Mercurial > repos > fabio > iwtomics
comparison testandplot.xml @ 56:9ceb3ffcd817 draft
Uploaded 20170608
| author | fabio |
|---|---|
| date | Thu, 08 Jun 2017 16:44:13 -0400 |
| parents | d49031ef33d5 |
| children | 7a806a3aeda1 |
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| 55:7698612e1dc7 | 56:9ceb3ffcd817 |
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| 165 <data format="rdata" name="iwtomicsrdata" label="${tool.name} on ${on_string}: IWTomicsData Object with Test Results" from_work_dir="iwtomics.testandplot.RData" /> | 165 <data format="rdata" name="iwtomicsrdata" label="${tool.name} on ${on_string}: IWTomicsData Object with Test Results" from_work_dir="iwtomics.testandplot.RData" /> |
| 166 <data format="tabular" name="iwtomicstests" label="${tool.name} on ${on_string}: Test IDs" from_work_dir="iwtomics.testandplot.tests.txt" /> | 166 <data format="tabular" name="iwtomicstests" label="${tool.name} on ${on_string}: Test IDs" from_work_dir="iwtomics.testandplot.tests.txt" /> |
| 167 <data format="tabular" name="iwtomicsselectedfeatures" label="${tool.name} on ${on_string}: Feature IDs" from_work_dir="iwtomics.testandplot.selectedfeatures.txt" /> | 167 <data format="tabular" name="iwtomicsselectedfeatures" label="${tool.name} on ${on_string}: Feature IDs" from_work_dir="iwtomics.testandplot.selectedfeatures.txt" /> |
| 168 </outputs> | 168 </outputs> |
| 169 | 169 |
| 170 <tests> | |
| 171 <test> | |
| 172 <param name="rdata" value="output_loadandplot/iwtomics.loadandplot.RData" ftype="rdata" /> | |
| 173 <param name="regionids" value="output_loadandplot/iwtomics.loadandplot.regions.txt" ftype="tabular" /> | |
| 174 <param name="featureids" value="output_loadandplot/iwtomics.loadandplot.features.txt" ftype="tabular" /> | |
| 175 <repeat name="regions"> | |
| 176 <param name="region0" value="2" /> | |
| 177 <param name="region1" value="1" /> | |
| 178 </repeat> | |
| 179 <repeat name="regions"> | |
| 180 <param name="region0" value="3" /> | |
| 181 <param name="region1" value="1" /> | |
| 182 </repeat> | |
| 183 <repeat name="regions"> | |
| 184 <param name="region0" value="4" /> | |
| 185 <param name="region1" value="1" /> | |
| 186 </repeat> | |
| 187 <param name="featureslist" value="1,2" /> | |
| 188 <param name="statistics" value="mean" /> | |
| 189 <param name="permutations" value="1000" /> | |
| 190 <param name="alpha" value="0.05" /> | |
| 191 <param name="average" value="TRUE" /> | |
| 192 <param name="size" value="TRUE" /> | |
| 193 <param name="plottype" value="boxplot" /> | |
| 194 <param name="prob0" value="0.25" /> | |
| 195 <param name="prob1" value="0.5" /> | |
| 196 <param name="prob2" value="0.75" /> | |
| 197 <param name="groupby" value="feature" /> | |
| 198 <param name="featurealphaplot" value="0.05" /> | |
| 199 <param name="featureonlysig" value="TRUE" /> | |
| 200 <output name="adjustedpvaluematrix" file="output_testandplot/iwtomics.testandplot.adjustedpvalue.matrix.txt" compare="sim_size" /> | |
| 201 <output name="iwtomicsrespdf" file="output_testandplot/iwtomics.testandplot.iwtomicstestresults.pdf" compare="sim_size" /> | |
| 202 <output name="iwtomicssumpdf" file="output_testandplot/iwtomics.testandplot.summaryplot.pdf" compare="sim_size" /> | |
| 203 <output name="iwtomicsrdata" file="output_testandplot/iwtomics.testandplot.RData" compare="sim_size" /> | |
| 204 <output name="iwtomicstests" file="output_testandplot/iwtomics.testandplot.tests.txt" /> | |
| 205 <output name="iwtomicsselectedfeatures" file="output_testandplot/iwtomics.testandplot.selectedfeatures.txt" /> | |
| 206 </test> | |
| 207 </tests> | |
| 208 | |
| 170 <help> | 209 <help> |
| 171 This tool statistically evaluates differences in genomic features between groups of regions along the genome. | 210 This tool statistically evaluates differences in genomic features between groups of regions along the genome. |
| 172 In particular, it implements the Interval-Wise Testing for omics data, an extended version of the Interval-Wise | 211 In particular, it implements the Interval-Wise Testing for omics data, an extended version of the Interval-Wise |
| 173 Testing for functional data presented in Pini and Vantini (2017). It allows to perform multiple two sample permutation | 212 Testing for functional data presented in Pini and Vantini (2017). It allows to perform multiple two sample permutation |
| 174 tests between pairs of region datasets, on several features. It returns the adjusted p-value curves for every test | 213 tests between pairs of region datasets, on several features. It returns the adjusted p-value curves for every test |