Mercurial > repos > bgruening > hicexplorer_chicplotviewpoint

comparison chicPlotViewpoint.xml @ 2:136ebddd6ec3 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
author iuc
date Wed, 11 Mar 2020 17:14:05 -0400
parents ae8bf5420df2
children dbf82dd7bdb3
comparison
equal deleted inserted replaced
1:61e2d34c5b99 2:136ebddd6ec3
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
17 #for $file in $interactionFiles: 17 #for $file in $interactionFiles:
18 #set identifier = @ESCAPE_IDENTIFIER_FILE@ 18 #set identifier = @ESCAPE_IDENTIFIER_FILE@
19 ln -s '$file' 'interactionFiles/$identifier' && 19 ln -s '$file' 'interactionFiles/$identifier' &&
20 #end for 20 #end for
21 21
35 35
36 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': 36 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
37 #set $interactonfileslist = ' '.join([ '\'interactionFiles/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ]) 37 #set $interactonfileslist = ' '.join([ '\'interactionFiles/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ])
38 #set $differentialfileslist = ' '.join([ '\'differentialFolder/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $differentialFiles ]) 38 #set $differentialfileslist = ' '.join([ '\'differentialFolder/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $differentialFiles ])
39 #set $significantfileslist = ' '.join([ '\'significantFolder/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $significantFiles ]) 39 #set $significantfileslist = ' '.join([ '\'significantFolder/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $significantFiles ])
40 40
41 #end if 41 #end if
42 42
43 @BINARY@ 43 @BINARY@
44 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': 44 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
45 --interactionFile $interactonfileslist 45 --interactionFile $interactonfileslist
46 #if $differentialFiles: 46 #if $differentialFiles:
47 --differentialTestResult $differentialfileslist 47 --differentialTestResult $differentialfileslist
48 #end if 48 #end if
49 49
50 #if $significantFiles: 50 #if $significantFiles:
51 --significantInteractions $significantfileslist 51 --significantInteractions $significantfileslist
52 #end if 52 #end if
53 53
54 -o out_plot.$image_file_format 54 -o out_plot.$image_file_format
55 #else: 55 #else:
56 --interactionFile $batchmode_conditional.interactionFilesOrderFile 56 --interactionFile $batchmode_conditional.interactionFilesOrderFile
77 --backgroundModelFile $backgroundModelFile 77 --backgroundModelFile $backgroundModelFile
78 #end if 78 #end if
79 79
80 #if $dpi: 80 #if $dpi:
81 --dpi $dpi 81 --dpi $dpi
82 #end if 82 #end if
83 83
84 #if $maxPValue: 84 #if $maxPValue:
85 --maxPValue $maxPValue 85 --maxPValue $maxPValue
86 #end if 86 #end if
87 87
107 ]]></command> 107 ]]></command>
108 <inputs> 108 <inputs>
109 <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/> 109 <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/>
110 <param name='differentialFiles' type="data" format="interval" label="Rejected H0 files" multiple="true" optional='true'/> 110 <param name='differentialFiles' type="data" format="interval" label="Rejected H0 files" multiple="true" optional='true'/>
111 <param name='significantFiles' type="data" format="interval" label="Significant interaction files" multiple="true" optional='true'/> 111 <param name='significantFiles' type="data" format="interval" label="Significant interaction files" multiple="true" optional='true'/>
112 112
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.' /> 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.' />
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.' /> 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.' />
115 <param argument="--backgroundModelFile" type="data" format='tabular' 115 <param argument="--backgroundModelFile" type="data" format='tabular'
116 label="Background model" 116 label="Background model"
117 help="The background file computed by chicViewpointBackgroundModel" optional='true'/> 117 help="The background file computed by chicViewpointBackgroundModel" optional='true'/>
118 118
119 <conditional name="batchmode_conditional"> 119 <conditional name="batchmode_conditional">
120 <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode"> 120 <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode">
121 <option value="optionBatchmode">Batch processing</option> 121 <option value="optionBatchmode">Batch processing</option>
122 <option value="optionSinglemode" selected="True">Single file processing</option> 122 <option value="optionSinglemode" selected="True">Single file processing</option>
123 </param> 123 </param>
124 <when value="optionBatchmode"> 124 <when value="optionBatchmode">
125 <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order"/> 125 <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order"/>
126 <param name='differentialFilesOrderFile' type="data" format="txt" label="Rejected H0 file order" optional='true'/> 126 <param name='differentialFilesOrderFile' type="data" format="txt" label="Rejected H0 file order" optional='true'/>
127 <param name='significantInteractionFilesOrderFile' type="data" format="txt" label="Significant file order" optional='true'/> 127 <param name='significantInteractionFilesOrderFile' type="data" format="txt" label="Significant file order" optional='true'/>
128 <param name='computeSampleNumber' type="integer" value='2' label="Plot n sample in one plot"/> 128 <param name='computeSampleNumber' type="integer" value='2' label="Plot n sample in one plot"/>
129 129
130 </when> 130 </when>
131 <when value="optionSinglemode"> 131 <when value="optionSinglemode">
132 </when> 132 </when>
133 </conditional> 133 </conditional>
134 134
135 135
136 <param argument="--maxPValue" type="float" optional="true" label="Max p-value" help="Maximum value of the plotted p-value."/> 136 <param argument="--maxPValue" type="float" optional="true" label="Max p-value" help="Maximum value of the plotted p-value."/>
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
152 152
153 </inputs> 153 </inputs>
154 <outputs> 154 <outputs>
155 <collection name="plotsCollection" type="list" label="cHi-C viewpoint plots"> 155 <collection name="plotsCollection" type="list" label="cHi-C viewpoint plots">
156 <discover_datasets pattern="__name_and_ext__" directory="plots" /> 156 <discover_datasets pattern="__name_and_ext__" directory="plots" />
157 </collection> 157 </collection>
158 158
159 </outputs> 159 </outputs>
160 <tests> 160 <tests>
161 <test> 161 <test>
162 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed"/> 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"/>
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.bed,cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed,cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.bed"/> 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"/>
164 <param name="significantFiles" value="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed"/> 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"/>
165 165
166 166
167 <conditional name="batchmode_conditional"> 167 <conditional name="batchmode_conditional">
168 <param name="batchmode_selector" value='optionBatchmode'/> 168 <param name="batchmode_selector" value='optionBatchmode'/>
169 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/> 169 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/>
170 <param name="differentialFilesOrderFile" value='cHi-C/chicDifferentialTest/rejectedFilesList.txt'/> 170 <param name="differentialFilesOrderFile" value='cHi-C/chicDifferentialTest/rejectedFilesList.txt'/>
171 <param name="significantInteractionFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_significant_files.txt'/> 171 <param name="significantInteractionFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_significant_files.txt'/>
172 <param name='computeSampleNumber' value='2'/> 172 <param name='computeSampleNumber' value='2'/>
173 </conditional> 173 </conditional>
174 <param name="pvalue" value='True'/> 174 <param name="pvalue" value='True'/>
175 <param name="alpha" value='0.5'/> 175 <param name="alpha" value='0.5'/>
176 <param name='backgroundModelFile' value='cHi-C/background.bed'/> 176 <param name='backgroundModelFile' value='cHi-C/background.txt'/>
177 <param name='xFold' value='1.5'/> 177 <param name='xFold' value='1.5'/>
178 <output_collection name="plotsCollection" type="list" count="3"> 178 <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'/> 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'/>
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'/> 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'/>
181 <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'/> 181 <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'/>
182 </output_collection> 182 </output_collection>
183 183
184 </test> 184 </test>
185 <test> 185 <test>
186 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed"/> 186 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt"/>
187 187
188 <conditional name="batchmode_conditional"> 188 <conditional name="batchmode_conditional">
189 <param name="batchmode_selector" value='optionSinglemode'/> 189 <param name="batchmode_selector" value='optionSinglemode'/>
190 </conditional> 190 </conditional>
191 191
192 <output_collection name="plotsCollection" type="list" count="1"> 192 <output_collection name="plotsCollection" type="list" count="1">
198 <help><![CDATA[ 198 <help><![CDATA[
199 199
200 Plot of viewpoints 200 Plot of viewpoints
201 ================== 201 ==================
202 202
203 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. 203 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.
204 204
205 An example usage is: 205 An example usage is:
206 206
207 `$ chicPlotViewpoint --interactionFile viewpoint1.bed viewpoint2.bed --range 500000 500000 --backgroundModelFile background_model.bed --pValue --outFileName viewpoint1_2.png --dpi 300` 207 `$ chicPlotViewpoint --interactionFile viewpoint1.txt viewpoint2.txt --range 500000 500000 --backgroundModelFile background_model.txt --pValue --outFileName viewpoint1_2.png --dpi 300`
208 208
209 209
210 In batch mode the list of file names and the folders containing the files need to be given: 210 In batch mode the list of file names and the folders containing the files need to be given:
211 211
212 `$ chicPlotViewpoint --interactionFile viewpoint_names.txt -interactionFileFolder viewpointFilesFolder --differentialTestResult rejected_H0.txt --differentialTestResultsFolder differentialFolder --range 500000 500000 --backgroundModelFile background_model.bed --pValue --outputFolder plotsFOlder --dpi 300 --threads 20` 212 `$ 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`
213 213
214 214
215 For more information about HiCExplorer please consider our documentation on readthedocs.io_ 215 For more information about HiCExplorer please consider our documentation on readthedocs.io_
216 216
217 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html 217 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html