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comparison plotCorrelation.xml @ 65:9bee2c86eeb1 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
author iuc
date Mon, 25 May 2015 05:16:10 -0400
parents 1d932daaa198
children
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64:627004611e98 65:9bee2c86eeb1
1 <tool id="deeptools_plotCorrelation" name="plotCorrelation" version="@WRAPPER_VERSION@.0"> 1 <tool id="deeptools_plotCorrelation" name="plotCorrelation" version="@WRAPPER_VERSION@.0">
2 <description>creates a heatmap for a score associated to genomic regions</description> 2 <description>creates a heatmap for a score associated to genomic regions</description>
3 <expand macro="requirements"/>
4 <expand macro="stdio" />
5 <macros> 3 <macros>
6 <token name="@BINARY@">heatmapper</token> 4 <token name="@BINARY@">heatmapper</token>
7 <import>deepTools_macros.xml</import> 5 <import>deepTools_macros.xml</import>
8 </macros> 6 </macros>
7 <expand macro="requirements"/>
9 <command> 8 <command>
10 <![CDATA[ 9 <![CDATA[
11 heatmapper 10 heatmapper
12 11
13 --matrixFile $matrixFile 12 --matrixFile $matrixFile
74 --startLabel '$advancedOpt.startLabel' 73 --startLabel '$advancedOpt.startLabel'
75 --endLabel '$advancedOpt.endLabel' 74 --endLabel '$advancedOpt.endLabel'
76 --refPointLabel '$advancedOpt.referencePointLabel' 75 --refPointLabel '$advancedOpt.referencePointLabel'
77 --regionsLabel '$advancedOpt.regionsLabel' 76 --regionsLabel '$advancedOpt.regionsLabel'
78 77
79 #if str($advancedOpt.plotTitle.value) != "None": 78 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
80 --plotTitle '$advancedOpt.plotTitle' 79 --plotTitle '$advancedOpt.plotTitle'
81 #end if 80 #end if
82 81
83 $advancedOpt.onePlotPerGroup 82 $advancedOpt.onePlotPerGroup
84 83
108 <param name="zMin" type="float" value="" size="3" 107 <param name="zMin" type="float" value="" size="3"
109 label="Minimum value for the heatmap intensities. Leave empty for automatic values"/> 108 label="Minimum value for the heatmap intensities. Leave empty for automatic values"/>
110 <param name="zMax" type="float" value="" size="3" 109 <param name="zMax" type="float" value="" size="3"
111 label="Maximum value for the heatmap intensities. Leave empty for automatic values"/> 110 label="Maximum value for the heatmap intensities. Leave empty for automatic values"/>
112 111
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" 112 <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"/> 113 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" 114 <param name="yMax" type="float" value="" size="3"
123 label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values"/> 115 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" 116 <param name="xAxisLabel" type="text" value="distance from TSS (bp)" size="200"
140 <option value="colorbar only">colorbar only</option> 132 <option value="colorbar only">colorbar only</option>
141 </param> 133 </param>
142 134
143 <param name="startLabel" type="text" value="TSS" size="10" 135 <param name="startLabel" type="text" value="TSS" size="10"
144 label="Label for the region start" 136 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;." /> 137 help ="[only for scale-regions mode] Label shown in the plot for the start of the region.
138 Default is TSS (transcription start site), but could be changed to anything, e.g. &quot;peak start&quot;. (--startLabel)" />
146 <param name="endLabel" type="text" value="TES" size="10" 139 <param name="endLabel" type="text" value="TES" size="10"
147 label="Label for the region end" 140 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)."/> 141 help="[only for scale-regions mode] Label shown in the plot for the region end. (--endLabel)"/>
149 142
150 <param name="referencePointLabel" type="text" value="TSS" size="10" 143 <param name="referencePointLabel" type="text" value="TSS" size="10"
151 label="Reference point label" 144 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." /> 145 help ="[only for scale-regions mode] Label shown in the plot for the reference-point.
146 Default is the same as the reference point selected (e.g. TSS),
147 but could be anything, e.g. &quot;peak start&quot; etc (--referencePointLabel)" />
153 <param name="regionsLabel" type="text" value="genes" size="30" 148 <param name="regionsLabel" type="text" value="genes" size="30"
154 label="Labels for the regions plotted in the heatmap" 149 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."> 150 help="If more than one region is being plotted a list of labels
151 separated by comma and limited by quotes, is required. For example, label1, label2. (--regionsLabel)">
156 <sanitizer> 152 <sanitizer>
157 <valid initial="string.printable"> 153 <valid initial="string.printable">
158 </valid> 154 </valid>
159 </sanitizer> 155 </sanitizer>
160 </param> 156 </param>
161 <param name="plotTitle" type="text" value="" size="30" 157
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)" /> 158 <expand macro="plotTitle" />
163 <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" 159 <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue=""
164 label="Do one plot per group" 160 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."/> 161 help="When computeMatrix was used on more than one group of genes,
162 the average plots for all the groups will be drawn in one panel by default.
163 If this option is set, each group will get its own plot, stacked on top of each other. (--onePlotPerGroup)"/>
166 164
167 <expand macro="kmeans_clustering" /> 165 <expand macro="kmeans_clustering" />
168 </when> 166 </when>
169 </conditional> 167 </conditional>
170 </inputs> 168 </inputs>