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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
author devteam
date Mon, 06 Jul 2020 18:11:20 +0000
parents aefbcaf15a94
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1:aefbcaf15a94 2:4bbfacecedd3
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="cummeRbund" name="cummeRbund" version="2.16.0"> 2 <tool id="cummeRbund" name="cummeRbund" version="@TOOL_VERSION@+galaxy1">
3 <description>visualize Cuffdiff output</description> 3 <description>visualize Cuffdiff output</description>
4 <macros> 4 <macros>
5 <import>cummeRbund_macros.xml</import> 5 <import>cummeRbund_macros.xml</import>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <requirement type="package" version="1.0.1">r-argparse</requirement> 8 <requirement type="package" version="1">fonts-conda-ecosystem</requirement>
9 <requirement type="package" version="2.16.0">bioconductor-cummerbund</requirement> 9 <requirement type="package" version="1.0.4">r-argparse</requirement>
10 <requirement type="package" version="3.4.1">r-base</requirement>
11 <requirement type="package" version="@TOOL_VERSION@">bioconductor-cummerbund</requirement>
10 </requirements> 12 </requirements>
11 <code file="cummeRbund_options.py"/> 13 <code file="cummeRbund_options.py"/>
12 <command detect_errors="aggressive"> 14 <command detect_errors="aggressive">
13 <![CDATA[ 15 <![CDATA[
14 #for i, p in enumerate($plots): 16 #for i, p in enumerate($plots):
15 Rscript $__tool_directory__/cummeRbund.R 17 Rscript --vanilla --slave '$__tool_directory__/cummeRbund.R'
16 --input "${input_database}" --width $p.width --height $p.height --type "${p.plot.type}" 18 --input '$input_database' --width $p.width --height $p.height --type "${p.plot.type}"
17 --outfile plot-${p.plot.type}-${i}.png 19 --outfile 'plot-${p.plot.type}-${i}.png'
18 #if $p.plot.type in ["density", "boxplot", "mds", "pca", "dendrogram"]: 20 #if $p.plot.type in ["density", "boxplot", "mds", "pca", "dendrogram"]:
19 $p.plot.replicates 21 $p.plot.replicates
20 #elif $p.plot.type == "scatter": 22 #elif $p.plot.type == "scatter":
21 $p.plot.smooth --x "$p.plot.x" --y "$p.plot.y" $p.plot.log10 23 $p.plot.smooth --x "$p.plot.x" --y "$p.plot.y" $p.plot.log10
22 #if $p.plot.multiple_genes.multiple_genes_selector == "yes": 24 #if $p.plot.multiple_genes.multiple_genes_selector == "yes":
23 --features $p.plot.multiple_genes.features --gene_selector 25 --features $p.plot.multiple_genes.features --gene_selector
24 #for gene in $p.plot.multiple_genes.genes: 26 #for gene in $p.plot.multiple_genes.genes:
25 --genes ${gene.gene_id} 27 --genes '$gene.gene_id'
26 #end for 28 #end for
27 #end if 29 #end if
28 #elif $p.plot.type == "maplot": 30 #elif $p.plot.type == "maplot":
29 --x "$p.plot.x" --y "$p.plot.y" $p.plot.count 31 --x "$p.plot.x" --y "$p.plot.y" $p.plot.count
30 #elif $p.plot.type == "volcano": 32 #elif $p.plot.type == "volcano":
31 --x "$p.plot.x" --y "$p.plot.y" 33 --x "$p.plot.x" --y "$p.plot.y"
32 #if $p.plot.multiple_genes.multiple_genes_selector == "yes": 34 #if $p.plot.multiple_genes.multiple_genes_selector == "yes":
33 --features $p.plot.multiple_genes.features --gene_selector 35 --features $p.plot.multiple_genes.features --gene_selector
34 #for gene in $p.plot.multiple_genes.genes: 36 #for gene in $p.plot.multiple_genes.genes:
35 --genes ${gene.gene_id} 37 --genes '$gene.gene_id'
36 #end for 38 #end for
37 #end if 39 #end if
38 #elif $p.plot.type == "heatmap": 40 #elif $p.plot.type == "heatmap":
39 --clustering "$p.plot.clustering" $p.plot.labcol $p.plot.labrow $p.plot.border --features $p.plot.features $p.plot.log10 41 --clustering "$p.plot.clustering" $p.plot.labcol $p.plot.labrow $p.plot.border --features $p.plot.features $p.plot.log10
40 #if len($p.plot.genes) > 0: 42 #if len($p.plot.genes) > 0:
41 --gene_selector 43 --gene_selector
42 #for gene in $p.plot.genes: 44 #for gene in $p.plot.genes:
43 --genes ${gene.gene_id} 45 --genes '$gene.gene_id'
44 #end for 46 #end for
45 #end if 47 #end if
46 #elif $p.plot.type == "cluster": 48 #elif $p.plot.type == "cluster":
47 --features $p.plot.features --k $p.plot.k --iter_max $p.plot.iter_max 49 --features $p.plot.features --k $p.plot.k --iter_max $p.plot.iter_max
48 #if len($p.plot.genes) > 0: 50 #if len($p.plot.genes) > 0:
49 #for gene in $p.plot.genes: 51 #for gene in $p.plot.genes:
50 --genes ${gene.gene_id} 52 --genes '$gene.gene_id'
51 #end for 53 #end for
52 #end if 54 #end if
53 #elif $p.plot.type in [ "expressionplot", "expressionbarplot" ]: 55 #elif $p.plot.type in [ "expressionplot", "expressionbarplot" ]:
54 #if $p.plot.type == "expressionplot": 56 #if $p.plot.type == "expressionplot":
55 $p.plot.draw_summary 57 $p.plot.draw_summary
56 #end if 58 #end if
57 --features $p.plot.features $p.plot.error_bars --genes ${p.plot.gene_id} $p.plot.replicates $p.plot.log10 59 --features $p.plot.features $p.plot.error_bars --genes '$p.plot.gene_id' $p.plot.replicates $p.plot.log10
58 #end if 60 #end if
59 #if $p.plot.type == "density": 61 #if $p.plot.type == "density":
60 $p.plot.log10 62 $p.plot.log10
61 #end if 63 #end if
62 > "${output}" 2>&1 ; 64 > '${output}' 2>&1 ;
63 #end for 65 #end for
64 ]]></command> 66 ]]></command>
65 <inputs> 67 <inputs>
66 <param name="input_database" type="data" format="sqlite" label="Select backend database (sqlite)" /> 68 <param name="input_database" type="data" format="sqlite" label="Select backend database (sqlite)" />
67 <repeat name="plots" title="Plots"> 69 <repeat name="plots" title="Plots">
173 <param name="type" value="maplot" /> 175 <param name="type" value="maplot" />
174 <param name="x" value="q1" /> 176 <param name="x" value="q1" />
175 <param name="y" value="q2" /> 177 <param name="y" value="q2" />
176 </conditional> 178 </conditional>
177 </repeat> 179 </repeat>
178 <output name="output" ftype="txt" file="maplot.txt" lines_diff="2"> 180 <output name="output" ftype="txt">
181 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
179 <discovered_dataset designation="maplot-0" ftype="png" file="maplot.png" /> 182 <discovered_dataset designation="maplot-0" ftype="png" file="maplot.png" />
180 </output> 183 </output>
181 </test> 184 </test>
182 <test> 185 <test>
183 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 186 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
188 <param name="type" value="scatter" /> 191 <param name="type" value="scatter" />
189 <param name="x" value="q1" /> 192 <param name="x" value="q1" />
190 <param name="y" value="q2" /> 193 <param name="y" value="q2" />
191 </conditional> 194 </conditional>
192 </repeat> 195 </repeat>
193 <output name="output" ftype="txt" file="scatter.txt" lines_diff="2"> 196 <output name="output" ftype="txt">
197 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
194 <discovered_dataset designation="scatter-0" ftype="png" file="scatter.png" /> 198 <discovered_dataset designation="scatter-0" ftype="png" file="scatter.png" />
195 </output> 199 </output>
196 </test> 200 </test>
197 <test> 201 <test>
198 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 202 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
201 <param name="height" value="960" /> 205 <param name="height" value="960" />
202 <conditional name="plot"> 206 <conditional name="plot">
203 <param name="type" value="dispersion" /> 207 <param name="type" value="dispersion" />
204 </conditional> 208 </conditional>
205 </repeat> 209 </repeat>
206 <output name="output" ftype="txt" file="dispersion.txt" lines_diff="2"> 210 <output name="output" ftype="txt">
211 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
207 <discovered_dataset designation="dispersion-0" ftype="png" file="dispersion.png" /> 212 <discovered_dataset designation="dispersion-0" ftype="png" file="dispersion.png" />
208 </output> 213 </output>
209 </test> 214 </test>
210 <test> 215 <test>
211 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 216 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
214 <param name="height" value="960" /> 219 <param name="height" value="960" />
215 <conditional name="plot"> 220 <conditional name="plot">
216 <param name="type" value="scatterMatrix" /> 221 <param name="type" value="scatterMatrix" />
217 </conditional> 222 </conditional>
218 </repeat> 223 </repeat>
219 <output name="output" ftype="txt" file="scatterMatrix.txt" lines_diff="2"> 224 <output name="output" ftype="txt">
225 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
220 <discovered_dataset designation="scatterMatrix-0" ftype="png" file="scatterMatrix.png" /> 226 <discovered_dataset designation="scatterMatrix-0" ftype="png" file="scatterMatrix.png" />
221 </output> 227 </output>
222 </test> 228 </test>
223 <test> 229 <test>
224 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 230 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
227 <param name="height" value="960" /> 233 <param name="height" value="960" />
228 <conditional name="plot"> 234 <conditional name="plot">
229 <param name="type" value="pca" /> 235 <param name="type" value="pca" />
230 </conditional> 236 </conditional>
231 </repeat> 237 </repeat>
232 <output name="output" ftype="txt" file="pca.txt" lines_diff="2"> 238 <output name="output" ftype="txt">
239 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
233 <discovered_dataset designation="pca-0" ftype="png" file="pca.png" /> 240 <discovered_dataset designation="pca-0" ftype="png" file="pca.png" />
234 </output> 241 </output>
235 </test> 242 </test>
236 <test> 243 <test>
237 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 244 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
242 <param name="type" value="expressionplot" /> 249 <param name="type" value="expressionplot" />
243 <param name="features" value="gene" /> 250 <param name="features" value="gene" />
244 <param name="gene_id" value="XLOC_000059" /> 251 <param name="gene_id" value="XLOC_000059" />
245 </conditional> 252 </conditional>
246 </repeat> 253 </repeat>
247 <output name="output" ftype="txt" file="expressionplot.txt" lines_diff="2"> 254 <output name="output" ftype="txt">
255 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
248 <discovered_dataset designation="expressionplot-0" ftype="png" file="expressionplot.png" /> 256 <discovered_dataset designation="expressionplot-0" ftype="png" file="expressionplot.png" />
249 </output> 257 </output>
250 </test> 258 </test>
251 <test> 259 <test>
252 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 260 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
257 <param name="features" value="gene" /> 265 <param name="features" value="gene" />
258 <param name="type" value="expressionbarplot" /> 266 <param name="type" value="expressionbarplot" />
259 <param name="gene_id" value="XLOC_000039" /> 267 <param name="gene_id" value="XLOC_000039" />
260 </conditional> 268 </conditional>
261 </repeat> 269 </repeat>
262 <output name="output" ftype="txt" file="expressionbarplot.txt" lines_diff="2"> 270 <output name="output" ftype="txt">
271 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
263 <discovered_dataset designation="expressionbarplot-0" ftype="png" file="expressionbarplot.png" /> 272 <discovered_dataset designation="expressionbarplot-0" ftype="png" file="expressionbarplot.png" />
264 </output> 273 </output>
265 </test> 274 </test>
266 <test> 275 <test>
267 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 276 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
276 <repeat name="genes"> 285 <repeat name="genes">
277 <param name="gene_id" value="XLOC_000037" /> 286 <param name="gene_id" value="XLOC_000037" />
278 </repeat> 287 </repeat>
279 </conditional> 288 </conditional>
280 </repeat> 289 </repeat>
281 <output name="output" ftype="txt" file="heatmap.txt" lines_diff="2"> 290 <output name="output" ftype="txt">
291 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
282 <discovered_dataset designation="heatmap-0" ftype="png" file="heatmap.png" /> 292 <discovered_dataset designation="heatmap-0" ftype="png" file="heatmap.png" />
283 </output> 293 </output>
284 </test> 294 </test>
285 <test> 295 <test>
286 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 296 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
289 <param name="height" value="960" /> 299 <param name="height" value="960" />
290 <conditional name="plot"> 300 <conditional name="plot">
291 <param name="type" value="density" /> 301 <param name="type" value="density" />
292 </conditional> 302 </conditional>
293 </repeat> 303 </repeat>
294 <output name="output" ftype="txt" file="density.txt" lines_diff="2"> 304 <output name="output" ftype="txt">
305 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
295 <discovered_dataset designation="density-0" ftype="png" file="density.png" /> 306 <discovered_dataset designation="density-0" ftype="png" file="density.png" />
296 </output> 307 </output>
297 </test> 308 </test>
298 <test> 309 <test>
299 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 310 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
302 <param name="height" value="960" /> 313 <param name="height" value="960" />
303 <conditional name="plot"> 314 <conditional name="plot">
304 <param name="type" value="dendrogram" /> 315 <param name="type" value="dendrogram" />
305 </conditional> 316 </conditional>
306 </repeat> 317 </repeat>
307 <output name="output" ftype="txt" file="dendrogram.txt" lines_diff="2"> 318 <output name="output" ftype="txt">
319 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
308 <discovered_dataset designation="dendrogram-0" ftype="png" file="dendrogram.png" /> 320 <discovered_dataset designation="dendrogram-0" ftype="png" file="dendrogram.png" />
309 </output> 321 </output>
310 </test> 322 </test>
311 <test> 323 <test>
312 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 324 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
317 <param name="type" value="volcano" /> 329 <param name="type" value="volcano" />
318 <param name="x" value="q1" /> 330 <param name="x" value="q1" />
319 <param name="y" value="q2" /> 331 <param name="y" value="q2" />
320 </conditional> 332 </conditional>
321 </repeat> 333 </repeat>
322 <output name="output" ftype="txt" file="volcano.txt" lines_diff="2"> 334 <output name="output" ftype="txt">
335 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
323 <discovered_dataset designation="volcano-0" ftype="png" file="volcano.png" /> 336 <discovered_dataset designation="volcano-0" ftype="png" file="volcano.png" />
324 </output> 337 </output>
325 </test> 338 </test>
326 <test> 339 <test>
327 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 340 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
330 <param name="height" value="960" /> 343 <param name="height" value="960" />
331 <conditional name="plot"> 344 <conditional name="plot">
332 <param name="type" value="boxplot" /> 345 <param name="type" value="boxplot" />
333 </conditional> 346 </conditional>
334 </repeat> 347 </repeat>
335 <output name="output" ftype="txt" file="boxplot.txt" lines_diff="2"> 348 <output name="output" ftype="txt">
349 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
336 <discovered_dataset designation="boxplot-0" ftype="png" file="boxplot.png" /> 350 <discovered_dataset designation="boxplot-0" ftype="png" file="boxplot.png" />
337 </output> 351 </output>
338 </test> 352 </test>
339 <test> 353 <test>
340 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 354 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
343 <param name="height" value="960" /> 357 <param name="height" value="960" />
344 <conditional name="plot"> 358 <conditional name="plot">
345 <param name="type" value="fpkmSCV" /> 359 <param name="type" value="fpkmSCV" />
346 </conditional> 360 </conditional>
347 </repeat> 361 </repeat>
348 <output name="output" ftype="txt" file="fpkmSCV.txt" lines_diff="2"> 362 <output name="output" ftype="txt">
363 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
349 <discovered_dataset designation="fpkmSCV-0" ftype="png" file="fpkmSCV.png" /> 364 <discovered_dataset designation="fpkmSCV-0" ftype="png" file="fpkmSCV.png" />
350 </output> 365 </output>
351 </test> 366 </test>
352 </tests> 367 </tests>
353 <help><![CDATA[ 368 <help><![CDATA[