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comparison heatmapper.xml @ 18:5ea8782d650c draft

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author bgruening
date Mon, 03 Feb 2014 13:44:35 -0500
parents ef65d6b68ccc
children 8c452f37c896
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17:ef65d6b68ccc 18:5ea8782d650c
1 <tool id="deeptools_heatmapper" name="heatmapper" version="1.0.2"> 1 <tool id="deeptools_heatmapper" name="heatmapper" version="1.0.3">
2 <description>creates a heatmap for a score associated to genomic regions</description> 2 <description>creates a heatmap for a score associated to genomic regions</description>
3 <expand macro="requirements"/> 3 <expand macro="requirements"/>
4 <expand macro="stdio" /> 4 <expand macro="stdio" />
5 <macros> 5 <macros>
6 <token name="@BINARY@">heatmapper</token>
6 <import>deepTools_macros.xml</import> 7 <import>deepTools_macros.xml</import>
7 </macros> 8 </macros>
8 <command> 9 <command>
9 heatmapper 10 heatmapper
10 11
78 --plotTitle '$advancedOpt.plotTitle' 79 --plotTitle '$advancedOpt.plotTitle'
79 #end if 80 #end if
80 81
81 $advancedOpt.onePlotPerGroup 82 $advancedOpt.onePlotPerGroup
82 83
83 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'yes': 84 @kmeans_clusterin@
84 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
85 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
86 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
87 #end if
88 #end if
89 #end if
90 85
91 #end if 86 #end if
92 </command> 87 </command>
93 <inputs> 88 <inputs>
94 <param name="matrixFile" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/> 89 <param name="matrixFile" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/>
145 <param name="heatmapWidth" type="float" value="7.5" min="1" max="100" label="Heatmap width in cm" help="The minimum value is 1 and the maximum is 100."/> 140 <param name="heatmapWidth" type="float" value="7.5" min="1" max="100" label="Heatmap width in cm" help="The minimum value is 1 and the maximum is 100."/>
146 <param name="heatmapHeight" type="float" value="25" min="3" max="100" label="Heatmap height in cm" help="The minimum value is 3 and the maximum is 100."/> 141 <param name="heatmapHeight" type="float" value="25" min="3" max="100" label="Heatmap height in cm" help="The minimum value is 3 and the maximum is 100."/>
147 142
148 <param name="whatToShow" type="select" label="What to show" help ="The default is to include a summary or profile plot on top of the heatmap and a heatmap colorbar."> 143 <param name="whatToShow" type="select" label="What to show" help ="The default is to include a summary or profile plot on top of the heatmap and a heatmap colorbar.">
149 <option value="plot, heatmap and colorbar" selected="true">summary plot, heatmap and colorbar</option> 144 <option value="plot, heatmap and colorbar" selected="true">summary plot, heatmap and colorbar</option>
150 <option value="plot only">summary plot only</option>
151 <option value="plot and heatmap">summary plot and heatmap (no colorbar)</option> 145 <option value="plot and heatmap">summary plot and heatmap (no colorbar)</option>
152 <option value="heatmap only">heatmap only</option> 146 <option value="heatmap only">heatmap only</option>
153 <option value="heatmap and colorbar">heatmap and colorbar</option> 147 <option value="heatmap and colorbar">heatmap and colorbar</option>
154 <option value="colorbar only">colorbar only</option> 148 <option value="colorbar only">colorbar only</option>
155 </param> 149 </param>
169 <param name="plotTitle" type="text" value="" size="30" label="Title of the plot" help="Title of the plot, to be printed on top of the generated image. Leave blank for no title." /> 163 <param name="plotTitle" type="text" value="" size="30" label="Title of the plot" help="Title of the plot, to be printed on top of the generated image. Leave blank for no title." />
170 <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" 164 <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue=""
171 label="Do one plot per group" 165 label="Do one plot per group"
172 help="When computeMatrix was used on more than one group of genes, the average plots for all the groups will be drawn in one panel by default. If this option is set, each group will get its own plot, stacked on top of each other."/> 166 help="When computeMatrix was used on more than one group of genes, the average plots for all the groups will be drawn in one panel by default. If this option is set, each group will get its own plot, stacked on top of each other."/>
173 167
174 <conditional name="used_multiple_regions"> 168 <expand macro="kmeans_clustering" />
175 <param name="used_multiple_regions_options" type="select" 169
176 label="Did you used multiple regions in ComputeMatrix?"
177 help="That option is only relevant if you want to cluster the results. Clustering is only available with one selected region in ComputeMatrix.">
178 <option value="no">No, I used only one region.</option>
179 <option value="yes">Yes, I used multiple regions.</option>
180 </param>
181 <when value="yes">
182 <conditional name="clustering">
183 <param name="clustering_options" type="select" label="Clustering algorithm">
184 <option value="none">No clustering</option>
185 <option value="kmeans">Kmeans clustering</option>
186 </param>
187 <when value="kmeans">
188 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
189 help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. Only works for data that is not grouped, otherwise only the first group will be clustered. If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) if a cluster has very few members compared to the total number or regions. (default: None)."/>
190 </when>
191 <when value="none" />
192 </conditional>
193 </when>
194 <when value="no" />
195 </conditional>
196 </when> 170 </when>
197 </conditional> 171 </conditional>
198 </inputs> 172 </inputs>
199 <outputs> 173 <outputs>
200 <expand macro="output_image_file_format" /> 174 <expand macro="output_image_file_format" />
222 196
223 .. image:: $PATH_TO_IMAGES/visual_hm_DmelPolII.png 197 .. image:: $PATH_TO_IMAGES/visual_hm_DmelPolII.png
224 :alt: Heatmap of RNA Polymerase II ChIP-seq 198 :alt: Heatmap of RNA Polymerase II ChIP-seq
225 199
226 200
201 You can find more details in the `heatmapper wiki`_.
202
203 .. _heatmapper wiki: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-heatmapper
204
205
227 ----- 206 -----
228
229 .. class:: infomark
230 207
231 @REFERENCES@ 208 @REFERENCES@
232 209
233 </help> 210 </help>
234 </tool> 211 </tool>