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author bgruening
date Thu, 14 Nov 2013 16:39:18 -0500
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1 <tool id="deeptools_heatmapper" name="heatmapper" version="1.0">
2 <description>creates a heatmap for a score associated to genomic regions</description>
3 <expand macro="requirements">
4 <requirement type="package" version="1.7.1">numpy</requirement>
5 <requirement type="package" version="1.2.1">matplotlib</requirement>
6 <requirement type="package" version="0.12.0">scipy</requirement>
7 </expand>
8 <macros>
9 <import>deepTools_macros.xml</import>
10 </macros>
11 <command>
12 heatmapper
13
14 --matrixFile $matrixFile
15 #if $output.showOutputSettings == "yes"
16 #set newoutFileName=str($outFileName)+"."+str($output.outFileFormat)
17 --outFileName $newoutFileName
18 #if $outFileNameData:
19 --outFileNameData '$outFileNameData'
20 #end if
21
22 #if $outFileNameMatrix:
23 --outFileNameMatrix '$outFileNameMatrix'
24 #end if
25
26 #if $outFileSortedRegions:
27 --outFileSortedRegions '$outFileSortedRegions'
28 #end if
29 #else
30 #set newoutFileName=str($outFileName)+".png"
31 --outFileName $newoutFileName
32 #end if
33
34 #if $advancedOpt.showAdvancedOpt == "yes"
35 #if $advancedOpt.sortRegions:
36 --sortRegions '$advancedOpt.sortRegions'
37 #end if
38
39 #if $advancedOpt.sortUsing:
40 --sortUsing '$advancedOpt.sortUsing'
41 #end if
42
43 #if $advancedOpt.averageTypeSummaryPlot:
44 --averageTypeSummaryPlot '$advancedOpt.averageTypeSummaryPlot'
45 #end if
46
47 #if str($advancedOpt.missingDataColor.value) != "None":
48 --missingDataColor '$advancedOpt.missingDataColor'
49 #end if
50
51 --colorMap '$advancedOpt.colorMap'
52
53 #if $advancedOpt.zMin:
54 --zMin $advancedOpt.zMin
55 #end if
56 #if $advancedOpt.zMax:
57 --zMax $advancedOpt.zMax
58 #end if
59
60 #if $advancedOpt.yMin:
61 --yMin $advancedOpt.yMin
62 #end if
63 #if $advancedOpt.yMax:
64 --yMax $advancedOpt.yMax
65 #end if
66
67 --xAxisLabel '$advancedOpt.xAxisLabel'
68 --yAxisLabel '$advancedOpt.yAxisLabel'
69
70 --heatmapWidth $advancedOpt.heatmapWidth
71 --heatmapHeight $advancedOpt.heatmapHeight
72
73 --whatToShow '$advancedOpt.whatToShow'
74
75 --startLabel '$advancedOpt.startLabel'
76 --endLabel '$advancedOpt.endLabel'
77 --refPointLabel '$advancedOpt.referencePointLabel'
78 --regionsLabel '$advancedOpt.regionsLabel'
79
80 #if str($advancedOpt.plotTitle.value) != "None":
81 --plotTitle '$advancedOpt.plotTitle'
82 #end if
83
84 $advancedOpt.onePlotPerGroup
85 #end if
86
87 ; mv $newoutFileName $outFileName
88 </command>
89 <inputs>
90 <param name="matrixFile" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/>
91
92 <expand macro="graphic_output_settings" />
93
94 <conditional name="advancedOpt" >
95 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
96 <option value="no" selected="true">no</option>
97 <option value="yes">yes</option>
98 </param>
99 <when value="no" />
100 <when value="yes">
101 <param name="sortRegions" type="select" label="Sort regions"
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.">
103 <option value="no">no ordering</option>
104 <option value="descend" selected="true">descending order</option>
105 <option value="ascend">ascending order</option>
106 </param>
107
108 <param name="sortUsing" type="select" label="Method used for sorting" help="For each row the method is computed." >
109 <option value="mean" selected="true">mean</option>
110 <option value="median">median</option>
111 <option value="min">min</option>
112 <option value="max">max</option>
113 <option value="sum">sum</option>
114 <option value="region_length">region length</option>
115 </param>
116
117 <param name="averageTypeSummaryPlot" type="select" label="Type of statistic that should be plotted in the summary image above the heatmap">
118 <option value="mean" selected="true">mean</option>
119 <option value="median">median</option>
120 <option value="min">min</option>
121 <option value="max">max</option>
122 <option value="sum">sum</option>
123 <option value="std">std</option>
124 </param>
125
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." />
127
128 <expand macro="colormap" />
129
130 <param name="zMin" type="float" value="" size="3" label="Minimum value for the heatmap intensities. Leave empty for automatic values" optional="true"/>
131 <param name="zMax" type="float" value="" size="3" label="Maximum value for the heatmap intensities. Leave empty for automatic values" optional="true"/>
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"/>
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"/>
134
135 <param name="xAxisLabel" type="text" value="distance from TSS (bp)" size="200" label="Description for the x-axis label" />
136 <param name="yAxisLabel" type="text" value="genes" size="30" label="Description for the y-axis label for the top panel" />
137
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."/>
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."/>
140
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.">
142 <option value="plot, heatmap and colorbar" selected="true">summary plot, heatmap and colorbar</option>
143 <option value="plot only">summary plot only</option>
144 <option value="plot and heatmap">summary plot and heatmap (no colorbar)</option>
145 <option value="heatmap only">heatmap only</option>
146 <option value="heatmap and colorbar">heatmap and colorbar</option>
147 <option value="colorbar only">colorbar only</option>
148 </param>
149
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;." />
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)."/>
152
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." />
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;."/>
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." />
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."/>
157
158
159 </when>
160 </conditional>
161
162 </inputs>
163 <outputs>
164 <data format="png" name="outFileName" label="${tool.name} image">
165 <change_format>
166 <when input="output.outFileFormat" value="pdf" format="pdf" />
167 <when input="output.outFileFormat" value="svg" format="svg" />
168 <when input="output.outFileFormat" value="eps" format="eps" />
169 <when input="output.outFileFormat" value="emf" format="emf" />
170 </change_format>
171 </data>
172 <data format="tabular" name="outFileNameData" label="${tool.name} raw plot data">
173 <filter>(output['showOutputSettings'] == 'yes' and output['saveData'] == True)</filter>
174 </data>
175 <data format="tabular" name="outFileNameMatrix" label="${tool.name} matrix of heatmap values">
176 <filter>(output['showOutputSettings'] == 'yes' and output['saveMatrix'] == True)</filter>
177 </data>
178 <data format="bed" name="outFileSortedRegions" label="${tool.name} sorted/filtered regions">
179 <filter>(output['showOutputSettings'] == 'yes' and output['saveSortedRegions'] == True)</filter>
180 </data>
181 </outputs>
182 <tests>
183 <test>
184 <param name="matrixFile" value="master.mat.gz" ftype="bgzip" />
185 <output name="outFileName" file="master.png" ftype="png" compare="sim_size" delta="100" />
186 </test>
187 </tests>
188 <help>
189
190 **What it does**
191
192 The heatmapper visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes.
193 Those values can be visualized individually along each of the regions provided by the user in INTERVAL or BED format.
194 In addition to the heatmap, an average profile plot is plotted on top of the heatmap (can be turned off by the user;
195 it can also be generated separately by the tool profiler).
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
197 with the different coloring options. If you would like to plot heatmaps for different groups of genomic regions individually,
198 e.g. one plot per chromosome, simply supply each group as an individual BED file.
199
200
201 .. image:: $PATH_TO_IMAGES/visual_hm_DmelPolII.png
202 :alt: Heatmap of RNA Polymerase II ChIP-seq
203
204
205 -----
206
207 .. class:: infomark
208
209 @REFERENCES@
210
211 </help>
212 </tool>