Mercurial > repos > bgruening > deeptools_plot_heatmap

comparison plotHeatmap.xml @ 42:2f2cd7085835 draft default tip

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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 810c1359b884661d3f5c7372be0f0f88c859a3b9
author bgruening
date Thu, 01 Jun 2023 10:18:08 +0000
parents 375e7508e571
children
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41:d09eab55cbc1 42:2f2cd7085835
1 <tool id="deeptools_plot_heatmap" name="plotHeatmap" version="@WRAPPER_VERSION@.1" profile="18.01"> 1 <tool id="deeptools_plot_heatmap" name="plotHeatmap" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
2 <description>creates a heatmap for score distributions across genomic regions</description> 2 <description>creates a heatmap for score distributions across genomic regions</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">plotHeatmap</token> 4 <token name="@BINARY@">plotHeatmap</token>
5 <import>deepTools_macros.xml</import> 5 <import>deepTools_macros.xml</import>
6 </macros> 6 </macros>
32 #if $advancedOpt.showAdvancedOpt == "yes" 32 #if $advancedOpt.showAdvancedOpt == "yes"
33 #if $advancedOpt.sortRegions: 33 #if $advancedOpt.sortRegions:
34 --sortRegions '$advancedOpt.sortRegions' 34 --sortRegions '$advancedOpt.sortRegions'
35 #end if 35 #end if
36 36
37 #if $advancedOpt.linesAtTickMarks:
38 --linesAtTickMarks
39 #end if
40
37 #if $advancedOpt.sortUsing: 41 #if $advancedOpt.sortUsing:
38 --sortUsing '$advancedOpt.sortUsing' 42 --sortUsing '$advancedOpt.sortUsing'
39 #end if 43 #end if
40 44
41 #if $advancedOpt.averageTypeSummaryPlot: 45 #if $advancedOpt.averageTypeSummaryPlot:
69 #end if 73 #end if
70 74
71 #if str($advancedOpt.yMin).strip() != "": 75 #if str($advancedOpt.yMin).strip() != "":
72 --yMin $advancedOpt.yMin 76 --yMin $advancedOpt.yMin
73 #end if 77 #end if
74 #if $advancedOpt.yMax: 78 #if str($advancedOpt.yMax).strip() != "":
75 --yMax $advancedOpt.yMax 79 --yMax $advancedOpt.yMax
80 #end if
81 #if str($advancedOpt.sortUsingSamples).strip() != "":
82 --sortUsingSamples $advancedOpt.sortUsingSamples
83 #end if
84 #if str($advancedOpt.clusterUsingSamples).strip() != "":
85 --clusterUsingSamples $advancedOpt.clusterUsingSamples
76 #end if 86 #end if
77 87
78 --xAxisLabel '$advancedOpt.xAxisLabel' 88 --xAxisLabel '$advancedOpt.xAxisLabel'
79 --yAxisLabel '$advancedOpt.yAxisLabel' 89 --yAxisLabel '$advancedOpt.yAxisLabel'
80 90
128 </param> 138 </param>
129 <when value="no" /> 139 <when value="no" />
130 <when value="yes"> 140 <when value="yes">
131 <expand macro="sortRegions" /> 141 <expand macro="sortRegions" />
132 <expand macro="sortUsing" /> 142 <expand macro="sortUsing" />
143 <param argument="--sortUsingSamples" type="text"
144 label="List of samples to be used for sorting"
145 help="List of sample numbers (order as in matrix), which are used by --sortUsing for sorting.
146 If no value is set, it uses all samples. Example: 1 3 (space separated!)" />
147 <sanitizer>
148 <valid initial="string.printable">
149 <add value=" "/>
150 </valid>
151 </sanitizer>
152 <param argument="--linesAtTickMarks" type="boolean" truevalue="--linesAtTickMarks" falsevalue=""
153 label="Draw dashed lines in heatmap above all tick marks?" />
133 <param argument="--averageTypeSummaryPlot" type="select" 154 <param argument="--averageTypeSummaryPlot" type="select"
134 label="Type of statistic that should be plotted in the summary image above the heatmap" 155 label="Type of statistic that should be plotted in the summary image above the heatmap"
135 help=""> 156 help="">
136 <option value="mean" selected="true">mean</option> 157 <option value="mean" selected="true">mean</option>
137 <option value="median">median</option> 158 <option value="median">median</option>
160 max="1.0" optional="True" 181 max="1.0" optional="True"
161 label="Alpha channel (transparency)" 182 label="Alpha channel (transparency)"
162 help="The alpha channel (transparency) to use for the heatmaps. The default is 1.0 and values must 183 help="The alpha channel (transparency) to use for the heatmaps. The default is 1.0 and values must
163 be between 0 and 1. A value of 0.0 would be fully transparent." /> 184 be between 0 and 1. A value of 0.0 would be fully transparent." />
164 185
165 <param argument="--colorList" type="text" value="" size="50" optional="True" 186 <param argument="--colorList" type="text" value="" optional="True"
166 label="List of colors for each heatmap. Separate lists by spaces and the colors in the list by comas" 187 label="List of colors for each heatmap. Separate lists by spaces and the colors in the list by comas"
167 help="The color of the heatmaps can be specified as a list of colors separated by comas with 188 help="The color of the heatmaps can be specified as a list of colors separated by comas with
168 not space in between. For example: white,blue white,green will set a color map from white 189 not space in between. For example: white,blue white,green will set a color map from white
169 to blue for the first heatmap and for white to green for the next heatmap."/> 190 to blue for the first heatmap and for white to green for the next heatmap."/>
170 <expand macro="zMin_zMax" /> 191 <expand macro="zMin_zMax" />
171 <param argument="--yMin" type="float" value="" size="3" optional="True" 192 <param argument="--yMin" type="float" value="" optional="True"
172 label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" help=""/> 193 label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" help=""/>
173 <param argument="--yMax" type="float" value="" size="3" optional="True" 194 <param argument="--yMax" type="float" value="" optional="True"
174 label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" help=""/> 195 label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" help=""/>
175 <param argument="--xAxisLabel" type="text" value="distance from TSS (bp)" size="200" 196 <param argument="--xAxisLabel" type="text" value="distance from TSS (bp)"
176 label="The x-axis label" help="" /> 197 label="The x-axis label" help="" />
177 <param argument="--yAxisLabel" type="text" value="genes" size="30" 198 <param argument="--yAxisLabel" type="text" value="genes"
178 label="The y-axis label for the top panel" help="" /> 199 label="The y-axis label for the top panel" help="" />
179 200
180 <param argument="--heatmapWidth" type="float" value="7.5" min="1" max="100" 201 <param argument="--heatmapWidth" type="float" value="7.5" min="1" max="100"
181 label="Heatmap width in cm" help="The minimum value is 1 and the maximum is 100."/> 202 label="Heatmap width in cm" help="The minimum value is 1 and the maximum is 100."/>
182 <param argument="--heatmapHeight" type="float" value="25" min="3" max="100" 203 <param argument="--heatmapHeight" type="float" value="25" min="3" max="100"
187 <option value="plot, heatmap and colorbar" selected="true">summary plot, heatmap and colorbar</option> 208 <option value="plot, heatmap and colorbar" selected="true">summary plot, heatmap and colorbar</option>
188 <option value="plot and heatmap">summary plot and heatmap (no colorbar)</option> 209 <option value="plot and heatmap">summary plot and heatmap (no colorbar)</option>
189 <option value="heatmap and colorbar">heatmap and colorbar</option> 210 <option value="heatmap and colorbar">heatmap and colorbar</option>
190 </param> 211 </param>
191 212
192 <param argument="--startLabel" type="text" value="TSS" size="10" 213 <param argument="--startLabel" type="text" value="TSS"
193 label="Label for the region start" 214 label="Label for the region start"
194 help ="Only for scale-regions mode. Label shown in the plot for the start of the region. Default is TSS (transcription start site), but could be changed to anything, e.g. &quot;peak start&quot;." /> 215 help ="Only for scale-regions mode. Label shown in the plot for the start of the region. Default is TSS (transcription start site), but could be changed to anything, e.g. &quot;peak start&quot;." />
195 <param argument="--endLabel" type="text" value="TES" size="10" 216 <param argument="--endLabel" type="text" value="TES"
196 label="Label for the region end" 217 label="Label for the region end"
197 help="Only for scale-regions mode. Label shown in the plot for the region end. Default is TES (transcription end site)."/> 218 help="Only for scale-regions mode. Label shown in the plot for the region end. Default is TES (transcription end site)."/>
198 219
199 <param argument="--referencePointLabel" type="text" value="TSS" size="10" 220 <param argument="--referencePointLabel" type="text" value="TSS"
200 label="Reference point label" 221 label="Reference point label"
201 help ="Label shown in the plot for the reference-point. Default is the same as the reference point selected (e.g. TSS), but could be anything, e.g. &quot;peak start&quot; etc." /> 222 help ="Label shown in the plot for the reference-point. Default is the same as the reference point selected (e.g. TSS), but could be anything, e.g. &quot;peak start&quot; etc." />
202 <param argument="--samplesLabel" type="text" size="30" 223 <param argument="--samplesLabel" type="text"
203 label="Labels for the samples (each bigwig) plotted" 224 label="Labels for the samples (each bigwig) plotted"
204 help="The default is to use the file name of the sample. The sample labels should be separated by 225 help="The default is to use the file name of the sample. The sample labels should be separated by
205 spaces and quoted if a label itself contains a space E.g. label-1 &quot;label 2&quot;"> 226 spaces and quoted if a label itself contains a space E.g. label-1 &quot;label 2&quot;">
206 <sanitizer> 227 <sanitizer>
207 <valid initial="string.printable"> 228 <valid initial="string.printable">
208 </valid> 229 </valid>
209 </sanitizer> 230 </sanitizer>
210 </param> 231 </param>
211 <param argument="--regionsLabel" type="text" size="30" 232 <param argument="--regionsLabel" type="text"
212 label="Labels for the regions plotted in the heatmap" 233 label="Labels for the regions plotted in the heatmap"
213 help="If more than one region is being plotted a list of labels separated by space is required. 234 help="If more than one region is being plotted a list of labels separated by space is required.
214 If a label itself contains a space, then quotes are needed. 235 If a label itself contains a space, then quotes are needed.
215 For example, label_1 &quot;label 2&quot;" /> 236 For example, label_1 &quot;label 2&quot;" />
216 237
220 <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue="" 241 <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue=""
221 label="Make one plot per group of regions" 242 label="Make one plot per group of regions"
222 help="The default is to make one plot per bigWig file, i.e., all samples next to each other. Choosing this option will make one plot per group of regions."/> 243 help="The default is to make one plot per bigWig file, i.e., all samples next to each other. Choosing this option will make one plot per group of regions."/>
223 244
224 <expand macro="kmeans_clustering" /> 245 <expand macro="kmeans_clustering" />
246 <param argument="--clusterUsingSamples" type="text"
247 label="List of samples to be used for clustering"
248 help="List of sample numbers (order as in matrix), which are used by --kmeans or --hclust for clustering.
249 If no value is set, it uses all samples. Example: 1 3 (space separated!)"/>
250 <sanitizer>
251 <valid initial="string.printable">
252 <add value=" "/>
253 </valid>
254 </sanitizer>
225 </when> 255 </when>
226 </conditional> 256 </conditional>
227 </inputs> 257 </inputs>
228 <outputs> 258 <outputs>
229 <expand macro="output_image_file_format" /> 259 <expand macro="output_image_file_format" />