Mercurial > repos > bgruening > deeptools
comparison computeMatrix.xml @ 13:b4c5dd45778a draft
Uploaded
| author | bgruening |
|---|---|
| date | Mon, 16 Dec 2013 04:36:19 -0500 |
| parents | 135f3bae5c56 |
| children | 5ea8782d650c |
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| 12:aea72b24dea0 | 13:b4c5dd45778a |
|---|---|
| 118 <param name="referencePoint" type="select" label="The reference point for the plotting"> | 118 <param name="referencePoint" type="select" label="The reference point for the plotting"> |
| 119 <option value="TSS" selected="true">beginning of region (e.g. TSS)</option> | 119 <option value="TSS" selected="true">beginning of region (e.g. TSS)</option> |
| 120 <option value="TES">end of region (e.g. TES)</option> | 120 <option value="TES">end of region (e.g. TES)</option> |
| 121 <option value="center">center of region</option> | 121 <option value="center">center of region</option> |
| 122 </param> | 122 </param> |
| 123 | |
| 124 <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."/> |
| 125 <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."/> |
| 126 | |
| 127 <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."/> | 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."/> |
| 128 </when> | 126 </when> |
| 129 </conditional> | 127 </conditional> |
| 130 | 128 |
| 131 <expand macro="graphic_output_settings" /> | 129 <expand macro="input_graphic_output_settings"> |
| 130 <expand macro="input_save_matrix_values" /> | |
| 131 </expand> | |
| 132 | 132 |
| 133 <conditional name="advancedOpt" > | 133 <conditional name="advancedOpt" > |
| 134 <param name="showAdvancedOpt" type="select" label="Show advanced options" > | 134 <param name="showAdvancedOpt" type="select" label="Show advanced options" > |
| 135 <option value="no" selected="true">no</option> | 135 <option value="no" selected="true">no</option> |
| 136 <option value="yes">yes</option> | 136 <option value="yes">yes</option> |
| 173 | 173 |
| 174 </inputs> | 174 </inputs> |
| 175 <outputs> | 175 <outputs> |
| 176 <data format="bgzip" name="outFileName" label="${tool.name} on ${on_string}: Matrix" /> | 176 <data format="bgzip" name="outFileName" label="${tool.name} on ${on_string}: Matrix" /> |
| 177 <expand macro="output_graphic_outputs" /> | 177 <expand macro="output_graphic_outputs" /> |
| 178 <expand macro="output_save_matrix_values" /> | |
| 178 </outputs> | 179 </outputs> |
| 179 <!-- | 180 <!-- |
| 180 computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1 | 181 computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1 |
| 181 --> | 182 --> |
| 182 <tests> | 183 <tests> |