Mercurial > repos > bgruening > deeptools
annotate plotCorrelation.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 | 1d932daaa198 |
| children |
| rev | line source |
|---|---|
| 62 | 1 <tool id="deeptools_plotCorrelation" name="plotCorrelation" 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:
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diff
changeset
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7 <expand macro="requirements"/> |
| 62 | 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:
62
diff
changeset
|
78 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "": |
| 62 | 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="corData" 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 | |
| 105 <expand macro="colormap" /> | |
| 106 | |
| 107 <param name="zMin" type="float" value="" size="3" | |
| 108 label="Minimum value for the heatmap intensities. Leave empty for automatic values"/> | |
| 109 <param name="zMax" type="float" value="" size="3" | |
| 110 label="Maximum value for the heatmap intensities. Leave empty for automatic values"/> | |
| 111 | |
| 112 <param name="yMin" type="float" value="" size="3" | |
| 113 label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values"/> | |
| 114 <param name="yMax" type="float" value="" size="3" | |
| 115 label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values"/> | |
| 116 <param name="xAxisLabel" type="text" value="distance from TSS (bp)" size="200" | |
| 117 label="Description for the x-axis label" /> | |
| 118 <param name="yAxisLabel" type="text" value="genes" size="30" | |
| 119 label="Description for the y-axis label for the top panel" /> | |
| 120 | |
| 121 <param name="heatmapWidth" type="float" value="7.5" min="1" max="100" | |
| 122 label="Heatmap width in cm" help="The minimum value is 1 and the maximum is 100."/> | |
| 123 <param name="heatmapHeight" type="float" value="25" min="3" max="100" | |
| 124 label="Heatmap height in cm" help="The minimum value is 3 and the maximum is 100."/> | |
| 125 | |
| 126 <param name="whatToShow" type="select" label="What to show" | |
| 127 help ="The default is to include a summary or profile plot on top of the heatmap and a heatmap colorbar."> | |
| 128 <option value="plot, heatmap and colorbar" selected="true">summary plot, heatmap and colorbar</option> | |
| 129 <option value="plot and heatmap">summary plot and heatmap (no colorbar)</option> | |
| 130 <option value="heatmap only">heatmap only</option> | |
| 131 <option value="heatmap and colorbar">heatmap and colorbar</option> | |
| 132 <option value="colorbar only">colorbar only</option> | |
| 133 </param> | |
| 134 | |
| 135 <param name="startLabel" type="text" value="TSS" size="10" | |
| 136 label="Label for the region start" | |
|
65
9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
62
diff
changeset
|
137 help ="[only for scale-regions mode] Label shown in the plot for the start of the region. |
|
9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
62
diff
changeset
|
138 Default is TSS (transcription start site), but could be changed to anything, e.g. "peak start". (--startLabel)" /> |
| 62 | 139 <param name="endLabel" type="text" value="TES" size="10" |
| 140 label="Label for the region end" | |
|
65
9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
62
diff
changeset
|
141 help="[only for scale-regions mode] Label shown in the plot for the region end. (--endLabel)"/> |
| 62 | 142 |
| 143 <param name="referencePointLabel" type="text" value="TSS" size="10" | |
| 144 label="Reference point label" | |
|
65
9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
62
diff
changeset
|
145 help ="[only for scale-regions mode] Label shown in the plot for the reference-point. |
|
9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
62
diff
changeset
|
146 Default is the same as the reference point selected (e.g. TSS), |
|
9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
62
diff
changeset
|
147 but could be anything, e.g. "peak start" etc (--referencePointLabel)" /> |
| 62 | 148 <param name="regionsLabel" type="text" value="genes" size="30" |
| 149 label="Labels for the regions plotted in the heatmap" | |
|
65
9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
62
diff
changeset
|
150 help="If more than one region is being plotted a list of labels |
|
9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
62
diff
changeset
|
151 separated by comma and limited by quotes, is required. For example, label1, label2. (--regionsLabel)"> |
| 62 | 152 <sanitizer> |
| 153 <valid initial="string.printable"> | |
| 154 </valid> | |
| 155 </sanitizer> | |
| 156 </param> | |
|
65
9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
62
diff
changeset
|
157 |
|
9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
62
diff
changeset
|
158 <expand macro="plotTitle" /> |
|
9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
62
diff
changeset
|
159 <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" |
|
9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
62
diff
changeset
|
160 label="Do one plot per group" |
|
9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
62
diff
changeset
|
161 help="When computeMatrix was used on more than one group of genes, |
|
9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
62
diff
changeset
|
162 the average plots for all the groups will be drawn in one panel by default. |
|
9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
62
diff
changeset
|
163 If this option is set, each group will get its own plot, stacked on top of each other. (--onePlotPerGroup)"/> |
| 62 | 164 |
| 165 <expand macro="kmeans_clustering" /> | |
| 166 </when> | |
| 167 </conditional> | |
| 168 </inputs> | |
| 169 <outputs> | |
| 170 <expand macro="output_image_file_format" /> | |
| 171 <expand macro="output_graphic_outputs" /> | |
| 172 <expand macro="output_save_matrix_values" /> | |
| 173 </outputs> | |
| 174 <tests> | |
| 175 <test> | |
| 176 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="bgzip" /> | |
| 177 <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="100" /> | |
| 178 </test> | |
| 179 </tests> | |
| 180 <help> | |
| 181 <![CDATA[ | |
| 182 **What it does** | |
| 183 | |
| 184 Tool for visualizing a correlation using either bamCorrelate or | |
| 185 bigwigCorrelate. Pearson or Spearman methods are available to compute correlation | |
| 186 coefficients. Results can be saved into a heat map image or as multiple | |
| 187 scatter plots. Further output files are optional. | |
| 188 | |
| 189 ----- | |
| 190 | |
| 191 @REFERENCES@ | |
| 192 ]]> | |
| 193 </help> | |
| 194 <expand macro="citations" /> | |
| 195 </tool> |