Mercurial > repos > iuc > mothur_get_oturep

comparison get.oturep.xml @ 5:2ac0e471b97a 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 13:55:52 -0400
parents 899ef1660676
children
comparison
equal deleted inserted replaced
4:f45e7f3675e2 5:2ac0e471b97a
129 <option value="name">Sequence Name</option> 129 <option value="name">Sequence Name</option>
130 <option value="number">Bin Number</option> 130 <option value="number">Bin Number</option>
131 <option value="size">Bin Size</option> 131 <option value="size">Bin Size</option>
132 <option value="group">Group</option> 132 <option value="group">Group</option>
133 </param> 133 </param>
134 <expand macro="param-savelog"/>
134 </inputs> 135 </inputs>
135 <outputs> 136 <outputs>
136 <expand macro="logfile-output"/> 137 <expand macro="logfile-output"/>
137 <collection name="names_out" type="list" label="${tool.name} on ${on_string}: rep.names"> 138 <collection name="names_out" type="list" label="${tool.name} on ${on_string}: rep.names">
138 <filter>method_condition['nameOrCount'].ext == "mothur.names"</filter> 139 <filter>method_condition['nameOrCount'].ext == "mothur.names"</filter>
159 <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/> 160 <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
160 <param name="nameOrCount" value="amazon1.names" ftype="mothur.names"/> 161 <param name="nameOrCount" value="amazon1.names" ftype="mothur.names"/>
161 <output_collection name="names_out" count="36"> 162 <output_collection name="names_out" count="36">
162 <element name="0.27" md5="39ff2858909d49633871d5a625585de5" ftype="mothur.names"/> 163 <element name="0.27" md5="39ff2858909d49633871d5a625585de5" ftype="mothur.names"/>
163 </output_collection> 164 </output_collection>
165 <param name="savelog" value="true"/>
164 <expand macro="logfile-test"/> 166 <expand macro="logfile-test"/>
165 </test> 167 </test>
166 <!-- test with distance / column / label select --> 168 <!-- test with distance / column / label select -->
167 <test> 169 <test>
168 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 170 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
172 <param name="nameOrCount" value="amazon1.names" ftype="mothur.names"/> 174 <param name="nameOrCount" value="amazon1.names" ftype="mothur.names"/>
173 <param name="label" value="unique,0.05,0.27,0.45"/> 175 <param name="label" value="unique,0.05,0.27,0.45"/>
174 <output_collection name="names_out" count="4"> 176 <output_collection name="names_out" count="4">
175 <element name="0.27" md5="be6dccdd3d4619c3ac465246c826209a" ftype="mothur.names"/> 177 <element name="0.27" md5="be6dccdd3d4619c3ac465246c826209a" ftype="mothur.names"/>
176 </output_collection> 178 </output_collection>
179 <param name="savelog" value="true"/>
177 <expand macro="logfile-test"/> 180 <expand macro="logfile-test"/>
178 </test> 181 </test>
179 <!-- test with distance / fasta / sorting --> 182 <!-- test with distance / fasta / sorting -->
180 <test> 183 <test>
181 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 184 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
189 <element name="0.27" md5="39ff2858909d49633871d5a625585de5" ftype="mothur.names"/> 192 <element name="0.27" md5="39ff2858909d49633871d5a625585de5" ftype="mothur.names"/>
190 </output_collection> 193 </output_collection>
191 <output_collection name="fasta_out" count="2"> 194 <output_collection name="fasta_out" count="2">
192 <element name="0.27" md5="a9d9622b6f5fcbe8acdc05df5484ffc4" ftype="fasta"/> 195 <element name="0.27" md5="a9d9622b6f5fcbe8acdc05df5484ffc4" ftype="fasta"/>
193 </output_collection> 196 </output_collection>
197 <param name="savelog" value="true"/>
194 <expand macro="logfile-test"/> 198 <expand macro="logfile-test"/>
195 </test> 199 </test>
196 <!-- test with distance / group file --> 200 <!-- test with distance / group file -->
197 <test> 201 <test>
198 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 202 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
205 <param name="group" value="amazon.groups" ftype="mothur.groups"/> 209 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
206 <param name="groups" value="forest,pasture"/> 210 <param name="groups" value="forest,pasture"/>
207 <output_collection name="names_out" count="8"> 211 <output_collection name="names_out" count="8">
208 <element name="0.27.pasture" md5="34f87d93fd9ebbefed9754f627f502fd" ftype="mothur.names"/> 212 <element name="0.27.pasture" md5="34f87d93fd9ebbefed9754f627f502fd" ftype="mothur.names"/>
209 </output_collection> 213 </output_collection>
214 <param name="savelog" value="true"/>
210 <expand macro="logfile-test"/> 215 <expand macro="logfile-test"/>
211 </test> 216 </test>
212 <!-- test with distance / count table --> 217 <!-- test with distance / count table -->
213 <test> 218 <test>
214 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 219 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
218 <param name="label" value="unique,0.05,0.27"/> 223 <param name="label" value="unique,0.05,0.27"/>
219 <param name="nameOrCount" value="amazon1.count_table" ftype="mothur.count_table"/> 224 <param name="nameOrCount" value="amazon1.count_table" ftype="mothur.count_table"/>
220 <output_collection name="count_out" count="3"> 225 <output_collection name="count_out" count="3">
221 <element name="0.27" md5="6b1afd712825af4bf8cb4ab8304df903" ftype="mothur.count_table"/> 226 <element name="0.27" md5="6b1afd712825af4bf8cb4ab8304df903" ftype="mothur.count_table"/>
222 </output_collection> 227 </output_collection>
228 <param name="savelog" value="true"/>
223 <expand macro="logfile-test"/> 229 <expand macro="logfile-test"/>
224 </test> 230 </test>
225 <!-- test with abundance / count / label --> 231 <!-- test with abundance / count / label -->
226 <!-- It seems that the content of the result file can vary from one execution to another with the same parameters --> 232 <!-- It seems that the content of the result file can vary from one execution to another with the same parameters -->
227 <test> 233 <test>
235 <assert_contents> 241 <assert_contents>
236 <has_text_matching expression="U68\w+\t36" /> 242 <has_text_matching expression="U68\w+\t36" />
237 </assert_contents> 243 </assert_contents>
238 </element> 244 </element>
239 </output_collection> 245 </output_collection>
246 <param name="savelog" value="true"/>
240 <expand macro="logfile-test"/> 247 <expand macro="logfile-test"/>
241 </test> 248 </test>
242 </tests> 249 </tests>
243 <help><![CDATA[ 250 <help><![CDATA[
244 251