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comparison masigpro.xml @ 2:db04ba860dab draft

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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