Mercurial > repos > bgruening > deeptools
comparison computeMatrix.xml @ 9:c53a73b8eef9 draft
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| author | bgruening |
|---|---|
| date | Tue, 10 Dec 2013 12:13:18 -0500 |
| parents | d957e25e18a3 |
| children | 135f3bae5c56 |
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| 8:1c5ed9126db6 | 9:c53a73b8eef9 |
|---|---|
| 113 </conditional> | 113 </conditional> |
| 114 </when> | 114 </when> |
| 115 | 115 |
| 116 <when value="reference-point"> | 116 <when value="reference-point"> |
| 117 <param name="referencePoint" type="select" label="The reference point for the plotting"> | 117 <param name="referencePoint" type="select" label="The reference point for the plotting"> |
| 118 <option value="TSS" selected="true">region start (TSS)</option> | 118 <option value="TSS" selected="true">beginning of region (e.g. TSS)</option> |
| 119 <option value="TES" selected="true">region end (TES)</option> | 119 <option value="TES">end of region (e.g. TES)</option> |
| 120 <option value="center" selected="true">center of the region</option> | 120 <option value="center">center of region</option> |
| 121 </param> | 121 </param> |
| 122 | |
| 122 <param name="nanAfterEnd" type="boolean" truevalue="--nanAfterEnd" falsevalue="" label="Discard any values after the region end" help="This is useful to visualize the region end when not using the scale-regions mode and when the reference-point is set to the TSS."/> | 123 <param name="nanAfterEnd" type="boolean" truevalue="--nanAfterEnd" falsevalue="" label="Discard any values after the region end" help="This is useful to visualize the region end when not using the scale-regions mode and when the reference-point is set to the TSS."/> |
| 123 <param name="beforeRegionStartLength" type="integer" value="1000" min="1" label="Distance upstream of the start site of the regions defined in the region file" help="If the regions are genes, this would be the distance upstream of the transcription start site."/> | 124 <param name="beforeRegionStartLength" type="integer" value="1000" min="1" label="Distance upstream of the start site of the regions defined in the region file" help="If the regions are genes, this would be the distance upstream of the transcription start site."/> |
| 124 | 125 |
| 125 <param name="afterRegionStartLength" type="integer" value="1000" min="1" label="Distance downstream of the end site of the given regions" help="If the regions are genes, this would be the distance downstream of the transcription end site."/> | 126 <param name="afterRegionStartLength" type="integer" value="1000" min="1" label="Distance downstream of the end site of the given regions" help="If the regions are genes, this would be the distance downstream of the transcription end site."/> |
| 126 </when> | 127 </when> |
| 127 </conditional> | 128 </conditional> |
| 128 | 129 |
| 129 <conditional name="output" > | 130 <conditional name="output" > |
| 130 <param name="showOutputSettings" type="select" label="Show additional output options" > | 131 <param name="showOutputSettings" type="select" label="Show additional output options" > |
| 131 <option value="no" selected="true">no</option> | 132 <option value="no" selected="true">no</option> |
| 132 <option value="yes">yes</option> | 133 <option value="yes">yes</option> |
| 133 </param> | 134 </param> |
| 134 <when value="no" /> | 135 <when value="no" /> |
| 135 <when value="yes"> | 136 <when value="yes"> |
| 136 <param name="saveData" type="boolean" label="Save the averages per matrix column into a text file" help="This corresponds to the underlying data used to plot a summary profile."/> | 137 <param name="saveData" type="boolean" label="Save the averages per matrix column into a text file" help="This corresponds to the underlying data used to plot a summary profile."/> |
| 137 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap" help="This matrix can easily be loaded into R or other programs."/> | 138 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap" help="This matrix can easily be loaded into R or other programs."/> |
| 138 <param name="saveSortedRegions" type="boolean" label="Save the regions after skiping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/> | 139 <param name="saveSortedRegions" type="boolean" label="Save the regions after skiping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/> |
| 139 </when> | 140 </when> |
| 140 </conditional> | 141 </conditional> |
| 141 | 142 |
| 142 <conditional name="advancedOpt" > | 143 <conditional name="advancedOpt" > |
| 143 <param name="showAdvancedOpt" type="select" label="Show advanced options" > | 144 <param name="showAdvancedOpt" type="select" label="Show advanced options" > |
| 144 <option value="no" selected="true">no</option> | 145 <option value="no" selected="true">no</option> |
| 180 </when> | 181 </when> |
| 181 </conditional> | 182 </conditional> |
| 182 | 183 |
| 183 </inputs> | 184 </inputs> |
| 184 <outputs> | 185 <outputs> |
| 185 <data format="bgzip" name="outFileName" label="${tool.name} on ${on_string}: matrix"> | 186 <data format="bgzip" name="outFileName" label="${tool.name} on ${on_string}: Matrix"> |
| 186 </data> | 187 </data> |
| 187 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: raw data"> | 188 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column"> |
| 188 <filter>(output['showOutputSettings'] == 'yes' and output['saveData'] == True)</filter> | 189 <filter> |
| 189 </data> | 190 (( |
| 190 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: matrix of values"> | 191 output['showOutputSettings'] == 'yes' and |
| 191 <filter>(output['showOutputSettings'] == 'yes' and output['saveMatrix'] == True)</filter> | 192 output['saveData'] is True |
| 193 )) | |
| 194 </filter> | |
| 195 </data> | |
| 196 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values"> | |
| 197 <filter> | |
| 198 (( | |
| 199 output['showOutputSettings'] == 'yes' and | |
| 200 output['saveMatrix'] is True | |
| 201 )) | |
| 202 </filter> | |
| 192 </data> | 203 </data> |
| 193 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions"> | 204 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions"> |
| 194 <filter>(output['showOutputSettings'] == 'yes' and output['saveSortedRegions'] == True)</filter> | 205 <filter> |
| 195 </data> | 206 (( |
| 207 output['showOutputSettings'] == 'yes' and | |
| 208 output['saveSortedRegions'] is True | |
| 209 )) | |
| 210 </filter> | |
| 211 </data> | |
| 196 </outputs> | 212 </outputs> |
| 197 <!-- | 213 <!-- |
| 198 computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1 | 214 computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1 |
| 199 --> | 215 --> |
| 200 <tests> | 216 <tests> |