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comparison edger.xml @ 7:47094543a5ff draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36
author iuc
date Thu, 08 Aug 2019 06:43:49 -0400
parents 7cf6248bc173
children ea85027d986c
comparison
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6:7cf6248bc173 7:47094543a5ff
1 <tool id="edger" name="edgeR" version="3.24.1"> 1 <tool id="edger" name="edgeR" version="3.24.1+galaxy1">
2 <description> 2 <description>
3 Perform differential expression of count data 3 Perform differential expression of count data
4 </description> 4 </description>
5 5
6 <requirements> 6 <requirements>
173 <when value="no" /> 173 <when value="no" />
174 </conditional> 174 </conditional>
175 175
176 <!-- Contrasts --> 176 <!-- Contrasts -->
177 <repeat name="rep_contrast" title="Contrast" min="1" default="1"> 177 <repeat name="rep_contrast" title="Contrast" min="1" default="1">
178 <param name="contrast" type="text" label="Contrast of Interest" help="Names of two groups to compare separated by a hyphen e.g. Mut-WT. If the order is Mut-WT the fold changes in the results will be up/down in Mut relative to WT. If you have more than one contrast enter each separately using the Insert Contrast button below. For more info, see Chapter 8 in the limma User's guide: https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf"> 178 <param name="contrast" type="text" label="Contrast of Interest" help="Names of two groups to compare separated by a hyphen e.g. Mut-WT. If the order is Mut-WT the fold changes in the results will be up/down in Mut relative to WT. If you have more than one contrast enter each separately using the Insert Contrast button below. For differences between contrasts use e.g. (MT.t1-MT.t0)-(WT.t1-WT.t0). For more info, see Chapter 8 in the limma User's guide: https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf or https://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf page 36 for nested comparisons.">
179 <validator type="empty_field" /> 179 <validator type="empty_field" />
180 <validator type="regex" message="Please only use letters, numbers or underscores">^[\w-]+$</validator> 180 <validator type="regex" message="Please only use letters, numbers, parentheses or underscores">^[\w\-()]+$</validator>
181 </param> 181 </param>
182 </repeat> 182 </repeat>
183 183
184 <!-- Filter Options --> 184 <!-- Filter Options -->
185 <section name="f" expanded="false" title="Filter Low Counts"> 185 <section name="f" expanded="false" title="Filter Low Counts">
307 <not_has_text text="likelihood ratio" /> 307 <not_has_text text="likelihood ratio" />
308 <not_has_text text="RData" /> 308 <not_has_text text="RData" />
309 </assert_contents> 309 </assert_contents>
310 </output> 310 </output>
311 </test> 311 </test>
312 <!-- Complex contrasts constructions -->
313 <test>
314 <param name="format" value="matrix" />
315 <param name="counts" value="matrix-complex.txt" />
316 <repeat name="rep_factor">
317 <param name="factorName" value="Genotype"/>
318 <param name="groupNames" value="MutA,MutA,MutA,MutB,MutB,MutB,WTA,WTA,WTA,WTB,WTB,WTB" />
319 </repeat>
320 <repeat name="rep_contrast">
321 <param name="contrast" value="(MutA-MutB)-(WTA-WTB)" />
322 </repeat>
323 <param name="normalisationOption" value="TMM" />
324 <output_collection name="outTables" count="1">
325 <element name="edgeR_(MutA-MutB)-(WTA-WTB)" ftype="tabular" >
326 <assert_contents>
327 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" />
328 <has_text_matching expression="11304.*15.53" />
329 </assert_contents>
330 </element>
331 </output_collection>
332 <output name="outReport" >
333 <assert_contents>
334 <has_text text="edgeR Analysis Output" />
335 <has_text text="quasi-likelihood" />
336 <not_has_text text="likelihood ratio" />
337 <not_has_text text="RData" />
338 </assert_contents>
339 </output>
340 </test>
312 <!-- Ensure annotation file input works --> 341 <!-- Ensure annotation file input works -->
313 <test> 342 <test>
314 <param name="format" value="matrix" /> 343 <param name="format" value="matrix" />
315 <param name="annoOpt" value="yes" /> 344 <param name="annoOpt" value="yes" />
316 <param name="geneanno" value="anno.txt" /> 345 <param name="geneanno" value="anno.txt" />