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comparison volcanoplot.xml @ 7:a363ba287b88 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 589795c240ea48accbb89cd0c3263f8eba301125
author iuc
date Wed, 15 May 2024 10:06:58 +0000
parents 83c573f2e73c
children 2f557f6abbfb
comparison
equal deleted inserted replaced
6:83c573f2e73c 7:a363ba287b88
1 <tool id="volcanoplot" name="Volcano Plot" version="0.0.5"> 1 <tool id="volcanoplot" name="Volcano Plot" version="0.0.6" profile="20.09">
2 <description>create a volcano plot</description> 2 <description>create a volcano plot</description>
3 <edam_topics> 3 <edam_topics>
4 <edam_topic>topic_0092</edam_topic> 4 <edam_topic>topic_0092</edam_topic>
5 </edam_topics> 5 </edam_topics>
6 <edam_operations> 6 <edam_operations>
143 max.overlaps = Inf, 143 max.overlaps = Inf,
144 show.legend = FALSE) 144 show.legend = FALSE)
145 #end if 145 #end if
146 #end if 146 #end if
147 147
148 #if not '$plot_options.title' 148 #if $plot_options.title:
149 p <- p + ggtitle('$plot_options.title') 149 p <- p + ggtitle('$plot_options.title')
150 #end if 150 #end if
151 151
152 #if not '$plot_options.xlab' 152 #if $plot_options.xlab:
153 p <- p + xlab('$plot_options.xlab') 153 p <- p + xlab('$plot_options.xlab')
154 #end if 154 #end if
155 155
156 #if not '$plot_options.ylab' 156 #if $plot_options.ylab:
157 p <- p + ylab('$plot_options.ylab') 157 p <- p + ylab('$plot_options.ylab')
158 #end if 158 #end if
159 159
160 #if not '$plot_options.xmin' and '$plot_options.xmax' 160 #if $plot_options.xmin and $plot_options.xmax:
161 p <- p + xlim('$plot_options.xmin', '$plot_options.xmax') 161 p <- p + xlim($plot_options.xmin, $plot_options.xmax)
162 #end if 162 #end if
163 163
164 #if not '$plot_options.ymax' 164 #if $plot_options.ymax:
165 p <- p + ylim(0, '$plot_options.ymax') 165 p <- p + ylim(0, $plot_options.ymax)
166 #end if 166 #end if
167 167
168 # Set legend title 168 # Set legend title
169 #if not '$plot_options.legend' 169 #if $plot_options.legend:
170 p <- p + theme(legend.title = '$plot_options.legend') 170 p <- p + guides(color = guide_legend(title = '$plot_options.legend'))
171 #else 171 #else
172 p <- p + theme(legend.title = element_blank()) 172 p <- p + theme(legend.title = element_blank())
173 #end if 173 #end if
174 174
175 # Print plot 175 # Print plot
189 <param name="header" type="select" label="File has header?" help="Does the differentially expressed results file contain a header row. The tool can auto-detect by checking if the first row in the P value column is a number or not. Default: Auto-detect"> 189 <param name="header" type="select" label="File has header?" help="Does the differentially expressed results file contain a header row. The tool can auto-detect by checking if the first row in the P value column is a number or not. Default: Auto-detect">
190 <option value="auto" selected="True">Auto-detect</option> 190 <option value="auto" selected="True">Auto-detect</option>
191 <option value="yes">Yes</option> 191 <option value="yes">Yes</option>
192 <option value="no">No</option> 192 <option value="no">No</option>
193 </param> 193 </param>
194 <param name="fdr_col" type="data_column" data_ref="input" label="FDR (adjusted P value)" /> 194 <param name="fdr_col" type="data_column" data_ref="input" label="FDR (adjusted P value) column number" />
195 <param name="pval_col" type="data_column" data_ref="input" label="P value (raw)" /> 195 <param name="pval_col" type="data_column" data_ref="input" label="P value (raw) column number" />
196 <param name="lfc_col" type="data_column" data_ref="input" label="Log Fold Change" /> 196 <param name="lfc_col" type="data_column" data_ref="input" label="Log Fold Change column number" />
197 <param name="label_col" type="data_column" data_ref="input" label="Labels" /> 197 <param name="label_col" type="data_column" data_ref="input" label="Labels column number" />
198 <param name="signif_thresh" type="float" max="1" value="0.05" label="Significance threshold" help="Default: 0.05"/> 198 <param name="signif_thresh" type="float" max="1" value="0.05" label="Significance threshold" help="Default: 0.05"/>
199 <param name="lfc_thresh" type="float" value="0" label="LogFC threshold to colour" help="Default: 0"/> 199 <param name="lfc_thresh" type="float" value="0" label="LogFC threshold to colour" help="Default: 0"/>
200 <conditional name="labels"> 200 <conditional name="labels">
201 <param name="label_select" type="select" label="Points to label" help="Select to label significant points or input labels from file. Default: None"> 201 <param name="label_select" type="select" label="Points to label" help="Select to label significant points or input labels from file. Default: None">
202 <option value="none" selected="True">None</option> 202 <option value="none" selected="True">None</option>
258 <param name="lfc_thresh" value="0" /> 258 <param name="lfc_thresh" value="0" />
259 <param name="label_select" value="file"/> 259 <param name="label_select" value="file"/>
260 <param name="label_file" ftype="tabular" value="labels.tab" /> 260 <param name="label_file" ftype="tabular" value="labels.tab" />
261 <output name="plot"> 261 <output name="plot">
262 <assert_contents> 262 <assert_contents>
263 <has_size value= "933832" delta="1000" /> 263 <has_size value= "933830" delta="1000" />
264 </assert_contents> 264 </assert_contents>
265 </output> 265 </output>
266 </test> 266 </test>
267 <test expect_num_outputs="2"> 267 <test expect_num_outputs="2">
268 <!-- Ensure rscript output works --> 268 <!-- Ensure rscript output works -->
319 .. _Volcano plot: https://en.wikipedia.org/wiki/Volcano_plot_(statistics) 319 .. _Volcano plot: https://en.wikipedia.org/wiki/Volcano_plot_(statistics)
320 .. _blog post: https://gettinggeneticsdone.blogspot.com/2016/01/ 320 .. _blog post: https://gettinggeneticsdone.blogspot.com/2016/01/
321 321
322 ]]></help> 322 ]]></help>
323 <citations> 323 <citations>
324 <citation type="doi">doi.org/10.1007/978-3-319-24277-4</citation>
324 </citations> 325 </citations>
325 </tool> 326 </tool>