Mercurial > repos > bgruening > deeptools
annotate heatmapper.xml @ 65:9bee2c86eeb1 draft
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 | f3140d17939e |
| children | 1dbd76a58d8b |
| 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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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
61
diff
changeset
|
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 | |
|
65
9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
61
diff
changeset
|
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" | |
| 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."> | |
| 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 | |
| 111 <param name="sortUsing" type="select" label="Method used for sorting" help="For each row the method is computed." > | |
| 112 <option value="mean" selected="true">mean</option> | |
| 113 <option value="median">median</option> | |
| 114 <option value="min">min</option> | |
| 115 <option value="max">max</option> | |
| 116 <option value="sum">sum</option> | |
| 117 <option value="region_length">region length</option> | |
| 118 </param> | |
| 119 | |
| 120 <param name="averageTypeSummaryPlot" type="select" label="Type of statistic that should be plotted in the summary image above the heatmap"> | |
| 121 <option value="mean" selected="true">mean</option> | |
| 122 <option value="median">median</option> | |
| 123 <option value="min">min</option> | |
| 124 <option value="max">max</option> | |
| 125 <option value="sum">sum</option> | |
| 126 <option value="std">std</option> | |
| 127 </param> | |
| 128 | |
| 129 <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." /> | |
| 131 | |
| 132 <expand macro="colormap" /> | |
| 133 | |
| 134 <param name="zMin" type="float" value="" size="3" | |
| 135 label="Minimum value for the heatmap intensities. Leave empty for automatic values"/> | |
| 136 <param name="zMax" type="float" value="" size="3" | |
| 137 label="Maximum value for the heatmap intensities. Leave empty for automatic values"/> | |
| 138 <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"/> | |
| 140 <param name="yMax" type="float" value="" size="3" | |
| 141 label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values"/> | |
| 142 <param name="xAxisLabel" type="text" value="distance from TSS (bp)" size="200" | |
| 143 label="Description for the x-axis label" /> | |
| 144 <param name="yAxisLabel" type="text" value="genes" size="30" | |
| 145 label="Description for the y-axis label for the top panel" /> | |
| 146 | |
| 147 <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."/> | |
| 149 <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."/> | |
| 151 | |
| 152 <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."> | |
| 154 <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> | |
| 156 <option value="heatmap only">heatmap only</option> | |
| 157 <option value="heatmap and colorbar">heatmap and colorbar</option> | |
| 158 <option value="colorbar only">colorbar only</option> | |
| 159 </param> | |
| 160 | |
| 161 <param name="startLabel" type="text" value="TSS" size="10" | |
| 162 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. "peak start"." /> | |
| 164 <param name="endLabel" type="text" value="TES" size="10" | |
| 165 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)."/> | |
| 167 | |
| 168 <param name="referencePointLabel" type="text" value="TSS" size="10" | |
| 169 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. "peak start" etc." /> | |
| 171 <param name="regionsLabel" type="text" value="genes" size="30" | |
| 172 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."> | |
| 174 <sanitizer> | |
| 175 <valid initial="string.printable"> | |
| 176 </valid> | |
| 177 </sanitizer> | |
| 178 </param> | |
|
65
9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
61
diff
changeset
|
179 <expand macro="plotTitle" /> |
| 61 | 180 <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" |
| 181 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."/> | |
| 183 | |
| 184 <expand macro="kmeans_clustering" /> | |
| 185 </when> | |
| 186 </conditional> | |
| 187 </inputs> | |
| 188 <outputs> | |
| 189 <expand macro="output_image_file_format" /> | |
| 190 <expand macro="output_graphic_outputs" /> | |
| 191 <expand macro="output_save_matrix_values" /> | |
| 192 </outputs> | |
| 193 <tests> | |
| 194 <test> | |
|
65
9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
61
diff
changeset
|
195 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_matrix" /> |
| 61 | 196 <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="100" /> |
| 197 </test> | |
| 198 </tests> | |
| 199 <help> | |
| 200 <![CDATA[ | |
| 201 **What it does** | |
| 202 | |
| 203 The heatmapper visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes. | |
| 204 Like profiler, it requires that computeMatrix was run first to calculate the values. | |
| 205 | |
| 206 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 | |
| 207 with the different coloring options. The most powerful option is the k-means clustering where you simply need to indicate the number of | |
| 208 groups with similar read distributions that you expect and the algorithm will do the sorting for you. | |
| 209 | |
| 210 Do check the examples on our help page with step-by-step protocols: https://github.com/fidelram/deepTools/wiki/Example-workflows | |
| 211 | |
| 212 | |
| 213 .. image:: $PATH_TO_IMAGES/visual_hm_DmelPolII.png | |
| 214 :alt: Heatmap of RNA Polymerase II ChIP-seq | |
| 215 | |
| 216 | |
| 217 You can find more details on the tool itself on the heatmapper wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-heatmapper | |
| 218 | |
| 219 | |
| 220 ----- | |
| 221 | |
| 222 @REFERENCES@ | |
| 223 ]]> | |
| 224 </help> | |
| 225 <expand macro="citations" /> | |
| 226 </tool> |