annotate heatmapper.xml @ 2:b5da81864541 draft

Uploaded
author bgruening
date Fri, 15 Nov 2013 11:02:32 -0500
parents d957e25e18a3
children 135f3bae5c56
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
1 <tool id="deeptools_heatmapper" name="heatmapper" version="1.0">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
2 <description>creates a heatmap for a score associated to genomic regions</description>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
3 <expand macro="requirements">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
4 <requirement type="package" version="1.7.1">numpy</requirement>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
5 <requirement type="package" version="1.2.1">matplotlib</requirement>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
6 <requirement type="package" version="0.12.0">scipy</requirement>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
7 </expand>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
8 <macros>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
9 <import>deepTools_macros.xml</import>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
10 </macros>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
11 <command>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
12 heatmapper
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
13
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
14 --matrixFile $matrixFile
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
15 #if $output.showOutputSettings == "yes"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
16 #set newoutFileName=str($outFileName)+"."+str($output.outFileFormat)
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
17 --outFileName $newoutFileName
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
18 #if $outFileNameData:
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
19 --outFileNameData '$outFileNameData'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
20 #end if
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
21
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
22 #if $outFileNameMatrix:
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
23 --outFileNameMatrix '$outFileNameMatrix'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
24 #end if
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
25
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
26 #if $outFileSortedRegions:
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
27 --outFileSortedRegions '$outFileSortedRegions'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
28 #end if
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
29 #else
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
30 #set newoutFileName=str($outFileName)+".png"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
31 --outFileName $newoutFileName
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
32 #end if
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
33
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
34 #if $advancedOpt.showAdvancedOpt == "yes"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
35 #if $advancedOpt.sortRegions:
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
36 --sortRegions '$advancedOpt.sortRegions'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
37 #end if
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
38
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
39 #if $advancedOpt.sortUsing:
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
40 --sortUsing '$advancedOpt.sortUsing'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
41 #end if
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
42
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
43 #if $advancedOpt.averageTypeSummaryPlot:
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
44 --averageTypeSummaryPlot '$advancedOpt.averageTypeSummaryPlot'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
45 #end if
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
46
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
47 #if str($advancedOpt.missingDataColor.value) != "None":
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
48 --missingDataColor '$advancedOpt.missingDataColor'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
49 #end if
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
50
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
51 --colorMap '$advancedOpt.colorMap'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
52
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
53 #if $advancedOpt.zMin:
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
54 --zMin $advancedOpt.zMin
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
55 #end if
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
56 #if $advancedOpt.zMax:
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
57 --zMax $advancedOpt.zMax
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
58 #end if
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
59
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
60 #if $advancedOpt.yMin:
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
61 --yMin $advancedOpt.yMin
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
62 #end if
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
63 #if $advancedOpt.yMax:
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
64 --yMax $advancedOpt.yMax
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
65 #end if
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
66
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
67 --xAxisLabel '$advancedOpt.xAxisLabel'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
68 --yAxisLabel '$advancedOpt.yAxisLabel'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
69
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
70 --heatmapWidth $advancedOpt.heatmapWidth
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
71 --heatmapHeight $advancedOpt.heatmapHeight
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
72
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
73 --whatToShow '$advancedOpt.whatToShow'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
74
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
75 --startLabel '$advancedOpt.startLabel'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
76 --endLabel '$advancedOpt.endLabel'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
77 --refPointLabel '$advancedOpt.referencePointLabel'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
78 --regionsLabel '$advancedOpt.regionsLabel'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
79
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
80 #if str($advancedOpt.plotTitle.value) != "None":
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
81 --plotTitle '$advancedOpt.plotTitle'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
82 #end if
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
83
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
84 $advancedOpt.onePlotPerGroup
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
85 #end if
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
86
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
87 ; mv $newoutFileName $outFileName
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
88 </command>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
89 <inputs>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
90 <param name="matrixFile" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
91
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
92 <expand macro="graphic_output_settings" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
93
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
94 <conditional name="advancedOpt" >
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
95 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
96 <option value="no" selected="true">no</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
97 <option value="yes">yes</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
98 </param>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
99 <when value="no" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
100 <when value="yes">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
101 <param name="sortRegions" type="select" label="Sort regions"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
102 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
103 <option value="no">no ordering</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
104 <option value="descend" selected="true">descending order</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
105 <option value="ascend">ascending order</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
106 </param>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
107
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
108 <param name="sortUsing" type="select" label="Method used for sorting" help="For each row the method is computed." >
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
109 <option value="mean" selected="true">mean</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
110 <option value="median">median</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
111 <option value="min">min</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
112 <option value="max">max</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
113 <option value="sum">sum</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
114 <option value="region_length">region length</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
115 </param>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
116
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
117 <param name="averageTypeSummaryPlot" type="select" label="Type of statistic that should be plotted in the summary image above the heatmap">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
118 <option value="mean" selected="true">mean</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
119 <option value="median">median</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
120 <option value="min">min</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
121 <option value="max">max</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
122 <option value="sum">sum</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
123 <option value="std">std</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
124 </param>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
125
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
126 <param name="missingDataColor" type="text" label="Missing data color" value="black" optional="true" help="If 'Represent missing data as zero' is not set, such cases will be colored in black by default. 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). Also color names can be used, see a list here: http://packages.python.org/ete2/reference/reference_svgcolors.html. Alternatively colors can be specified using the #rrggbb notation." />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
127
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
128 <expand macro="colormap" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
129
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
130 <param name="zMin" type="float" value="" size="3" label="Minimum value for the heatmap intensities. Leave empty for automatic values" optional="true"/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
131 <param name="zMax" type="float" value="" size="3" label="Maximum value for the heatmap intensities. Leave empty for automatic values" optional="true"/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
132 <param name="yMin" type="float" value="" size="3" label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" optional="true"/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
133 <param name="yMax" type="float" value="" size="3" label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" optional="true"/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
134
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
135 <param name="xAxisLabel" type="text" value="distance from TSS (bp)" size="200" label="Description for the x-axis label" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
136 <param name="yAxisLabel" type="text" value="genes" size="30" label="Description for the y-axis label for the top panel" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
137
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
138 <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."/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
139 <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."/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
140
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
141 <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.">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
142 <option value="plot, heatmap and colorbar" selected="true">summary plot, heatmap and colorbar</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
143 <option value="plot only">summary plot only</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
144 <option value="plot and heatmap">summary plot and heatmap (no colorbar)</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
145 <option value="heatmap only">heatmap only</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
146 <option value="heatmap and colorbar">heatmap and colorbar</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
147 <option value="colorbar only">colorbar only</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
148 </param>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
149
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
150 <param name="startLabel" type="text" value="TSS" size="10" label="Label for the region start" 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;." />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
151 <param name="endLabel" type="text" value="TES" size="10" label="Label for the region end" help="[only for scale-regions mode] Label shown in the plot for the region end. Default is TES (transcription end site)."/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
152
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
153 <param name="referencePointLabel" type="text" value="TSS" size="10" label="Reference point label" help ="[only for scale-regions mode] 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." />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
154 <param name="regionsLabel" type="text" value="genes" size="30" label="Labels for the regions plotted in the heatmap" help="If more than one region is being plotted a list of labels separated by comma and limited by quotes, is required. For example, &quot;label1, label2&quot;."/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
155 <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." />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
156 <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" label="Do one plot per group" help="When the region file contains groups separated by &quot;#&quot;, the default is to plot the averages for the distinct plots in one plot. If this option is set, each group will get its own plot, stacked on top of each other."/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
157
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
158
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
159 </when>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
160 </conditional>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
161
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
162 </inputs>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
163 <outputs>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
164 <data format="png" name="outFileName" label="${tool.name} image">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
165 <change_format>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
166 <when input="output.outFileFormat" value="pdf" format="pdf" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
167 <when input="output.outFileFormat" value="svg" format="svg" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
168 <when input="output.outFileFormat" value="eps" format="eps" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
169 <when input="output.outFileFormat" value="emf" format="emf" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
170 </change_format>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
171 </data>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
172 <data format="tabular" name="outFileNameData" label="${tool.name} raw plot data">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
173 <filter>(output['showOutputSettings'] == 'yes' and output['saveData'] == True)</filter>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
174 </data>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
175 <data format="tabular" name="outFileNameMatrix" label="${tool.name} matrix of heatmap values">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
176 <filter>(output['showOutputSettings'] == 'yes' and output['saveMatrix'] == True)</filter>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
177 </data>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
178 <data format="bed" name="outFileSortedRegions" label="${tool.name} sorted/filtered regions">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
179 <filter>(output['showOutputSettings'] == 'yes' and output['saveSortedRegions'] == True)</filter>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
180 </data>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
181 </outputs>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
182 <tests>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
183 <test>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
184 <param name="matrixFile" value="master.mat.gz" ftype="bgzip" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
185 <output name="outFileName" file="master.png" ftype="png" compare="sim_size" delta="100" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
186 </test>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
187 </tests>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
188 <help>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
189
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
190 **What it does**
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
191
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
192 The heatmapper visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes.
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
193 Those values can be visualized individually along each of the regions provided by the user in INTERVAL or BED format.
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
194 In addition to the heatmap, an average profile plot is plotted on top of the heatmap (can be turned off by the user;
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
195 it can also be generated separately by the tool profiler).
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
196 We implemented vast optional parameters and we encourage you to play around with the min/max values displayed in the heatmap as well as
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
197 with the different coloring options. If you would like to plot heatmaps for different groups of genomic regions individually,
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
198 e.g. one plot per chromosome, simply supply each group as an individual BED file.
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
199
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
200
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
201 .. image:: $PATH_TO_IMAGES/visual_hm_DmelPolII.png
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
202 :alt: Heatmap of RNA Polymerase II ChIP-seq
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
203
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
204
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
205 -----
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
206
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
207 .. class:: infomark
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
208
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
209 @REFERENCES@
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
210
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
211 </help>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
212 </tool>