Mercurial > repos > iuc > mothur_cluster_split

comparison cluster.split.xml @ 5:f14e393f1641 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 38a2bbee32eaaceeb22d7549b13dbc0c613ee173
author iuc
date Tue, 20 Mar 2018 14:04:03 -0400
parents 063229a11154
children 9546bb7c1b61
comparison
equal deleted inserted replaced
4:cc7fbbceb25f 5:f14e393f1641
175 <param argument="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - distance matrix is too large to fit in RAM" 175 <param argument="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - distance matrix is too large to fit in RAM"
176 help="If your job fails due to not enough memory error, set this to true to rerun"/> 176 help="If your job fails due to not enough memory error, set this to true to rerun"/>
177 <param argument="cluster" type="boolean" falsevalue="false" truevalue="true" checked="true" label="perform clustering?" 177 <param argument="cluster" type="boolean" falsevalue="false" truevalue="true" checked="true" label="perform clustering?"
178 help="indicate whether you want to run the clustering or just split the distance matrix"/> 178 help="indicate whether you want to run the clustering or just split the distance matrix"/>
179 <param argument="runsensspec" type="boolean" truevalue="true" falsevalue="false" checked="true" label="runsensspec" help="run the sens.spec command on the completed list file"/> 179 <param argument="runsensspec" type="boolean" truevalue="true" falsevalue="false" checked="true" label="runsensspec" help="run the sens.spec command on the completed list file"/>
180 <expand macro="param-savelog"/>
180 </inputs> 181 </inputs>
181 <outputs> 182 <outputs>
182 <expand macro="logfile-output"/> 183 <expand macro="logfile-output"/>
183 <data name="rabund" format="mothur.rabund" from_work_dir="splitby.*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"> 184 <data name="rabund" format="mothur.rabund" from_work_dir="splitby.*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)">
184 <filter>splitby['nameOrCount'].ext != "mothur.count_table"</filter> 185 <filter>splitby['nameOrCount'].ext != "mothur.count_table"</filter>
227 <assert_contents> 228 <assert_contents>
228 <has_line_matching expression="^unique(\t\d+)+$"/> 229 <has_line_matching expression="^unique(\t\d+)+$"/>
229 <has_text text="0.03"/> 230 <has_text text="0.03"/>
230 </assert_contents> 231 </assert_contents>
231 </output> 232 </output>
233 <param name="savelog" value="true"/>
232 <expand macro="logfile-test"/> 234 <expand macro="logfile-test"/>
233 </test> 235 </test>
234 <test><!-- test with cluster false --> 236 <test><!-- test with cluster false -->
235 <param name="splitmethod" value="distance"/> 237 <param name="splitmethod" value="distance"/>
236 <param name="format" value="phylip"/> 238 <param name="format" value="phylip"/>
258 <assert_contents> 260 <assert_contents>
259 <has_line_matching expression="^U\d+\tU\d+\t\d+\.\d+$"/> 261 <has_line_matching expression="^U\d+\tU\d+\t\d+\.\d+$"/>
260 </assert_contents> 262 </assert_contents>
261 </element> 263 </element>
262 </output_collection> 264 </output_collection>
265 <param name="savelog" value="true"/>
263 <expand macro="logfile-test"/> 266 <expand macro="logfile-test"/>
264 </test> 267 </test>
265 <test><!-- test with classify method (mothur.names input file) --> 268 <test><!-- test with classify method (mothur.names input file) -->
266 <param name="splitmethod" value="classify"/> 269 <param name="splitmethod" value="classify"/>
267 <param name="format" value="column"/> 270 <param name="format" value="column"/>
270 <param name="taxonomy" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/> 273 <param name="taxonomy" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
271 <param name="method" value="average"/> 274 <param name="method" value="average"/>
272 <output name="otulist" md5="d6eba624ad79759c530b9bc3285a1361" ftype="mothur.list"/> 275 <output name="otulist" md5="d6eba624ad79759c530b9bc3285a1361" ftype="mothur.list"/>
273 <output name="rabund" md5="2a165e1e40644fccb8cc9f53d8915bc3" ftype="mothur.rabund"/> 276 <output name="rabund" md5="2a165e1e40644fccb8cc9f53d8915bc3" ftype="mothur.rabund"/>
274 <output name="sabund" md5="7aad8a9ca0eade414d6eba1f8bef960f" ftype="mothur.sabund"/> 277 <output name="sabund" md5="7aad8a9ca0eade414d6eba1f8bef960f" ftype="mothur.sabund"/>
278 <param name="savelog" value="true"/>
275 <expand macro="logfile-test"/> 279 <expand macro="logfile-test"/>
276 </test> 280 </test>
277 <test><!-- test with classify method (mothur.count_table input file) --> 281 <test><!-- test with classify method (mothur.count_table input file) -->
278 <param name="splitmethod" value="classify"/> 282 <param name="splitmethod" value="classify"/>
279 <param name="format" value="column"/> 283 <param name="format" value="column"/>
280 <param name="dist" value="amazon.pair.dist" ftype="mothur.pair.dist"/> 284 <param name="dist" value="amazon.pair.dist" ftype="mothur.pair.dist"/>
281 <param name="nameOrCount" value="amazon.count_table" ftype="mothur.count_table"/> 285 <param name="nameOrCount" value="amazon.count_table" ftype="mothur.count_table"/>
282 <param name="taxonomy" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/> 286 <param name="taxonomy" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
283 <param name="method" value="average"/> 287 <param name="method" value="average"/>
284 <output name="otulist" md5="c5c28330434d3e773221f635d04d6af9" ftype="mothur.list"/> 288 <output name="otulist" md5="c5c28330434d3e773221f635d04d6af9" ftype="mothur.list"/>
289 <param name="savelog" value="true"/>
285 <expand macro="logfile-test"/> 290 <expand macro="logfile-test"/>
286 </test> 291 </test>
287 <test><!-- test with fasta --> 292 <test><!-- test with fasta -->
288 <param name="splitmethod" value="fasta"/> 293 <param name="splitmethod" value="fasta"/>
289 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/> 294 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
292 <param name="cutoff" value="9999"/> 297 <param name="cutoff" value="9999"/>
293 <param name="method" value="average"/> 298 <param name="method" value="average"/>
294 <output name="otulist" md5="a1279248cf2bc1094e0046b2cff1b785" ftype="mothur.list"/> 299 <output name="otulist" md5="a1279248cf2bc1094e0046b2cff1b785" ftype="mothur.list"/>
295 <output name="rabund" md5="65ec9f326cd92fc607679b9902ec8430" ftype="mothur.rabund"/> 300 <output name="rabund" md5="65ec9f326cd92fc607679b9902ec8430" ftype="mothur.rabund"/>
296 <output name="sabund" md5="854d3acd15f64299c5d9d9e18f2d51b4" ftype="mothur.sabund"/> 301 <output name="sabund" md5="854d3acd15f64299c5d9d9e18f2d51b4" ftype="mothur.sabund"/>
302 <param name="savelog" value="true"/>
297 <expand macro="logfile-test"/> 303 <expand macro="logfile-test"/>
298 </test> 304 </test>
299 <test><!-- test with vsearch executable (agc/dgc method) --> 305 <test><!-- test with vsearch executable (agc/dgc method) -->
300 <param name="splitmethod" value="fasta"/> 306 <param name="splitmethod" value="fasta"/>
301 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/> 307 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
303 <param name="taxonomy" value="amazon.align_head.wang.taxonomy" ftype="mothur.seq.taxonomy"/> 309 <param name="taxonomy" value="amazon.align_head.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
304 <param name="method" value="agc"/> 310 <param name="method" value="agc"/>
305 <output name="otulist" md5="0fbc5bf21331538dd50b6586c4005edc" ftype="mothur.list"/> 311 <output name="otulist" md5="0fbc5bf21331538dd50b6586c4005edc" ftype="mothur.list"/>
306 <output name="rabund" md5="dcccca11d9fa7a186cd93e9d4592f832" ftype="mothur.rabund"/> 312 <output name="rabund" md5="dcccca11d9fa7a186cd93e9d4592f832" ftype="mothur.rabund"/>
307 <output name="sabund" md5="167815924b1b2b4d4e5e7468d41256cb" ftype="mothur.sabund"/> 313 <output name="sabund" md5="167815924b1b2b4d4e5e7468d41256cb" ftype="mothur.sabund"/>
314 <param name="savelog" value="true"/>
308 <expand macro="logfile-test"/> 315 <expand macro="logfile-test"/>
309 </test> 316 </test>
310 <test><!-- test with opticlust method --> 317 <test><!-- test with opticlust method -->
311 <param name="splitmethod" value="distance"/> 318 <param name="splitmethod" value="distance"/>
312 <param name="format" value="phylip"/> 319 <param name="format" value="phylip"/>
334 <assert_contents> 341 <assert_contents>
335 <expand macro="test-sensspec-format"/> 342 <expand macro="test-sensspec-format"/>
336 <has_text text="0.03"/> 343 <has_text text="0.03"/>
337 </assert_contents> 344 </assert_contents>
338 </output> 345 </output>
346 <param name="savelog" value="true"/>
339 <expand macro="logfile-test"/> 347 <expand macro="logfile-test"/>
340 </test> 348 </test>
341 </tests> 349 </tests>
342 <help><![CDATA[ 350 <help><![CDATA[
343 351