Mercurial > repos > bgruening > deeptools_plot_profile

comparison plotProfiler.xml @ 3:c73c5d2c94b3 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c
author bgruening
date Wed, 09 Mar 2016 18:36:45 -0500
parents 466df17b2d67
children af7e456ef4f9
comparison
equal deleted inserted replaced
2:0b9bc8b4d0c1 3:c73c5d2c94b3
56 #if $advancedOpt.yMin: 56 #if $advancedOpt.yMin:
57 --yMin $advancedOpt.yMin 57 --yMin $advancedOpt.yMin
58 #end if 58 #end if
59 #if $advancedOpt.yMax: 59 #if $advancedOpt.yMax:
60 --yMax $advancedOpt.yMax 60 --yMax $advancedOpt.yMax
61 #end if
62
63 #if $advancedOpt.outFileNameData:
64 --outFileNameData "$output_outFileNameData"
61 #end if 65 #end if
62 66
63 @KMEANS_CLUSTERING@ 67 @KMEANS_CLUSTERING@
64 68
65 #end if 69 #end if
152 156
153 <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue="" 157 <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue=""
154 label="Make one plot per group of regions" 158 label="Make one plot per group of regions"
155 help="The default is to make one plot per bigWig file, i.e., all samples next to each other. Choosing this option will make one plot per group of regions. " /> 159 help="The default is to make one plot per bigWig file, i.e., all samples next to each other. Choosing this option will make one plot per group of regions. " />
156 160
161 <param argument="--outFileNameData" type="boolean" label="Save the data underlying the average profile"
162 help="This option will create an additional output file." />
157 163
158 <param argument="--yMin" type="float" value="" size="3" optional="true" 164 <param argument="--yMin" type="float" value="" size="3" optional="true"
159 label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values"/> 165 label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values"/>
160 <param argument="--yMax" type="float" value="" size="3" optional="true" 166 <param argument="--yMax" type="float" value="" size="3" optional="true"
161 label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" /> 167 label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" />
166 </conditional> 172 </conditional>
167 </inputs> 173 </inputs>
168 <outputs> 174 <outputs>
169 <expand macro="output_image_file_format" /> 175 <expand macro="output_image_file_format" />
170 <expand macro="output_graphic_outputs" /> 176 <expand macro="output_graphic_outputs" />
177
178 <data format="tabular" name="output_outFileNameData" label="${tool.name} on ${on_string}: Underlying data">
179 <filter>outFileNameData</filter>
180 </data>
181
171 </outputs> 182 </outputs>
172 <tests> 183 <tests>
173 <test> 184 <test>
174 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" /> 185 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
175 <output name="outFileName" file="profiler_result1.png" ftype="png" compare="sim_size" delta="4000" /> 186 <output name="outFileName" file="profiler_result1.png" ftype="png" compare="sim_size" delta="4000" />
176 </test> 187 </test>
177 <test> 188 <test>
178 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" /> 189 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
179 <param name="showAdvancedOpt" value="yes" /> 190 <param name="showAdvancedOpt" value="yes" />
180 <param name="showScaleRegionsOpt" value="yes" /> 191 <param name="showScaleRegionsOpt" value="yes" />
192 <param name="outFileNameData" value="True" />
181 <output name="outFileName" file="profiler_result2.png" ftype="png" compare="sim_size" delta="4000" /> 193 <output name="outFileName" file="profiler_result2.png" ftype="png" compare="sim_size" delta="4000" />
194 <output name="output_outFileNameData" file="profiler_result2.tabular" ftype="tabular" />
182 </test> 195 </test>
183 </tests> 196 </tests>
184 <help> 197 <help>
185 <![CDATA[ 198 <![CDATA[
186 199