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comparison plotCorrelation.xml @ 0:b2886915ce68 draft default tip

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author bgruening
date Tue, 10 Feb 2015 03:21:34 -0500
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1 <tool id="deeptools_plotCorrelation" name="plotCorrelation" version="@WRAPPER_VERSION@.0">
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 <![CDATA[
11 heatmapper
12
13 --matrixFile $matrixFile
14 --outFileName $outFileName
15
16 #if $output.showOutputSettings == "yes"
17 --plotFileFormat $output.outFileFormat
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 --plotFileFormat 'png'
31 #end if
32
33 #if $advancedOpt.showAdvancedOpt == "yes"
34 #if $advancedOpt.sortRegions:
35 --sortRegions '$advancedOpt.sortRegions'
36 #end if
37
38 #if $advancedOpt.sortUsing:
39 --sortUsing '$advancedOpt.sortUsing'
40 #end if
41
42 #if $advancedOpt.averageTypeSummaryPlot:
43 --averageTypeSummaryPlot '$advancedOpt.averageTypeSummaryPlot'
44 #end if
45
46 #if str($advancedOpt.missingDataColor.value) != "None":
47 --missingDataColor '$advancedOpt.missingDataColor'
48 #end if
49
50 --colorMap '$advancedOpt.colorMap'
51
52 #if str($advancedOpt.zMin).strip() != "":
53 --zMin $advancedOpt.zMin
54 #end if
55 #if $advancedOpt.zMax:
56 --zMax $advancedOpt.zMax
57 #end if
58
59 #if str($advancedOpt.yMin).strip() != "":
60 --yMin $advancedOpt.yMin
61 #end if
62 #if $advancedOpt.yMax:
63 --yMax $advancedOpt.yMax
64 #end if
65
66 --xAxisLabel '$advancedOpt.xAxisLabel'
67 --yAxisLabel '$advancedOpt.yAxisLabel'
68
69 --heatmapWidth $advancedOpt.heatmapWidth
70 --heatmapHeight $advancedOpt.heatmapHeight
71
72 --whatToShow '$advancedOpt.whatToShow'
73
74 --startLabel '$advancedOpt.startLabel'
75 --endLabel '$advancedOpt.endLabel'
76 --refPointLabel '$advancedOpt.referencePointLabel'
77 --regionsLabel '$advancedOpt.regionsLabel'
78
79 #if str($advancedOpt.plotTitle.value) != "None":
80 --plotTitle '$advancedOpt.plotTitle'
81 #end if
82
83 $advancedOpt.onePlotPerGroup
84
85 @KMEANS_CLUSTERING@
86
87 #end if
88 ]]>
89 </command>
90 <inputs>
91 <param name="corData" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/>
92
93 <expand macro="input_graphic_output_settings">
94 <expand macro="input_image_file_format" />
95 <expand macro="input_save_matrix_values" />
96 </expand>
97
98 <conditional name="advancedOpt" >
99 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
100 <option value="no" selected="true">no</option>
101 <option value="yes">yes</option>
102 </param>
103 <when value="no" />
104 <when value="yes">
105
106 <expand macro="colormap" />
107
108 <param name="zMin" type="float" value="" size="3"
109 label="Minimum value for the heatmap intensities. Leave empty for automatic values"/>
110 <param name="zMax" type="float" value="" size="3"
111 label="Maximum value for the heatmap intensities. Leave empty for automatic values"/>
112
113 <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
114 label="Plot the correlation value"
115 help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/>
116
117
118
119
120 <param name="yMin" type="float" value="" size="3"
121 label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values"/>
122 <param name="yMax" type="float" value="" size="3"
123 label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values"/>
124 <param name="xAxisLabel" type="text" value="distance from TSS (bp)" size="200"
125 label="Description for the x-axis label" />
126 <param name="yAxisLabel" type="text" value="genes" size="30"
127 label="Description for the y-axis label for the top panel" />
128
129 <param name="heatmapWidth" type="float" value="7.5" min="1" max="100"
130 label="Heatmap width in cm" help="The minimum value is 1 and the maximum is 100."/>
131 <param name="heatmapHeight" type="float" value="25" min="3" max="100"
132 label="Heatmap height in cm" help="The minimum value is 3 and the maximum is 100."/>
133
134 <param name="whatToShow" type="select" label="What to show"
135 help ="The default is to include a summary or profile plot on top of the heatmap and a heatmap colorbar.">
136 <option value="plot, heatmap and colorbar" selected="true">summary plot, heatmap and colorbar</option>
137 <option value="plot and heatmap">summary plot and heatmap (no colorbar)</option>
138 <option value="heatmap only">heatmap only</option>
139 <option value="heatmap and colorbar">heatmap and colorbar</option>
140 <option value="colorbar only">colorbar only</option>
141 </param>
142
143 <param name="startLabel" type="text" value="TSS" size="10"
144 label="Label for the region start"
145 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;." />
146 <param name="endLabel" type="text" value="TES" size="10"
147 label="Label for the region end"
148 help="[only for scale-regions mode] Label shown in the plot for the region end. Default is TES (transcription end site)."/>
149
150 <param name="referencePointLabel" type="text" value="TSS" size="10"
151 label="Reference point label"
152 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." />
153 <param name="regionsLabel" type="text" value="genes" size="30"
154 label="Labels for the regions plotted in the heatmap"
155 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.">
156 <sanitizer>
157 <valid initial="string.printable">
158 </valid>
159 </sanitizer>
160 </param>
161 <param name="plotTitle" type="text" value="" size="30"
162 label="Title of the plot" help="Title of the plot, to be printed on top of the generated image. Leave blank for no title. (--plotTitle)" />
163 <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue=""
164 label="Do one plot per group"
165 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."/>
166
167 <expand macro="kmeans_clustering" />
168 </when>
169 </conditional>
170 </inputs>
171 <outputs>
172 <expand macro="output_image_file_format" />
173 <expand macro="output_graphic_outputs" />
174 <expand macro="output_save_matrix_values" />
175 </outputs>
176 <tests>
177 <test>
178 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="bgzip" />
179 <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="100" />
180 </test>
181 </tests>
182 <help>
183 <![CDATA[
184 **What it does**
185
186 Tool for visualizing a correlation using either bamCorrelate or
187 bigwigCorrelate. Pearson or Spearman methods are available to compute correlation
188 coefficients. Results can be saved into a heat map image or as multiple
189 scatter plots. Further output files are optional.
190
191 -----
192
193 @REFERENCES@
194 ]]>
195 </help>
196 <expand macro="citations" />
197 </tool>