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comparison heatmapper.xml @ 66:1dbd76a58d8b draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
author galaxyp
date Sat, 30 May 2015 13:55:46 -0400
parents 9bee2c86eeb1
children 5f7c4d7930e2
comparison
equal deleted inserted replaced
65:9bee2c86eeb1 66:1dbd76a58d8b
100 <option value="yes">yes</option> 100 <option value="yes">yes</option>
101 </param> 101 </param>
102 <when value="no" /> 102 <when value="no" />
103 <when value="yes"> 103 <when value="yes">
104 <param name="sortRegions" type="select" label="Sort regions" 104 <param name="sortRegions" type="select" label="Sort regions"
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."> 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)">
106 <option value="no">no ordering</option> 106 <option value="no">no ordering</option>
107 <option value="descend" selected="true">descending order</option> 107 <option value="descend" selected="true">descending order</option>
108 <option value="ascend">ascending order</option> 108 <option value="ascend">ascending order</option>
109 </param> 109 </param>
110 110
111 <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)">
112 <option value="mean" selected="true">mean</option> 113 <option value="mean" selected="true">mean</option>
113 <option value="median">median</option> 114 <option value="median">median</option>
114 <option value="min">min</option> 115 <option value="min">min</option>
115 <option value="max">max</option> 116 <option value="max">max</option>
116 <option value="sum">sum</option> 117 <option value="sum">sum</option>
117 <option value="region_length">region length</option> 118 <option value="region_length">region length</option>
118 </param> 119 </param>
119 120
120 <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)">
121 <option value="mean" selected="true">mean</option> 124 <option value="mean" selected="true">mean</option>
122 <option value="median">median</option> 125 <option value="median">median</option>
123 <option value="min">min</option> 126 <option value="min">min</option>
124 <option value="max">max</option> 127 <option value="max">max</option>
125 <option value="sum">sum</option> 128 <option value="sum">sum</option>
126 <option value="std">std</option> 129 <option value="std">std</option>
127 </param> 130 </param>
128 131
129 <param name="missingDataColor" type="text" value="black" optional="true" label="Missing data color" 132 <param name="missingDataColor" type="text" value="black" optional="true" label="Missing data color"
130 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." /> 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)" />
131 137
132 <expand macro="colormap" /> 138 <expand macro="colormap" />
133 139
134 <param name="zMin" type="float" value="" size="3" 140 <param name="zMin" type="float" value="" size="3"
135 label="Minimum value for the heatmap intensities. Leave empty for automatic values"/> 141 label="Minimum value for the heatmap intensities. Leave empty for automatic values" help="(--zMin)"/>
136 <param name="zMax" type="float" value="" size="3" 142 <param name="zMax" type="float" value="" size="3"
137 label="Maximum value for the heatmap intensities. Leave empty for automatic values"/> 143 label="Maximum value for the heatmap intensities. Leave empty for automatic values" help="(--zMax)"/>
138 <param name="yMin" type="float" value="" size="3" 144 <param name="yMin" type="float" value="" size="3"
139 label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values"/> 145 label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" help="(--yMin)"/>
140 <param name="yMax" type="float" value="" size="3" 146 <param name="yMax" type="float" value="" size="3"
141 label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values"/> 147 label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" help="(--yMax)"/>
142 <param name="xAxisLabel" type="text" value="distance from TSS (bp)" size="200" 148 <param name="xAxisLabel" type="text" value="distance from TSS (bp)" size="200"
143 label="Description for the x-axis label" /> 149 label="Description for the x-axis label" help="(--xAxisLabel)"/>
144 <param name="yAxisLabel" type="text" value="genes" size="30" 150 <param name="yAxisLabel" type="text" value="genes" size="30"
145 label="Description for the y-axis label for the top panel" /> 151 label="Description for the y-axis label for the top panel" help="(--yAxisLabel)"/>
146 152
147 <param name="heatmapWidth" type="float" value="7.5" min="1" max="100" 153 <param name="heatmapWidth" type="float" value="7.5" min="1" max="100"
148 label="Heatmap width in cm" help="The minimum value is 1 and the maximum is 100."/> 154 label="Heatmap width in cm" help="The minimum value is 1 and the maximum is 100."/>
149 <param name="heatmapHeight" type="float" value="25" min="3" max="100" 155 <param name="heatmapHeight" type="float" value="25" min="3" max="100"
150 label="Heatmap height in cm" help="The minimum value is 3 and the maximum is 100."/> 156 label="Heatmap height in cm" help="The minimum value is 3 and the maximum is 100."/>
151 157
152 <param name="whatToShow" type="select" label="What to show" 158 <param name="whatToShow" type="select" label="What to show"
153 help ="The default is to include a summary or profile plot on top of the heatmap and a heatmap colorbar."> 159 help ="The default is to include a summary or profile plot on top of the heatmap and a heatmap colorbar. (--whatToShow)">
154 <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>
155 <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>
156 <option value="heatmap only">heatmap only</option> 162 <option value="heatmap only">heatmap only</option>
157 <option value="heatmap and colorbar">heatmap and colorbar</option> 163 <option value="heatmap and colorbar">heatmap and colorbar</option>
158 <option value="colorbar only">colorbar only</option> 164 <option value="colorbar only">colorbar only</option>
159 </param> 165 </param>
160 166
161 <param name="startLabel" type="text" value="TSS" size="10" 167 <param name="startLabel" type="text" value="TSS" size="10"
162 label="Label for the region start" 168 label="Label for the region start"
163 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;." /> 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)" />
164 <param name="endLabel" type="text" value="TES" size="10" 170 <param name="endLabel" type="text" value="TES" size="10"
165 label="Label for the region end" 171 label="Label for the region end"
166 help="[only for scale-regions mode] Label shown in the plot for the region end. Default is TES (transcription end site)."/> 172 help="Only for scale-regions mode. Label shown in the plot for the region end. Default is TES (transcription end site). (--endLabel)"/>
167 173
168 <param name="referencePointLabel" type="text" value="TSS" size="10" 174 <param name="referencePointLabel" type="text" value="TSS" size="10"
169 label="Reference point label" 175 label="Reference point label"
170 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." /> 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)" />
171 <param name="regionsLabel" type="text" value="genes" size="30" 177 <param name="regionsLabel" type="text" value="genes" size="30"
172 label="Labels for the regions plotted in the heatmap" 178 label="Labels for the regions plotted in the heatmap"
173 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)">
174 <sanitizer> 180 <sanitizer>
175 <valid initial="string.printable"> 181 <valid initial="string.printable">
176 </valid> 182 </valid>
177 </sanitizer> 183 </sanitizer>
178 </param> 184 </param>
179 <expand macro="plotTitle" /> 185 <expand macro="plotTitle" />
180 <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" 186 <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue=""
181 label="Do one plot per group" 187 label="Do one plot per group"
182 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)"/>
183 190
184 <expand macro="kmeans_clustering" /> 191 <expand macro="kmeans_clustering" />
185 </when> 192 </when>
186 </conditional> 193 </conditional>
187 </inputs> 194 </inputs>
190 <expand macro="output_graphic_outputs" /> 197 <expand macro="output_graphic_outputs" />
191 <expand macro="output_save_matrix_values" /> 198 <expand macro="output_save_matrix_values" />
192 </outputs> 199 </outputs>
193 <tests> 200 <tests>
194 <test> 201 <test>
195 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_matrix" /> 202 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
196 <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="100" /> 203 <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="100" />
197 </test> 204 </test>
198 </tests> 205 </tests>
199 <help> 206 <help>
200 <![CDATA[ 207 <![CDATA[