name='computeSampleNumber' value='2'/> 174 <param name='computeSampleNumber' value='2'/>
173 </conditional> 175 </conditional>
174 <param name="pvalue" value='True'/> 176 <param name="pvalue" value='True'/>
175 <param name="alpha" value='0.5'/> 177 <param name="truncateZeroPvalues" value='True'/>
178
179 <!-- <param name="alpha" value='0.5'/> -->
176 <param name='backgroundModelFile' value='cHi-C/background.txt'/> 180 <param name='backgroundModelFile' value='cHi-C/background.txt'/>
177 <param name='xFold' value='1.5'/> 181 <param name='xFold' value='1.5'/>
178 <output_collection name="plotsCollection" type="list" count="3"> 182 <output_collection name="plotsCollection" type="list" count="3">
179 <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'/> 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'/>
180 <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'/> 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'/>
192 <output_collection name="plotsCollection" type="list" count="1"> 196 <output_collection name="plotsCollection" type="list" count="1">
193 <element name="out_plot" file="cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png" ftype="png" compare='sim_size' delta='40000'/> 197 <element name="out_plot" file="cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png" ftype="png" compare='sim_size' delta='40000'/>
194 198
195 </output_collection> 199 </output_collection>
196 </test> 200 </test>
201
202 <test>
203 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt"/>
204
205 <conditional name="batchmode_conditional">
206 <param name="batchmode_selector" value='optionSinglemode'/>
207 </conditional>
208
209 <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'/>
211
212 </output_collection>
213 </test>
197 </tests> 214 </tests>
198 <help><![CDATA[ 215 <help><![CDATA[
199 216
200 Plot of viewpoints 217 Plot of viewpoints
201 ================== 218 ==================