annotate heatmapper.xml @ 20:69ff16ba27bd draft

Uploaded
author bgruening
date Mon, 03 Feb 2014 15:47:26 -0500
parents 5ea8782d650c
children 8c452f37c896
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
18
5ea8782d650c Uploaded
bgruening
parents: 17
diff changeset
1 <tool id="deeptools_heatmapper" name="heatmapper" version="1.0.3">
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
2 <description>creates a heatmap for a score associated to genomic regions</description>
10
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
3 <expand macro="requirements"/>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
4 <expand macro="stdio" />
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
5 <macros>
18
5ea8782d650c Uploaded
bgruening
parents: 17
diff changeset
6 <token name="@BINARY@">heatmapper</token>
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
7 <import>deepTools_macros.xml</import>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
8 </macros>
10
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
9 <command>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
10 heatmapper
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
11
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
12 --matrixFile $matrixFile
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
13 --outFileName $outFileName
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
14
10
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
15 #if $output.showOutputSettings == "yes"
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
16 --plotFileFormat $output.outFileFormat
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
17 #if $outFileNameData:
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
18 --outFileNameData '$outFileNameData'
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
19 #end if
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
20
10
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
21 #if $outFileNameMatrix:
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
22 --outFileNameMatrix '$outFileNameMatrix'
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
23 #end if
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
24
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
25 #if $outFileSortedRegions:
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
26 --outFileSortedRegions '$outFileSortedRegions'
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
27 #end if
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
28 #else
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
29 --plotFileFormat 'png'
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
30 #end if
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
31
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
32 #if $advancedOpt.showAdvancedOpt == "yes"
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
33 #if $advancedOpt.sortRegions:
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
34 --sortRegions '$advancedOpt.sortRegions'
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
35 #end if
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
36
10
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
37 #if $advancedOpt.sortUsing:
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
38 --sortUsing '$advancedOpt.sortUsing'
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
39 #end if
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
40
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
41 #if $advancedOpt.averageTypeSummaryPlot:
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
42 --averageTypeSummaryPlot '$advancedOpt.averageTypeSummaryPlot'
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
43 #end if
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
44
10
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
45 #if str($advancedOpt.missingDataColor.value) != "None":
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
46 --missingDataColor '$advancedOpt.missingDataColor'
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
47 #end if
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
48
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
49 --colorMap '$advancedOpt.colorMap'
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
50
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
51 #if $advancedOpt.zMin:
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
52 --zMin $advancedOpt.zMin
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
53 #end if
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
54 #if $advancedOpt.zMax:
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
55 --zMax $advancedOpt.zMax
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
56 #end if
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
57
10
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
58 #if $advancedOpt.yMin:
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
59 --yMin $advancedOpt.yMin
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
60 #end if
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
61 #if $advancedOpt.yMax:
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
62 --yMax $advancedOpt.yMax
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
63 #end if
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
64
10
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
65 --xAxisLabel '$advancedOpt.xAxisLabel'
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
66 --yAxisLabel '$advancedOpt.yAxisLabel'
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
67
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
68 --heatmapWidth $advancedOpt.heatmapWidth
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
69 --heatmapHeight $advancedOpt.heatmapHeight
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
70
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
71 --whatToShow '$advancedOpt.whatToShow'
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
72
10
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
73 --startLabel '$advancedOpt.startLabel'
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
74 --endLabel '$advancedOpt.endLabel'
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
75 --refPointLabel '$advancedOpt.referencePointLabel'
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
76 --regionsLabel '$advancedOpt.regionsLabel'
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
77
10
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
78 #if str($advancedOpt.plotTitle.value) != "None":
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
79 --plotTitle '$advancedOpt.plotTitle'
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
80 #end if
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
81
10
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
82 $advancedOpt.onePlotPerGroup
12
aea72b24dea0 Uploaded
bgruening
parents: 11
diff changeset
83
18
5ea8782d650c Uploaded
bgruening
parents: 17
diff changeset
84 @kmeans_clusterin@
12
aea72b24dea0 Uploaded
bgruening
parents: 11
diff changeset
85
10
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
86 #end if
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
87 </command>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
88 <inputs>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
89 <param name="matrixFile" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/>
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
90
13
b4c5dd45778a Uploaded
bgruening
parents: 12
diff changeset
91 <expand macro="input_graphic_output_settings">
11
baf4283e2d7f Uploaded
bgruening
parents: 10
diff changeset
92 <expand macro="input_image_file_format" />
13
b4c5dd45778a Uploaded
bgruening
parents: 12
diff changeset
93 <expand macro="input_save_matrix_values" />
11
baf4283e2d7f Uploaded
bgruening
parents: 10
diff changeset
94 </expand>
10
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
95
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
96 <conditional name="advancedOpt" >
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
97 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
98 <option value="no" selected="true">no</option>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
99 <option value="yes">yes</option>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
100 </param>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
101 <when value="no" />
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
102 <when value="yes">
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
103 <param name="sortRegions" type="select" label="Sort regions"
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
104 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
105 <option value="no">no ordering</option>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
106 <option value="descend" selected="true">descending order</option>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
107 <option value="ascend">ascending order</option>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
108 </param>
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
109
10
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
110 <param name="sortUsing" type="select" label="Method used for sorting" help="For each row the method is computed." >
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
111 <option value="mean" selected="true">mean</option>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
112 <option value="median">median</option>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
113 <option value="min">min</option>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
114 <option value="max">max</option>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
115 <option value="sum">sum</option>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
116 <option value="region_length">region length</option>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
117 </param>
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
118
10
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
119 <param name="averageTypeSummaryPlot" type="select" label="Type of statistic that should be plotted in the summary image above the heatmap">
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
120 <option value="mean" selected="true">mean</option>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
121 <option value="median">median</option>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
122 <option value="min">min</option>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
123 <option value="max">max</option>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
124 <option value="sum">sum</option>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
125 <option value="std">std</option>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
126 </param>
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
127
10
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
128 <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." />
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
129
10
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
130 <expand macro="colormap" />
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
131
10
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
132 <param name="zMin" type="float" value="" size="3" label="Minimum value for the heatmap intensities. Leave empty for automatic values" optional="true"/>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
133 <param name="zMax" type="float" value="" size="3" label="Maximum value for the heatmap intensities. Leave empty for automatic values" optional="true"/>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
134 <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"/>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
135 <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"/>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
136
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
137 <param name="xAxisLabel" type="text" value="distance from TSS (bp)" size="200" label="Description for the x-axis label" />
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
138 <param name="yAxisLabel" type="text" value="genes" size="30" label="Description for the y-axis label for the top panel" />
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
139
10
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
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."/>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
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."/>
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
142
10
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
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.">
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
144 <option value="plot, heatmap and colorbar" selected="true">summary plot, heatmap and colorbar</option>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
145 <option value="plot and heatmap">summary plot and heatmap (no colorbar)</option>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
146 <option value="heatmap only">heatmap only</option>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
147 <option value="heatmap and colorbar">heatmap and colorbar</option>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
148 <option value="colorbar only">colorbar only</option>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
149 </param>
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
150
10
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
151 <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;." />
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
152 <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)."/>
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
153
10
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
154 <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." />
17
ef65d6b68ccc Uploaded
bgruening
parents: 13
diff changeset
155 <param name="regionsLabel" type="text" value="genes" size="30"
ef65d6b68ccc Uploaded
bgruening
parents: 13
diff changeset
156 label="Labels for the regions plotted in the heatmap"
ef65d6b68ccc Uploaded
bgruening
parents: 13
diff changeset
157 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.">
ef65d6b68ccc Uploaded
bgruening
parents: 13
diff changeset
158 <sanitizer>
ef65d6b68ccc Uploaded
bgruening
parents: 13
diff changeset
159 <valid initial="string.printable">
ef65d6b68ccc Uploaded
bgruening
parents: 13
diff changeset
160 </valid>
ef65d6b68ccc Uploaded
bgruening
parents: 13
diff changeset
161 </sanitizer>
ef65d6b68ccc Uploaded
bgruening
parents: 13
diff changeset
162 </param>
10
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
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." />
17
ef65d6b68ccc Uploaded
bgruening
parents: 13
diff changeset
164 <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue=""
ef65d6b68ccc Uploaded
bgruening
parents: 13
diff changeset
165 label="Do one plot per group"
ef65d6b68ccc Uploaded
bgruening
parents: 13
diff changeset
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."/>
12
aea72b24dea0 Uploaded
bgruening
parents: 11
diff changeset
167
18
5ea8782d650c Uploaded
bgruening
parents: 17
diff changeset
168 <expand macro="kmeans_clustering" />
5ea8782d650c Uploaded
bgruening
parents: 17
diff changeset
169
10
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
170 </when>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
171 </conditional>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
172 </inputs>
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
173 <outputs>
13
b4c5dd45778a Uploaded
bgruening
parents: 12
diff changeset
174 <expand macro="output_image_file_format" />
b4c5dd45778a Uploaded
bgruening
parents: 12
diff changeset
175 <expand macro="output_graphic_outputs" />
b4c5dd45778a Uploaded
bgruening
parents: 12
diff changeset
176 <expand macro="output_save_matrix_values" />
10
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
177 </outputs>
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
178 <tests>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
179 <test>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
180 <param name="matrixFile" value="master.mat.gz" ftype="bgzip" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
181 <output name="outFileName" file="master.png" ftype="png" compare="sim_size" delta="100" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
182 </test>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
183 </tests>
10
135f3bae5c56 Uploaded
bgruening
parents: 0
diff changeset
184 <help>
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
185
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
186 **What it does**
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
187
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
188 The heatmapper visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes.
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
189 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
190 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
191 it can also be generated separately by the tool profiler).
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
192 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
193 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
194 e.g. one plot per chromosome, simply supply each group as an individual BED file.
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
195
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
196
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
197 .. image:: $PATH_TO_IMAGES/visual_hm_DmelPolII.png
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
198 :alt: Heatmap of RNA Polymerase II ChIP-seq
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
199
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
200
18
5ea8782d650c Uploaded
bgruening
parents: 17
diff changeset
201 You can find more details in the `heatmapper wiki`_.
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
202
18
5ea8782d650c Uploaded
bgruening
parents: 17
diff changeset
203 .. _heatmapper wiki: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-heatmapper
5ea8782d650c Uploaded
bgruening
parents: 17
diff changeset
204
5ea8782d650c Uploaded
bgruening
parents: 17
diff changeset
205
5ea8782d650c Uploaded
bgruening
parents: 17
diff changeset
206 -----
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
207
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
208 @REFERENCES@
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
209
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
210 </help>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
211 </tool>