Mercurial > repos > iuc > masigpro
comparison masigpro.xml @ 2:db04ba860dab draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 54ebbdebc9861af600371928cb9915095941c231
author | iuc |
---|---|
date | Thu, 13 Jul 2017 18:23:17 -0400 |
parents | cc96abdef027 |
children | 83f8b5ceff43 |
comparison
equal
deleted
inserted
replaced
1:cc96abdef027 | 2:db04ba860dab |
---|---|
1 <tool id="masigpro" name="maSigPro" version="1.49.3.0"> | 1 <tool id="masigpro" name="maSigPro" version="1.49.3.1"> |
2 <description>Significant Gene Expression Profile Differences in Time Course Gene Expression Data</description> | 2 <description>Significant Gene Expression Profile Differences in Time Course Gene Expression Data</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="1.49.3">bioconductor-masigpro</requirement> | 4 <requirement type="package" version="1.49.3">bioconductor-masigpro</requirement> |
5 <requirement type="package" version="1.3.2">r-optparse</requirement> | 5 <requirement type="package" version="1.3.2">r-optparse</requirement> |
6 <requirement type="package" version="4.4">sed</requirement> | 6 <requirement type="package" version="4.4">sed</requirement> |
68 --vars '$getSiggenes.vars' | 68 --vars '$getSiggenes.vars' |
69 --significant_intercept '$getSiggenes.significant_intercept' | 69 --significant_intercept '$getSiggenes.significant_intercept' |
70 #if $pdf.pdf_selector: | 70 #if $pdf.pdf_selector: |
71 --cluster_data $pdf.seeGenes.clusterData | 71 --cluster_data $pdf.seeGenes.clusterData |
72 -k $pdf.seeGenes.k | 72 -k $pdf.seeGenes.k |
73 --print_cluster $pdf.seeGenes.print_cluster | |
73 --cluster_method $pdf.seeGenes.clustering.clusterMethod | 74 --cluster_method $pdf.seeGenes.clustering.clusterMethod |
74 #if str($pdf.seeGenes.clustering.clusterMethod) == "hclust": | 75 #if str($pdf.seeGenes.clustering.clusterMethod) == "hclust": |
75 --distance $pdf.seeGenes.clustering.distance | 76 --distance $pdf.seeGenes.clustering.distance |
76 --agglo_method $pdf.seeGenes.clustering.aggloMethod | 77 --agglo_method $pdf.seeGenes.clustering.aggloMethod |
77 #end if | 78 #end if |
275 In case ‘data’ is a ‘get.siggenes’ object, this is given by | 276 In case ‘data’ is a ‘get.siggenes’ object, this is given by |
276 providing the element names of the list | 277 providing the element names of the list |
277 ‘c(sig.profiles,coefficients,t.score)’ of their list | 278 ‘c(sig.profiles,coefficients,t.score)’ of their list |
278 position (1,2 or 3)." /> | 279 position (1,2 or 3)." /> |
279 <param name="k" type="integer" label="Number of clusters for data partioning" value="9" /> | 280 <param name="k" type="integer" label="Number of clusters for data partioning" value="9" /> |
281 <param name="print_cluster" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" | |
282 label="Add cluster information to summary file?" | |
283 help="Adds columns with the cluster assignment for each gene." /> | |
280 <conditional name="clustering"> | 284 <conditional name="clustering"> |
281 <param name="clusterMethod" label="Cluster Method" type="select" | 285 <param name="clusterMethod" label="Cluster Method" type="select" |
282 help="clustering method for data partioning. Currently | 286 help="clustering method for data partioning. Currently |
283 ‘hclust’, ‘kmeans’ and ‘Mclust’ are supported"> | 287 ‘hclust’, ‘kmeans’ and ‘Mclust’ are supported"> |
284 <option selected="True" value="hclust">hclust</option> | 288 <option selected="True" value="hclust">hclust</option> |
311 </when> | 315 </when> |
312 <when value="kmeans"> | 316 <when value="kmeans"> |
313 <param name="iterMax" type="integer" label="Maximum number of iterations" value="500" | 317 <param name="iterMax" type="integer" label="Maximum number of iterations" value="500" |
314 help="Maximum number of iterations when ‘cluster.method’ is ‘kmeans’" /> | 318 help="Maximum number of iterations when ‘cluster.method’ is ‘kmeans’" /> |
315 </when> | 319 </when> |
320 <when value="Mclust"> | |
321 </when> | |
316 </conditional> | 322 </conditional> |
317 <param name="colorMode" label="Color Mode" type="select" help="Color scale for plotting profiles. Can be either ‘rainbow’ or ‘gray’"> | 323 <param name="colorMode" label="Color Mode" type="select" help="Color scale for plotting profiles. Can be either ‘rainbow’ or ‘gray’"> |
318 <option selected="True" value="rainbow">Rainbow</option> | 324 <option selected="True" value="rainbow">Rainbow</option> |
319 <option value="gray">Gray</option> | 325 <option value="gray">Gray</option> |
320 </param> | 326 </param> |
326 help="Graphical parameter maginfication to be used for x labels in plotting functions" /> | 332 help="Graphical parameter maginfication to be used for x labels in plotting functions" /> |
327 <param name="legend" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Add legend to plotting profiles?" | 333 <param name="legend" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Add legend to plotting profiles?" |
328 help="Indicating whether legend must be added when plotting profiles" /> | 334 help="Indicating whether legend must be added when plotting profiles" /> |
329 </section> | 335 </section> |
330 </when> | 336 </when> |
337 <when value="0"> | |
338 </when> | |
331 </conditional> | 339 </conditional> |
332 </inputs> | 340 </inputs> |
333 <outputs> | 341 <outputs> |
334 <data format="tabular" name="masigpro_out" label="maSigPro result file on ${on_string}"> | 342 <data format="txt" name="data_out" label="maSigPro data file on ${on_string}"> |
343 <filter> | |
344 (( | |
345 source['source_selector'] == 'advanced' and | |
346 source['enable_output'] == True | |
347 )) | |
348 </filter> | |
335 </data> | 349 </data> |
336 <data format="txt" name="edesign_out" label="maSigPro edesign file on ${on_string}"> | 350 <data format="txt" name="edesign_out" label="maSigPro edesign file on ${on_string}"> |
337 <filter> | 351 <filter> |
338 (( | 352 (( |
339 source['source_selector'] == 'advanced' and | 353 source['source_selector'] == 'advanced' and |
340 source['enable_output'] == True | 354 source['enable_output'] == True |
341 )) | 355 )) |
342 </filter> | 356 </filter> |
343 </data> | 357 </data> |
344 <data format="txt" name="data_out" label="maSigPro data file on ${on_string}"> | |
345 <filter> | |
346 (( | |
347 source['source_selector'] == 'advanced' and | |
348 source['enable_output'] == True | |
349 )) | |
350 </filter> | |
351 </data> | |
352 <data format="pdf" name="pdf_out" from_work_dir="Results.pdf" label="maSigPro Plot file on ${on_string}"> | 358 <data format="pdf" name="pdf_out" from_work_dir="Results.pdf" label="maSigPro Plot file on ${on_string}"> |
353 <filter> | 359 <filter> |
354 (( | 360 (( |
355 pdf['pdf_selector'] == True | 361 pdf['pdf_selector'] == True |
356 )) | 362 )) |
357 </filter> | 363 </filter> |
364 </data> | |
365 <data format="tabular" name="masigpro_out" label="maSigPro result file on ${on_string}"> | |
358 </data> | 366 </data> |
359 </outputs> | 367 </outputs> |
360 <tests> | 368 <tests> |
361 <test> | 369 <test> |
362 <param name="source_selector" value="advanced" /> | 370 <param name="source_selector" value="advanced" /> |
395 <param name="edesign" value="edesign_out.txt" /> | 403 <param name="edesign" value="edesign_out.txt" /> |
396 <param name="data" value="data_out.txt" /> | 404 <param name="data" value="data_out.txt" /> |
397 <output name="masigpro_out" file="masigpro_out.tab" /> | 405 <output name="masigpro_out" file="masigpro_out.tab" /> |
398 <output name="pdf_out" file="Results.pdf" /> | 406 <output name="pdf_out" file="Results.pdf" /> |
399 </test> | 407 </test> |
408 <test> | |
409 <param name="source_selector" value="defaults" /> | |
410 <param name="edesign" value="edesign_out.txt" /> | |
411 <param name="data" value="data_out.txt" /> | |
412 <param name="print_cluster" value="FALSE" /> | |
413 <output name="masigpro_out" file="masigpro_out_no_cluster.tab" /> | |
414 <output name="pdf_out" file="Results.pdf" /> | |
415 </test> | |
400 </tests> | 416 </tests> |
401 <help> | 417 <help> |
402 <![CDATA[ | 418 <![CDATA[ |
403 .. class:: infomark | 419 .. class:: infomark |
404 | 420 |