Mercurial > repos > bgruening > deeptools
annotate heatmapper.xml @ 72:c56a8c021315 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
| author | bgruening |
|---|---|
| date | Fri, 18 Sep 2015 10:03:38 -0400 |
| parents | 1dbd76a58d8b |
| children | 5f7c4d7930e2 |
| rev | line source |
|---|---|
| 61 | 1 <tool id="deeptools_heatmapper" name="heatmapper" version="@WRAPPER_VERSION@.0"> |
| 2 <description>creates a heatmap for a score associated to genomic regions</description> | |
| 3 <macros> | |
| 4 <token name="@BINARY@">heatmapper</token> | |
| 5 <import>deepTools_macros.xml</import> | |
| 6 </macros> | |
|
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7 <expand macro="requirements"/> |
| 61 | 8 <command> |
| 9 <![CDATA[ | |
| 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 '$advancedOpt.colorMap' | |
| 50 | |
| 51 #if str($advancedOpt.zMin).strip() != "": | |
| 52 --zMin $advancedOpt.zMin | |
| 53 #end if | |
| 54 #if $advancedOpt.zMax: | |
| 55 --zMax $advancedOpt.zMax | |
| 56 #end if | |
| 57 | |
| 58 #if str($advancedOpt.yMin).strip() != "": | |
| 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 | |
|
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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78 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "": |
| 61 | 79 --plotTitle '$advancedOpt.plotTitle' |
| 80 #end if | |
| 81 | |
| 82 $advancedOpt.onePlotPerGroup | |
| 83 | |
| 84 @KMEANS_CLUSTERING@ | |
| 85 | |
| 86 #end if | |
| 87 ]]> | |
| 88 </command> | |
| 89 <inputs> | |
| 90 <param name="matrixFile" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/> | |
| 91 | |
| 92 <expand macro="input_graphic_output_settings"> | |
| 93 <expand macro="input_image_file_format" /> | |
| 94 <expand macro="input_save_matrix_values" /> | |
| 95 </expand> | |
| 96 | |
| 97 <conditional name="advancedOpt" > | |
| 98 <param name="showAdvancedOpt" type="select" label="Show advanced options" > | |
| 99 <option value="no" selected="true">no</option> | |
| 100 <option value="yes">yes</option> | |
| 101 </param> | |
| 102 <when value="no" /> | |
| 103 <when value="yes"> | |
| 104 <param name="sortRegions" type="select" label="Sort regions" | |
|
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
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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)"> |
| 61 | 106 <option value="no">no ordering</option> |
| 107 <option value="descend" selected="true">descending order</option> | |
| 108 <option value="ascend">ascending order</option> | |
| 109 </param> | |
| 110 | |
|
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1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
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111 <param name="sortUsing" type="select" label="Method used for sorting" |
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1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
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112 help="For each row the method is computed. (--sortUsing)"> |
| 61 | 113 <option value="mean" selected="true">mean</option> |
| 114 <option value="median">median</option> | |
| 115 <option value="min">min</option> | |
| 116 <option value="max">max</option> | |
| 117 <option value="sum">sum</option> | |
| 118 <option value="region_length">region length</option> | |
| 119 </param> | |
| 120 | |
|
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1dbd76a58d8b
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121 <param name="averageTypeSummaryPlot" type="select" |
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1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
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122 label="Type of statistic that should be plotted in the summary image above the heatmap" |
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1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
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123 help="(--averageTypeSummaryPlot)"> |
| 61 | 124 <option value="mean" selected="true">mean</option> |
| 125 <option value="median">median</option> | |
| 126 <option value="min">min</option> | |
| 127 <option value="max">max</option> | |
| 128 <option value="sum">sum</option> | |
| 129 <option value="std">std</option> | |
| 130 </param> | |
| 131 | |
| 132 <param name="missingDataColor" type="text" value="black" optional="true" label="Missing data color" | |
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1dbd76a58d8b
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133 help="If 'Represent missing data as zero' is not set, such cases will be colored in black by default. |
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1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
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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). |
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1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
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135 Also color names can be used, see a list here: http://packages.python.org/ete2/reference/reference_svgcolors.html. |
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1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
galaxyp
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136 Alternatively colors can be specified using the #rrggbb notation. (--missingDataColor)" /> |
| 61 | 137 |
| 138 <expand macro="colormap" /> | |
| 139 | |
| 140 <param name="zMin" type="float" value="" size="3" | |
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1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
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141 label="Minimum value for the heatmap intensities. Leave empty for automatic values" help="(--zMin)"/> |
| 61 | 142 <param name="zMax" type="float" value="" size="3" |
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1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
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143 label="Maximum value for the heatmap intensities. Leave empty for automatic values" help="(--zMax)"/> |
| 61 | 144 <param name="yMin" type="float" value="" size="3" |
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1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
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145 label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" help="(--yMin)"/> |
| 61 | 146 <param name="yMax" type="float" value="" size="3" |
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1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
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147 label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" help="(--yMax)"/> |
| 61 | 148 <param name="xAxisLabel" type="text" value="distance from TSS (bp)" size="200" |
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1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
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149 label="Description for the x-axis label" help="(--xAxisLabel)"/> |
| 61 | 150 <param name="yAxisLabel" type="text" value="genes" size="30" |
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1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
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151 label="Description for the y-axis label for the top panel" help="(--yAxisLabel)"/> |
| 61 | 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" | |
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1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
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159 help ="The default is to include a summary or profile plot on top of the heatmap and a heatmap colorbar. (--whatToShow)"> |
| 61 | 160 <option value="plot, heatmap and colorbar" selected="true">summary plot, heatmap and colorbar</option> |
| 161 <option value="plot and heatmap">summary plot and heatmap (no colorbar)</option> | |
| 162 <option value="heatmap only">heatmap only</option> | |
| 163 <option value="heatmap and colorbar">heatmap and colorbar</option> | |
| 164 <option value="colorbar only">colorbar only</option> | |
| 165 </param> | |
| 166 | |
| 167 <param name="startLabel" type="text" value="TSS" size="10" | |
| 168 label="Label for the region start" | |
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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. "peak start". (--startLabel)" /> |
| 61 | 170 <param name="endLabel" type="text" value="TES" size="10" |
| 171 label="Label for the region end" | |
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172 help="Only for scale-regions mode. Label shown in the plot for the region end. Default is TES (transcription end site). (--endLabel)"/> |
| 61 | 173 |
| 174 <param name="referencePointLabel" type="text" value="TSS" size="10" | |
| 175 label="Reference point label" | |
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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. "peak start" etc. (--referencePointLabel)" /> |
| 61 | 177 <param name="regionsLabel" type="text" value="genes" size="30" |
| 178 label="Labels for the regions plotted in the heatmap" | |
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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)"> |
| 61 | 180 <sanitizer> |
| 181 <valid initial="string.printable"> | |
| 182 </valid> | |
| 183 </sanitizer> | |
| 184 </param> | |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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185 <expand macro="plotTitle" /> |
| 61 | 186 <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" |
| 187 label="Do one plot per group" | |
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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. |
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1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
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189 If this option is set, each group will get its own plot, stacked on top of each other. (--onePlotPerGroup)"/> |
| 61 | 190 |
| 191 <expand macro="kmeans_clustering" /> | |
| 192 </when> | |
| 193 </conditional> | |
| 194 </inputs> | |
| 195 <outputs> | |
| 196 <expand macro="output_image_file_format" /> | |
| 197 <expand macro="output_graphic_outputs" /> | |
| 198 <expand macro="output_save_matrix_values" /> | |
| 199 </outputs> | |
| 200 <tests> | |
| 201 <test> | |
|
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
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202 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" /> |
| 61 | 203 <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="100" /> |
| 204 </test> | |
| 205 </tests> | |
| 206 <help> | |
| 207 <![CDATA[ | |
| 208 **What it does** | |
| 209 | |
| 210 The heatmapper visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes. | |
| 211 Like profiler, it requires that computeMatrix was run first to calculate the values. | |
| 212 | |
| 213 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 | |
| 214 with the different coloring options. The most powerful option is the k-means clustering where you simply need to indicate the number of | |
| 215 groups with similar read distributions that you expect and the algorithm will do the sorting for you. | |
| 216 | |
| 217 Do check the examples on our help page with step-by-step protocols: https://github.com/fidelram/deepTools/wiki/Example-workflows | |
| 218 | |
| 219 | |
| 220 .. image:: $PATH_TO_IMAGES/visual_hm_DmelPolII.png | |
| 221 :alt: Heatmap of RNA Polymerase II ChIP-seq | |
| 222 | |
| 223 | |
| 224 You can find more details on the tool itself on the heatmapper wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-heatmapper | |
| 225 | |
| 226 | |
| 227 ----- | |
| 228 | |
| 229 @REFERENCES@ | |
| 230 ]]> | |
| 231 </help> | |
| 232 <expand macro="citations" /> | |
| 233 </tool> |