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comparison limma_voom.xml @ 8:87f26da8078e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
author iuc
date Tue, 15 May 2018 02:36:21 -0400
parents 5a722ae502b3
children a30e66a28451
comparison
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7:5a722ae502b3 8:87f26da8078e
1 <tool id="limma_voom" name="limma" version="3.34.9.3"> 1 <tool id="limma_voom" name="limma" version="3.34.9.4">
2 <description> 2 <description>
3 Perform differential expression with limma-voom or limma-trend 3 Perform differential expression with limma-voom or limma-trend
4 </description> 4 </description>
5 5
6 <requirements> 6 <requirements>
68 -y 68 -y
69 #elif $f.filt.cformat.samples.count_select == 'sample': 69 #elif $f.filt.cformat.samples.count_select == 'sample':
70 -s '$f.filt.cformat.samples.cntSampleReq' 70 -s '$f.filt.cformat.samples.cntSampleReq'
71 #end if 71 #end if
72 #end if 72 #end if
73 #end if
74
75 #if $out.plots:
76 -P $out.plots
73 #end if 77 #end if
74 78
75 #if $out.normCounts: 79 #if $out.normCounts:
76 -x 80 -x
77 #end if 81 #end if
200 <when value="no" /> 204 <when value="no" />
201 </conditional> 205 </conditional>
202 206
203 <!-- Contrasts --> 207 <!-- Contrasts -->
204 <repeat name="rep_contrast" title="Contrast" min="1" default="1"> 208 <repeat name="rep_contrast" title="Contrast" min="1" default="1">
205 <param name="contrast" type="text" label="Contrast of Interest" help="Names of two groups to compare separated by a hyphen e.g. Mut-WT. If the order is Mut-WT the fold changes in the results will be up/down in Mut relative to WT. If you have more than one contrast enter each separately using the Insert Contrast button below. For more info, see Chapter 8 in the limma User's guide: https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf"> 209 <param name="contrast" type="text" label="Contrast of Interest" help="Names of two groups to compare separated by a hyphen e.g. Mut-WT. If the order is Mut-WT the fold changes in the results will be up/down in Mut relative to WT. If you have more than one contrast enter each separately using the Insert Contrast button below. For differences between contrasts use e.g. (Mut1-WT)-(Mut2-WT). For more info, see Chapter 8 in the limma User's guide: https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf">
206 <validator type="empty_field" /> 210 <validator type="empty_field" />
207 <validator type="regex" message="Please only use letters, numbers or underscores">^[\w-]+$</validator> 211 <validator type="regex" message="Please only use letters, numbers or underscores">^[\(\w\)-]+$</validator>
208 </param> 212 </param>
209 </repeat> 213 </repeat>
210 214
211 <!-- Filter Options --> 215 <!-- Filter Options -->
212 <section name="f" expanded="false" title="Filter Low Counts"> 216 <section name="f" expanded="false" title="Filter Low Counts">
248 </conditional> 252 </conditional>
249 </section> 253 </section>
250 254
251 <!-- Output Options --> 255 <!-- Output Options -->
252 <section name="out" expanded="false" title="Output Options"> 256 <section name="out" expanded="false" title="Output Options">
257 <param name="plots" type="select" display="checkboxes" multiple="True" optional="True" label="Additional Plots" help="Select additional plots to output in the report and as PDFs">
258 <option value="d">Density Plots (if filtering)</option>
259 <option value="c">CpmsVsCounts Plots (if filtering on cpms)</option>
260 <option value="b">Box Plots (if normalising)</option>
261 <option value="x">MDS Extra (Dims 2vs3 and 3vs4)</option>
262 <option value="m">MD Plots for individual samples</option>
263 <option value="h">Heatmaps (top DE genes) </option>
264 <option value="s">Stripcharts (top DE genes)</option>
265 </param>
253 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false" 266 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
254 label="Output Normalised Counts Table?" 267 label="Output Normalised Counts Table?"
255 help="Output a file containing the normalised counts, these are in log2 counts per million (logCPM). Default: No"> 268 help="Output a file containing the normalised counts, these are in log2 counts per million (logCPM). Default: No">
256 </param> 269 </param>
257 <param name="rscript" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used will be provided as a text file in the output. Default: No"/> 270 <param name="rscript" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used will be provided as a text file in the output. Default: No"/>
276 <option value="none">None</option> 289 <option value="none">None</option>
277 </param> 290 </param>
278 <param name="treat" type="boolean" truevalue="1" falsevalue="0" checked="False" 291 <param name="treat" type="boolean" truevalue="1" falsevalue="0" checked="False"
279 label="Test significance relative to a fold-change threshold (TREAT)" 292 label="Test significance relative to a fold-change threshold (TREAT)"
280 help="If you want to apply a cut-off on a fold change the TREAT function can be used, see Help section below. Default: No"/> 293 help="If you want to apply a cut-off on a fold change the TREAT function can be used, see Help section below. Default: No"/>
281 <param name="topgenes" type="integer" value="10" min="0" 294 <param name="topgenes" type="integer" value="10" min="0" max="100"
282 label="Number of genes to highlight in Volcano plot and Heatmap" 295 label="Number of genes to highlight in Volcano plot, Heatmap and Stripcharts"
283 help="The top DE genes will be highlighted in the Volcano plot for each contrast and output in a heatmap PDF. Default: 10."/> 296 help="The top DE genes will be highlighted in the Volcano plot for each contrast and can be output in heatmap and stripchart PDFs (max 100). Default: 10."/>
284 <param name="normalisationOption" type="select" label="Normalisation Method" help="Default: TMM"> 297 <param name="normalisationOption" type="select" label="Normalisation Method" help="Default: TMM">
285 <option value="TMM" selected="true">TMM</option> 298 <option value="TMM" selected="true">TMM</option>
286 <option value="RLE">RLE</option> 299 <option value="RLE">RLE</option>
287 <option value="upperquartile">Upperquartile</option> 300 <option value="upperquartile">Upperquartile</option>
288 <option value="none">None (Don't normalise)</option> 301 <option value="none">None (Don't normalise)</option>