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comparison heatmapper.xml @ 26:2ad3b027dfcd draft

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author bgruening
date Thu, 06 Feb 2014 06:40:05 -0500
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1 <tool id="deeptools_heatmapper" name="heatmapper" version="1.0.4">
2 <description>creates a heatmap for a score associated to genomic regions</description>
3 <expand macro="requirements"/>
4 <expand macro="stdio" />
5 <macros>
6 <token name="@BINARY@">heatmapper</token>
7 <import>deepTools_macros.xml</import>
8 </macros>
9 <command>
10 heatmapper
11
12 --matrixFile $matrixFile
13 --outFileName $outFileName
14
15 #if $output.showOutputSettings == "yes"
16 --plotFileFormat $output.outFileFormat
17 #if $outFileNameData:
18 --outFileNameData '$outFileNameData'
19 #end if
20
21 #if $outFileNameMatrix:
22 --outFileNameMatrix '$outFileNameMatrix'
23 #end if
24
25 #if $outFileSortedRegions:
26 --outFileSortedRegions '$outFileSortedRegions'
27 #end if
28 #else
29 --plotFileFormat 'png'
30 #end if
31
32 #if $advancedOpt.showAdvancedOpt == "yes"
33 #if $advancedOpt.sortRegions:
34 --sortRegions '$advancedOpt.sortRegions'
35 #end if
36
37 #if $advancedOpt.sortUsing:
38 --sortUsing '$advancedOpt.sortUsing'
39 #end if
40
41 #if $advancedOpt.averageTypeSummaryPlot:
42 --averageTypeSummaryPlot '$advancedOpt.averageTypeSummaryPlot'
43 #end if
44
45 #if str($advancedOpt.missingDataColor.value) != "None":
46 --missingDataColor '$advancedOpt.missingDataColor'
47 #end if
48
49 --colorMap '$advancedOpt.colorMap'
50
51 #if $advancedOpt.zMin:
52 --zMin $advancedOpt.zMin
53 #end if
54 #if $advancedOpt.zMax:
55 --zMax $advancedOpt.zMax
56 #end if
57
58 #if $advancedOpt.yMin:
59 --yMin $advancedOpt.yMin
60 #end if
61 #if $advancedOpt.yMax:
62 --yMax $advancedOpt.yMax
63 #end if
64
65 --xAxisLabel '$advancedOpt.xAxisLabel'
66 --yAxisLabel '$advancedOpt.yAxisLabel'
67
68 --heatmapWidth $advancedOpt.heatmapWidth
69 --heatmapHeight $advancedOpt.heatmapHeight
70
71 --whatToShow '$advancedOpt.whatToShow'
72
73 --startLabel '$advancedOpt.startLabel'
74 --endLabel '$advancedOpt.endLabel'
75 --refPointLabel '$advancedOpt.referencePointLabel'
76 --regionsLabel '$advancedOpt.regionsLabel'
77
78 #if str($advancedOpt.plotTitle.value) != "None":
79 --plotTitle '$advancedOpt.plotTitle'
80 #end if
81
82 $advancedOpt.onePlotPerGroup
83
84 @kmeans_clusterin@
85
86 #end if
87 </command>
88 <inputs>
89 <param name="matrixFile" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/>
90
91 <expand macro="input_graphic_output_settings">
92 <expand macro="input_image_file_format" />
93 <expand macro="input_save_matrix_values" />
94 </expand>
95
96 <conditional name="advancedOpt" >
97 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
98 <option value="no" selected="true">no</option>
99 <option value="yes">yes</option>
100 </param>
101 <when value="no" />
102 <when value="yes">
103 <param name="sortRegions" type="select" label="Sort regions"
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.">
105 <option value="no">no ordering</option>
106 <option value="descend" selected="true">descending order</option>
107 <option value="ascend">ascending order</option>
108 </param>
109
110 <param name="sortUsing" type="select" label="Method used for sorting" help="For each row the method is computed." >
111 <option value="mean" selected="true">mean</option>
112 <option value="median">median</option>
113 <option value="min">min</option>
114 <option value="max">max</option>
115 <option value="sum">sum</option>
116 <option value="region_length">region length</option>
117 </param>
118
119 <param name="averageTypeSummaryPlot" type="select" label="Type of statistic that should be plotted in the summary image above the heatmap">
120 <option value="mean" selected="true">mean</option>
121 <option value="median">median</option>
122 <option value="min">min</option>
123 <option value="max">max</option>
124 <option value="sum">sum</option>
125 <option value="std">std</option>
126 </param>
127
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." />
129
130 <expand macro="colormap" />
131
132 <param name="zMin" type="float" value="" size="3" label="Minimum value for the heatmap intensities. Leave empty for automatic values" optional="true"/>
133 <param name="zMax" type="float" value="" size="3" label="Maximum value for the heatmap intensities. Leave empty for automatic values" optional="true"/>
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"/>
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"/>
136
137 <param name="xAxisLabel" type="text" value="distance from TSS (bp)" size="200" label="Description for the x-axis label" />
138 <param name="yAxisLabel" type="text" value="genes" size="30" label="Description for the y-axis label for the top panel" />
139
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."/>
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."/>
142
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.">
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>
146 <option value="heatmap only">heatmap only</option>
147 <option value="heatmap and colorbar">heatmap and colorbar</option>
148 <option value="colorbar only">colorbar only</option>
149 </param>
150
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;." />
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)."/>
153
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." />
155 <param name="regionsLabel" type="text" value="genes" size="30"
156 label="Labels for the regions plotted in the heatmap"
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.">
158 <sanitizer>
159 <valid initial="string.printable">
160 </valid>
161 </sanitizer>
162 </param>
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." />
164 <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue=""
165 label="Do one plot per group"
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."/>
167
168 <expand macro="kmeans_clustering" />
169
170 </when>
171 </conditional>
172 </inputs>
173 <outputs>
174 <expand macro="output_image_file_format" />
175 <expand macro="output_graphic_outputs" />
176 <expand macro="output_save_matrix_values" />
177 </outputs>
178 <tests>
179 <test>
180 <param name="matrixFile" value="master.mat.gz" ftype="bgzip" />
181 <output name="outFileName" file="master.png" ftype="png" compare="sim_size" delta="100" />
182 </test>
183 </tests>
184 <help>
185
186 **What it does**
187
188 The heatmapper visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes.
189 Like profiler, it requires that computeMatrix was run first to calculate the values.
190
191 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
192 with the different coloring options. The most powerful option is the k-means clustering where you simply need to indicate the number of
193 groups with similar read distributions that you expect and the algorithm will do the sorting for you.
194
195 Do check the examples on our help page with step-by-step protocols: https://github.com/fidelram/deepTools/wiki/Example-workflows
196
197
198 .. image:: $PATH_TO_IMAGES/visual_hm_DmelPolII.png
199 :alt: Heatmap of RNA Polymerase II ChIP-seq
200
201
202 You can find more details on the tool itself on the heatmapper wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-heatmapper
203
204
205 -----
206
207 @REFERENCES@
208
209 </help>
210 </tool>