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comparison plotHeatmap.xml @ 7:aaf01404686f draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 54a10cf268ca9a5399f13458a1b218be7891bd41
author bgruening
date Wed, 23 Dec 2015 03:54:30 -0500
parents 59f925c67e2f
children 8ed7e3b6a16c
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6:59f925c67e2f 7:aaf01404686f
30 30
31 #if $advancedOpt.showAdvancedOpt == "yes" 31 #if $advancedOpt.showAdvancedOpt == "yes"
32 #if $advancedOpt.sortRegions: 32 #if $advancedOpt.sortRegions:
33 --sortRegions '$advancedOpt.sortRegions' 33 --sortRegions '$advancedOpt.sortRegions'
34 #end if 34 #end if
35 35
36 #if $advancedOpt.sortUsing: 36 #if $advancedOpt.sortUsing:
37 --sortUsing '$advancedOpt.sortUsing' 37 --sortUsing '$advancedOpt.sortUsing'
38 #end if 38 #end if
39 39
40 #if $advancedOpt.averageTypeSummaryPlot: 40 #if $advancedOpt.averageTypeSummaryPlot:
67 --heatmapWidth $advancedOpt.heatmapWidth 67 --heatmapWidth $advancedOpt.heatmapWidth
68 --heatmapHeight $advancedOpt.heatmapHeight 68 --heatmapHeight $advancedOpt.heatmapHeight
69 69
70 --whatToShow '$advancedOpt.whatToShow' 70 --whatToShow '$advancedOpt.whatToShow'
71 71
72 --startLabel '$advancedOpt.startLabel' 72 --startLabel '$advancedOpt.startLabel'
73 --endLabel '$advancedOpt.endLabel' 73 --endLabel '$advancedOpt.endLabel'
74 --refPointLabel '$advancedOpt.referencePointLabel' 74 --refPointLabel '$advancedOpt.referencePointLabel'
75 --regionsLabel '$advancedOpt.regionsLabel' 75 --regionsLabel '$advancedOpt.regionsLabel'
76 76
77 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "": 77 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
78 --plotTitle '$advancedOpt.plotTitle' 78 --plotTitle '$advancedOpt.plotTitle'
79 #end if 79 #end if
80 80
81 $advancedOpt.perGroup 81 $advancedOpt.onePlotPerGroup
82 82
83 @KMEANS_CLUSTERING@ 83 @KMEANS_CLUSTERING@
84 84
85 #end if 85 #end if
86 ]]> 86 ]]>
111 <option value="max">max</option> 111 <option value="max">max</option>
112 <option value="sum">sum</option> 112 <option value="sum">sum</option>
113 <option value="std">std</option> 113 <option value="std">std</option>
114 </param> 114 </param>
115 115
116 <param argument="--missingDataColor" type="text" value="black" optional="true" label="Missing data color" 116 <param argument="--missingDataColor" type="text" value="black" optional="true" label="Missing data color"
117 help="If 'Represent missing data as zero' is not set, such cases will be colored in black by default. 117 help="If 'Represent missing data as zero' is not set, such cases will be colored in black by default.
118 By using this parameter a different color can be set. A value between 0 and 1 will be used for a gray scale (black is 0). 118 By using this parameter a different color can be set. A value between 0 and 1 will be used for a gray scale (black is 0).
119 Also color names can be used, see a list here: http://packages.python.org/ete2/reference/reference_svgcolors.html. 119 Also color names can be used, see a list here: http://packages.python.org/ete2/reference/reference_svgcolors.html.
120 Alternatively colors can be specified using the #rrggbb notation." /> 120 Alternatively colors can be specified using the #rrggbb notation." />
121 121
141 141
142 <param argument="--whatToShow" type="select" label="What to show" 142 <param argument="--whatToShow" type="select" label="What to show"
143 help ="The default is to include a summary or profile plot on top of the heatmap and a heatmap colorbar."> 143 help ="The default is to include a summary or profile plot on top of the heatmap and a heatmap colorbar.">
144 <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>
145 <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>
146 <option value="heatmap only">heatmap only</option>
146 <option value="heatmap and colorbar">heatmap and colorbar</option> 147 <option value="heatmap and colorbar">heatmap and colorbar</option>
148 <option value="colorbar only">colorbar only</option>
147 </param> 149 </param>
148 150
149 <param argument="--startLabel" type="text" value="TSS" size="10" 151 <param argument="--startLabel" type="text" value="TSS" size="10"
150 label="Label for the region start" 152 label="Label for the region start"
151 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;." /> 153 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;." />
154 help="Only for scale-regions mode. Label shown in the plot for the region end. Default is TES (transcription end site)."/> 156 help="Only for scale-regions mode. Label shown in the plot for the region end. Default is TES (transcription end site)."/>
155 157
156 <param argument="--referencePointLabel" type="text" value="TSS" size="10" 158 <param argument="--referencePointLabel" type="text" value="TSS" size="10"
157 label="Reference point label" 159 label="Reference point label"
158 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." /> 160 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." />
159 <param argument="--regionsLabel" type="text" value="genes" size="30" 161 <param argument="--regionsLabel" type="text" value="genes" size="30"
160 label="Labels for the regions plotted in the heatmap" 162 label="Labels for the regions plotted in the heatmap"
161 help="If more than one region is being plotted a list of labels separated by comma and limited by quotes, is required. For example, label1, label2."> 163 help="If more than one region is being plotted a list of labels separated by comma and limited by quotes, is required. For example, label1, label2.">
162 <sanitizer> 164 <sanitizer>
163 <valid initial="string.printable"> 165 <valid initial="string.printable">
164 </valid> 166 </valid>
165 </sanitizer> 167 </sanitizer>
166 </param> 168 </param>
167 <expand macro="plotTitle" /> 169 <expand macro="plotTitle" />
168 <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue="" 170 <param argument="--onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue=""
169 label="Do one plot per group" 171 label="Do one plot per group"
170 help="When clustering is applied to the data, or the computematrix was performed on file containing 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.
171 groups separated by &quot;#&quot;, plot the groups next to each other. The default is to plot 173 If this option is set, each group will get its own plot, stacked on top of each other."/>
172 the samples next to each other. If this option is set, each group (or cluster) will get its own plot,
173 with different samples stacked on top of each other."/>
174 174
175 <expand macro="kmeans_clustering" /> 175 <expand macro="kmeans_clustering" />
176 </when> 176 </when>
177 </conditional> 177 </conditional>
178 </inputs> 178 </inputs>
197 <![CDATA[ 197 <![CDATA[
198 **What it does** 198 **What it does**
199 199
200 The heatmapper visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes. 200 The heatmapper visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes.
201 Like profiler, it requires that computeMatrix was run first to calculate the values. 201 Like profiler, it requires that computeMatrix was run first to calculate the values.
202 202
203 We implemented vast optional parameters to optimize the visual output and we encourage you to play around with the min/max values 203 We implemented vast optional parameters to optimize the visual output and we encourage you to play around with the min/max values displayed in the heatmap as well as
204 displayed in the heatmap as well as with the different coloring options. The most powerful option is the k-means/hirarchichal clustering 204 with the different coloring options. The most powerful option is the k-means clustering where you simply need to indicate the number of
205 where you simply need to indicate the number of groups with similar read distributions that you expect and the algorithm will do the sorting for you. 205 groups with similar read distributions that you expect and the algorithm will do the sorting for you.
206
207 Do check the examples on our help page with step-by-step protocols: https://github.com/fidelram/deepTools/wiki/Example-workflows
206 208
207 209
208 .. image:: $PATH_TO_IMAGES/visual_hm_DmelPolII.png 210 .. image:: $PATH_TO_IMAGES/visual_hm_DmelPolII.png
209 :alt: Heatmap of RNA Polymerase II ChIP-seq 211 :alt: Heatmap of RNA Polymerase II ChIP-seq
210 212
211 213
212 You can find more details on the tool on the plotHeatmap doc page: https://deeptools.readthedocs.org/en/release-1.6/content/tools/plotHeatmap.html 214 You can find more details on the tool itself on the heatmapper wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-heatmapper
213 215
214 216
215 ----- 217 -----
216 218
217 @REFERENCES@ 219 @REFERENCES@