Mercurial > repos > fabio > iwtomics

comparison plotwithscale.xml @ 56:9ceb3ffcd817 draft

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Uploaded 20170608
author fabio
date Thu, 08 Jun 2017 16:44:13 -0400
parents d49031ef33d5
children 7a806a3aeda1
comparison
equal deleted inserted replaced
55:7698612e1dc7 56:9ceb3ffcd817
130 </conditional> 130 </conditional>
131 </section> 131 </section>
132 </inputs> 132 </inputs>
133 133
134 <outputs> 134 <outputs>
135 <!--<data format="txt" name="stackerr" label="iwtomics.testandplot.stackerr.txt" from_work_dir="iwtomics.testandplot.stackerr.txt" />--> 135 <!--<data format="txt" name="stackerr" label="iwtomics.testandplot.stackerr.txt" from_work_dir="iwtomics.plotwithscale.stackerr.txt" />-->
136 <data format="txt" name="adjustedpvalue" label="${tool.name} on ${on_string}: Adjusted p-value" from_work_dir="iwtomics.testandplot.adjustedpvalue.txt" /> 136 <data format="txt" name="adjustedpvalue" label="${tool.name} on ${on_string}: Adjusted p-value" from_work_dir="iwtomics.plotwithscale.adjustedpvalue.txt" />
137 <data format="pdf" name="iwtomicsrespdf" label="${tool.name} on ${on_string}: Plotted Test Results" from_work_dir="iwtomics.testandplot.iwtomicstestresults.pdf" /> 137 <data format="pdf" name="iwtomicsrespdf" label="${tool.name} on ${on_string}: Plotted Test Results" from_work_dir="iwtomics.plotwithscale.iwtomicstestresults.pdf" />
138 <data format="pdf" name="iwtomicssumpdf" label="${tool.name} on ${on_string}: Summary Plot" from_work_dir="iwtomics.testandplot.summaryplot.pdf" /> 138 <data format="pdf" name="iwtomicssumpdf" label="${tool.name} on ${on_string}: Summary Plot" from_work_dir="iwtomics.plotwithscale.summaryplot.pdf" />
139 </outputs> 139 </outputs>
140
141 <tests>
142 <test>
143 <param name="rdata" value="output_testandplot/iwtomics.testandplot.RData" ftype="rdata" />
144 <param name="testids" value="output_testandplot/iwtomics.testandplot.tests.txt" ftype="tabular" />
145 <param name="featureids" value="output_testandplot/iwtomics.testandplot.selectedfeatures.txt" ftype="tabular" />
146 <repeat name="thresholdontestscale">
147 <param name="test" value="1" />
148 <param name="feature" value="1" />
149 <param name="scale" value="10" />
150 </repeat>
151 <repeat name="thresholdontestscale">
152 <param name="test" value="1,2,3" />
153 <param name="feature" value="2" />
154 <param name="scale" value="20" />
155 </repeat>
156 <param name="alpha" value="0.05" />
157 <param name="average" value="TRUE" />
158 <param name="size" value="TRUE" />
159 <param name="plottype" value="boxplot" />
160 <param name="prob0" value="0.25" />
161 <param name="prob1" value="0.5" />
162 <param name="prob2" value="0.75" />
163 <param name="groupby" value="feature" />
164 <param name="featurealphaplot" value="0.05" />
165 <param name="featureonlysig" value="TRUE" />
166 <output name="adjustedpvalue" file="output_plotwithscale/iwtomics.plotwithscale.adjustedpvalue.txt" compare="sim_size" />
167 <output name="iwtomicsrespdf" file="output_plotwithscale/iwtomics.plotwithscale.iwtomicstestresults.pdf" compare="sim_size" />
168 <output name="iwtomicssumpdf" file="output_plotwithscale/iwtomics.plotwithscale.summaryplot.pdf" compare="sim_size" />
169 </test>
170 </tests>
140 171
141 <help> 172 <help>
142 This tool allows to select the scale for the Interval-Wise Testing results. In particular, it returns the p-value curves 173 This tool allows to select the scale for the Interval-Wise Testing results. In particular, it returns the p-value curves
143 for the different tests performed at the selected scale, and it creates a graphical representation of the 174 for the different tests performed at the selected scale, and it creates a graphical representation of the
144 Interval-Wise Testing results and a summary plot (optional) at the selected scale. 175 Interval-Wise Testing results and a summary plot (optional) at the selected scale.