Mercurial > repos > bgruening > deeptools
comparison heatmapper.xml @ 17:ef65d6b68ccc draft
Uploaded
| author | bgruening |
|---|---|
| date | Sat, 21 Dec 2013 14:26:06 -0500 |
| parents | b4c5dd45778a |
| children | 5ea8782d650c |
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| 16:16310f8b24d5 | 17:ef65d6b68ccc |
|---|---|
| 78 --plotTitle '$advancedOpt.plotTitle' | 78 --plotTitle '$advancedOpt.plotTitle' |
| 79 #end if | 79 #end if |
| 80 | 80 |
| 81 $advancedOpt.onePlotPerGroup | 81 $advancedOpt.onePlotPerGroup |
| 82 | 82 |
| 83 #if $advancedOpt.clustering.clustering_options == 'kmeans': | 83 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'yes': |
| 84 #if int($advancedOpt.clustering.k_kmeans) > 0: | 84 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans': |
| 85 --kmeans $advancedOpt.clustering.k_kmeans | 85 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0: |
| 86 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans | |
| 87 #end if | |
| 86 #end if | 88 #end if |
| 87 #end if | 89 #end if |
| 88 | 90 |
| 89 #end if | 91 #end if |
| 90 </command> | 92 </command> |
| 154 | 156 |
| 155 <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. "peak start"." /> | 157 <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. "peak start"." /> |
| 156 <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)."/> | 158 <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)."/> |
| 157 | 159 |
| 158 <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. "peak start" etc." /> | 160 <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. "peak start" etc." /> |
| 159 <param name="regionsLabel" type="text" value="genes" size="30" label="Labels for the regions plotted in the heatmap" 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"."/> | 161 <param name="regionsLabel" type="text" value="genes" size="30" |
| 162 label="Labels for the regions plotted in the heatmap" | |
| 163 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."> | |
| 164 <sanitizer> | |
| 165 <valid initial="string.printable"> | |
| 166 </valid> | |
| 167 </sanitizer> | |
| 168 </param> | |
| 160 <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." /> | 169 <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." /> |
| 161 <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" label="Do one plot per group" help="When the region file contains groups separated by "#", the default is to plot the averages for the distinct plots in one plot. If this option is set, each group will get its own plot, stacked on top of each other."/> | 170 <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" |
| 162 | 171 label="Do one plot per group" |
| 163 <conditional name="clustering"> | 172 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."/> |
| 164 <param name="clustering_options" type="select" label="Clustering algorithm"> | 173 |
| 165 <option value="none">No clustering</option> | 174 <conditional name="used_multiple_regions"> |
| 166 <option value="kmeans">Kmeans clustering</option> | 175 <param name="used_multiple_regions_options" type="select" |
| 176 label="Did you used multiple regions in ComputeMatrix?" | |
| 177 help="That option is only relevant if you want to cluster the results. Clustering is only available with one selected region in ComputeMatrix."> | |
| 178 <option value="no">No, I used only one region.</option> | |
| 179 <option value="yes">Yes, I used multiple regions.</option> | |
| 167 </param> | 180 </param> |
| 168 <when value="kmeans"> | 181 <when value="yes"> |
| 169 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" | 182 <conditional name="clustering"> |
| 170 help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. Only works for data that is not grouped, otherwise only the first group will be clustered. If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) if a cluster has very few members compared to the total number or regions. (default: None)."/> | 183 <param name="clustering_options" type="select" label="Clustering algorithm"> |
| 184 <option value="none">No clustering</option> | |
| 185 <option value="kmeans">Kmeans clustering</option> | |
| 186 </param> | |
| 187 <when value="kmeans"> | |
| 188 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" | |
| 189 help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. Only works for data that is not grouped, otherwise only the first group will be clustered. If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) if a cluster has very few members compared to the total number or regions. (default: None)."/> | |
| 190 </when> | |
| 191 <when value="none" /> | |
| 192 </conditional> | |
| 171 </when> | 193 </when> |
| 172 <when value="none" /> | 194 <when value="no" /> |
| 173 </conditional> | 195 </conditional> |
| 174 | |
| 175 | |
| 176 </when> | 196 </when> |
| 177 </conditional> | 197 </conditional> |
| 178 </inputs> | 198 </inputs> |
| 179 <outputs> | 199 <outputs> |
| 180 <expand macro="output_image_file_format" /> | 200 <expand macro="output_image_file_format" /> |