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comparison heatmapper.xml @ 30:5231f398d784 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
author bgruening
date Tue, 20 Oct 2015 14:43:12 -0400
parents 3a2aab18a217
children
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29:3a2aab18a217 30:5231f398d784
1 <tool id="deeptools_heatmapper" name="heatmapper" version="@WRAPPER_VERSION@.0"> 1 <tool id="deeptools_heatmapper" name="heatmapper" 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>
9 <![CDATA[
10 heatmapper 10 heatmapper
11 11
12 --matrixFile $matrixFile 12 --matrixFile $matrixFile
13 --outFileName $outFileName 13 --outFileName $outFileName
14 14
73 --startLabel '$advancedOpt.startLabel' 73 --startLabel '$advancedOpt.startLabel'
74 --endLabel '$advancedOpt.endLabel' 74 --endLabel '$advancedOpt.endLabel'
75 --refPointLabel '$advancedOpt.referencePointLabel' 75 --refPointLabel '$advancedOpt.referencePointLabel'
76 --regionsLabel '$advancedOpt.regionsLabel' 76 --regionsLabel '$advancedOpt.regionsLabel'
77 77
78 #if str($advancedOpt.plotTitle.value) != "None": 78 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
79 --plotTitle '$advancedOpt.plotTitle' 79 --plotTitle '$advancedOpt.plotTitle'
80 #end if 80 #end if
81 81
82 $advancedOpt.onePlotPerGroup 82 $advancedOpt.onePlotPerGroup
83 83
84 @kmeans_clusterin@ 84 @KMEANS_CLUSTERING@
85 85
86 #end if 86 #end if
87 ]]>
87 </command> 88 </command>
88 <inputs> 89 <inputs>
89 <param name="matrixFile" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/> 90 <param name="matrixFile" format="deeptools_compute_matrix_archive" type="data" label="Matrix file from the computeMatrix tool"/>
90 91
91 <expand macro="input_graphic_output_settings"> 92 <expand macro="input_graphic_output_settings">
92 <expand macro="input_image_file_format" /> 93 <expand macro="input_image_file_format" />
93 <expand macro="input_save_matrix_values" /> 94 <expand macro="input_save_matrix_values" />
94 </expand> 95 </expand>
99 <option value="yes">yes</option> 100 <option value="yes">yes</option>
100 </param> 101 </param>
101 <when value="no" /> 102 <when value="no" />
102 <when value="yes"> 103 <when value="yes">
103 <param name="sortRegions" type="select" label="Sort regions" 104 <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 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region. (--sortRegions)">
105 <option value="no">no ordering</option> 106 <option value="no">no ordering</option>
106 <option value="descend" selected="true">descending order</option> 107 <option value="descend" selected="true">descending order</option>
107 <option value="ascend">ascending order</option> 108 <option value="ascend">ascending order</option>
108 </param> 109 </param>
109 110
110 <param name="sortUsing" type="select" label="Method used for sorting" help="For each row the method is computed." > 111 <param name="sortUsing" type="select" label="Method used for sorting"
112 help="For each row the method is computed. (--sortUsing)">
111 <option value="mean" selected="true">mean</option> 113 <option value="mean" selected="true">mean</option>
112 <option value="median">median</option> 114 <option value="median">median</option>
113 <option value="min">min</option> 115 <option value="min">min</option>
114 <option value="max">max</option> 116 <option value="max">max</option>
115 <option value="sum">sum</option> 117 <option value="sum">sum</option>
116 <option value="region_length">region length</option> 118 <option value="region_length">region length</option>
117 </param> 119 </param>
118 120
119 <param name="averageTypeSummaryPlot" type="select" label="Type of statistic that should be plotted in the summary image above the heatmap"> 121 <param name="averageTypeSummaryPlot" type="select"
122 label="Type of statistic that should be plotted in the summary image above the heatmap"
123 help="(--averageTypeSummaryPlot)">
120 <option value="mean" selected="true">mean</option> 124 <option value="mean" selected="true">mean</option>
121 <option value="median">median</option> 125 <option value="median">median</option>
122 <option value="min">min</option> 126 <option value="min">min</option>
123 <option value="max">max</option> 127 <option value="max">max</option>
124 <option value="sum">sum</option> 128 <option value="sum">sum</option>
125 <option value="std">std</option> 129 <option value="std">std</option>
126 </param> 130 </param>
127 131
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." /> 132 <param name="missingDataColor" type="text" value="black" optional="true" label="Missing data color"
133 help="If 'Represent missing data as zero' is not set, such cases will be colored in black by default.
134 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).
135 Also color names can be used, see a list here: http://packages.python.org/ete2/reference/reference_svgcolors.html.
136 Alternatively colors can be specified using the #rrggbb notation. (--missingDataColor)" />
129 137
130 <expand macro="colormap" /> 138 <expand macro="colormap" />
131 139
132 <param name="zMin" type="float" value="" size="3" label="Minimum value for the heatmap intensities. Leave empty for automatic values" optional="true"/> 140 <param name="zMin" type="float" value="" size="3"
133 <param name="zMax" type="float" value="" size="3" label="Maximum value for the heatmap intensities. Leave empty for automatic values" optional="true"/> 141 label="Minimum value for the heatmap intensities. Leave empty for automatic values" help="(--zMin)"/>
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"/> 142 <param name="zMax" type="float" value="" size="3"
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"/> 143 label="Maximum value for the heatmap intensities. Leave empty for automatic values" help="(--zMax)"/>
136 144 <param name="yMin" type="float" value="" size="3"
137 <param name="xAxisLabel" type="text" value="distance from TSS (bp)" size="200" label="Description for the x-axis label" /> 145 label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" help="(--yMin)"/>
138 <param name="yAxisLabel" type="text" value="genes" size="30" label="Description for the y-axis label for the top panel" /> 146 <param name="yMax" type="float" value="" size="3"
139 147 label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" help="(--yMax)"/>
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."/> 148 <param name="xAxisLabel" type="text" value="distance from TSS (bp)" size="200"
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."/> 149 label="Description for the x-axis label" help="(--xAxisLabel)"/>
142 150 <param name="yAxisLabel" type="text" value="genes" size="30"
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."> 151 label="Description for the y-axis label for the top panel" help="(--yAxisLabel)"/>
152
153 <param name="heatmapWidth" type="float" value="7.5" min="1" max="100"
154 label="Heatmap width in cm" help="The minimum value is 1 and the maximum is 100."/>
155 <param name="heatmapHeight" type="float" value="25" min="3" max="100"
156 label="Heatmap height in cm" help="The minimum value is 3 and the maximum is 100."/>
157
158 <param name="whatToShow" type="select" label="What to show"
159 help ="The default is to include a summary or profile plot on top of the heatmap and a heatmap colorbar. (--whatToShow)">
144 <option value="plot, heatmap and colorbar" selected="true">summary plot, heatmap and colorbar</option> 160 <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> 161 <option value="plot and heatmap">summary plot and heatmap (no colorbar)</option>
146 <option value="heatmap only">heatmap only</option> 162 <option value="heatmap only">heatmap only</option>
147 <option value="heatmap and colorbar">heatmap and colorbar</option> 163 <option value="heatmap and colorbar">heatmap and colorbar</option>
148 <option value="colorbar only">colorbar only</option> 164 <option value="colorbar only">colorbar only</option>
149 </param> 165 </param>
150 166
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;." /> 167 <param name="startLabel" type="text" value="TSS" size="10"
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)."/> 168 label="Label for the region start"
153 169 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;. (--startLabel)" />
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." /> 170 <param name="endLabel" type="text" value="TES" size="10"
171 label="Label for the region end"
172 help="Only for scale-regions mode. Label shown in the plot for the region end. Default is TES (transcription end site). (--endLabel)"/>
173
174 <param name="referencePointLabel" type="text" value="TSS" size="10"
175 label="Reference point label"
176 help ="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. (--referencePointLabel)" />
155 <param name="regionsLabel" type="text" value="genes" size="30" 177 <param name="regionsLabel" type="text" value="genes" size="30"
156 label="Labels for the regions plotted in the heatmap" 178 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."> 179 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. (--regionsLabel)">
158 <sanitizer> 180 <sanitizer>
159 <valid initial="string.printable"> 181 <valid initial="string.printable">
160 </valid> 182 </valid>
161 </sanitizer> 183 </sanitizer>
162 </param> 184 </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." /> 185 <expand macro="plotTitle" />
164 <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" 186 <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue=""
165 label="Do one plot per group" 187 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."/> 188 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.
189 If this option is set, each group will get its own plot, stacked on top of each other. (--onePlotPerGroup)"/>
167 190
168 <expand macro="kmeans_clustering" /> 191 <expand macro="kmeans_clustering" />
169
170 </when> 192 </when>
171 </conditional> 193 </conditional>
172 </inputs> 194 </inputs>
173 <outputs> 195 <outputs>
174 <expand macro="output_image_file_format" /> 196 <expand macro="output_image_file_format" />
175 <expand macro="output_graphic_outputs" /> 197 <expand macro="output_graphic_outputs" />
176 <expand macro="output_save_matrix_values" /> 198 <expand macro="output_save_matrix_values" />
177 </outputs> 199 </outputs>
178 <tests> 200 <tests>
179 <test> 201 <test>
180 <param name="matrixFile" value="master.mat.gz" ftype="bgzip" /> 202 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
181 <output name="outFileName" file="master.png" ftype="png" compare="sim_size" delta="100" /> 203 <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="100" />
182 </test> 204 </test>
183 </tests> 205 </tests>
184 <help> 206 <help>
185 207 <![CDATA[
186 **What it does** 208 **What it does**
187 209
188 The heatmapper visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes. 210 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. 211 Like profiler, it requires that computeMatrix was run first to calculate the values.
190 212
203 225
204 226
205 ----- 227 -----
206 228
207 @REFERENCES@ 229 @REFERENCES@
208 230 ]]>
209 </help> 231 </help>
210 <expand macro="citations" /> 232 <expand macro="citations" />
211 </tool> 233 </tool>