Mercurial > repos > iuc > mothur_sub_sample

comparison sub.sample.xml @ 4:90c49ac0776e 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 14:16:54 -0400
parents 1f5904c5ee42
children 5986c72bbe25
comparison
equal deleted inserted replaced
3:1f5904c5ee42 4:90c49ac0776e
142 </when> 142 </when>
143 </conditional> 143 </conditional>
144 <param name="size" type="integer" value="" min="1" optional="true" label="size - If set, the number of samples to pick"/> 144 <param name="size" type="integer" value="" min="1" optional="true" label="size - If set, the number of samples to pick"/>
145 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> 145 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
146 <param name="taxonomy" type="data" format="mothur.seq.taxonomy,mothur.ref.taxonomy" optional="true" label="taxonomy - allows a taxonomy file"/> 146 <param name="taxonomy" type="data" format="mothur.seq.taxonomy,mothur.ref.taxonomy" optional="true" label="taxonomy - allows a taxonomy file"/>
147 <expand macro="param-savelog"/>
147 </inputs> 148 </inputs>
148 <outputs> 149 <outputs>
149 <expand macro="logfile-output"/> 150 <expand macro="logfile-output"/>
150 <data name="fasta_out" format_source="otu" from_work_dir="input_otu*.subsample.*" label="${tool.name} on ${on_string}: subsample.fasta"> 151 <data name="fasta_out" format_source="otu" from_work_dir="input_otu*.subsample.*" label="${tool.name} on ${on_string}: subsample.fasta">
151 <filter>input['format'] == 'fasta'</filter> 152 <filter>input['format'] == 'fasta'</filter>
184 <has_text text="label"/> 185 <has_text text="label"/>
185 <has_text text="numOtus"/> 186 <has_text text="numOtus"/>
186 </assert_contents> 187 </assert_contents>
187 </element> 188 </element>
188 </output_collection> 189 </output_collection>
190 <param name="savelog" value="true"/>
189 <expand macro="logfile-test"/> 191 <expand macro="logfile-test"/>
190 </test> 192 </test>
191 <test><!-- test with list and group file and label select--> 193 <test><!-- test with list and group file and label select-->
192 <param name="format" value="list"/> 194 <param name="format" value="list"/>
193 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 195 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
201 <has_text text="label"/> 203 <has_text text="label"/>
202 <has_text text="numOtus"/> 204 <has_text text="numOtus"/>
203 </assert_contents> 205 </assert_contents>
204 </element> 206 </element>
205 </output_collection> 207 </output_collection>
208 <param name="savelog" value="true"/>
206 <expand macro="logfile-test"/> 209 <expand macro="logfile-test"/>
207 </test> 210 </test>
208 <test><!-- test with fasta and taxonomy --> 211 <test><!-- test with fasta and taxonomy -->
209 <param name="format" value="fasta"/> 212 <param name="format" value="fasta"/>
210 <param name="otu" value="amazon.fasta" ftype="fasta"/> 213 <param name="otu" value="amazon.fasta" ftype="fasta"/>
217 <output name="taxonomy_out" ftype="mothur.seq.taxonomy"> 220 <output name="taxonomy_out" ftype="mothur.seq.taxonomy">
218 <assert_contents> 221 <assert_contents>
219 <has_line_matching expression="^U[0-9]+\tBacteria.*$"/> 222 <has_line_matching expression="^U[0-9]+\tBacteria.*$"/>
220 </assert_contents> 223 </assert_contents>
221 </output> 224 </output>
225 <param name="savelog" value="true"/>
222 <expand macro="logfile-test"/> 226 <expand macro="logfile-test"/>
223 </test> 227 </test>
224 <test><!-- test with fasta and group file and name file --> 228 <test><!-- test with fasta and group file and name file -->
225 <param name="format" value="fasta"/> 229 <param name="format" value="fasta"/>
226 <param name="otu" value="amazon.fasta" ftype="fasta"/> 230 <param name="otu" value="amazon.fasta" ftype="fasta"/>
241 <output name="names_out" ftype="mothur.names"> 245 <output name="names_out" ftype="mothur.names">
242 <assert_contents> 246 <assert_contents>
243 <has_line_matching expression="^U[0-9]+\tU[0-9]+$"/> 247 <has_line_matching expression="^U[0-9]+\tU[0-9]+$"/>
244 </assert_contents> 248 </assert_contents>
245 </output> 249 </output>
250 <param name="savelog" value="true"/>
246 <expand macro="logfile-test"/> 251 <expand macro="logfile-test"/>
247 </test> 252 </test>
248 <test><!-- test with shared --> 253 <test><!-- test with shared -->
249 <param name="format" value="shared"/> 254 <param name="format" value="shared"/>
250 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 255 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
258 <has_text text="forest"/> 263 <has_text text="forest"/>
259 <not_has_text text="pasture"/> 264 <not_has_text text="pasture"/>
260 </assert_contents> 265 </assert_contents>
261 </element> 266 </element>
262 </output_collection> 267 </output_collection>
268 <param name="savelog" value="true"/>
263 <expand macro="logfile-test"/> 269 <expand macro="logfile-test"/>
264 </test> 270 </test>
265 <test><!-- test with rabund --> 271 <test><!-- test with rabund -->
266 <param name="format" value="rabund"/> 272 <param name="format" value="rabund"/>
267 <param name="otu" value="amazon.an.rabund" ftype="mothur.rabund"/> 273 <param name="otu" value="amazon.an.rabund" ftype="mothur.rabund"/>
269 <assert_contents> 275 <assert_contents>
270 <has_text text="unique"/> 276 <has_text text="unique"/>
271 <has_text text="0.55"/> 277 <has_text text="0.55"/>
272 </assert_contents> 278 </assert_contents>
273 </output> 279 </output>
280 <param name="savelog" value="true"/>
274 <expand macro="logfile-test"/> 281 <expand macro="logfile-test"/>
275 </test> 282 </test>
276 <test><!-- test with sabund --> 283 <test><!-- test with sabund -->
277 <param name="format" value="sabund"/> 284 <param name="format" value="sabund"/>
278 <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/> 285 <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/>
280 <assert_contents> 287 <assert_contents>
281 <has_text text="unique"/> 288 <has_text text="unique"/>
282 <has_text text="0.55"/> 289 <has_text text="0.55"/>
283 </assert_contents> 290 </assert_contents>
284 </output> 291 </output>
292 <param name="savelog" value="true"/>
285 <expand macro="logfile-test"/> 293 <expand macro="logfile-test"/>
286 </test> 294 </test>
287 </tests> 295 </tests>
288 <help><![CDATA[ 296 <help><![CDATA[
289 297