Mercurial > repos > iuc > mothur_get_sharedseqs

comparison get.sharedseqs.xml @ 5:779fb6464cd5 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 38a2bbee32eaaceeb22d7549b13dbc0c613ee173
author iuc
date Tue, 20 Mar 2018 14:15:21 -0400
parents 30f2529d9cc6
children
comparison
equal deleted inserted replaced
4:66956c649bd2 5:779fb6464cd5
124 </conditional> 124 </conditional>
125 <param name="output" type="select" label="output - select the output format" help="accnos can be used with get.seqs, list.seqs and remove.seqs"> 125 <param name="output" type="select" label="output - select the output format" help="accnos can be used with get.seqs, list.seqs and remove.seqs">
126 <option value="" selected="true">default: (name group bin_number)</option> 126 <option value="" selected="true">default: (name group bin_number)</option>
127 <option value="accnos">accnos (name)</option> 127 <option value="accnos">accnos (name)</option>
128 </param> 128 </param>
129 <expand macro="param-savelog"/>
129 </inputs> 130 </inputs>
130 <outputs> 131 <outputs>
131 <expand macro="logfile-output"/> 132 <expand macro="logfile-output"/>
132 <collection name="sharedseqs" type="list" label="${tool.name} on ${on_string}: shared.seqs"> 133 <collection name="sharedseqs" type="list" label="${tool.name} on ${on_string}: shared.seqs">
133 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.shared\.seqs" format="tabular"/> 134 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.shared\.seqs" format="tabular"/>
148 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 149 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
149 <param name="selection" value="shared"/> 150 <param name="selection" value="shared"/>
150 <output_collection name="sharedseqs" count="35"> 151 <output_collection name="sharedseqs" count="35">
151 <element name="0.41.unique.forest_pasture" md5="e07fe8acfa12d6f61a9efee88d91be54" ftype="tabular"/> 152 <element name="0.41.unique.forest_pasture" md5="e07fe8acfa12d6f61a9efee88d91be54" ftype="tabular"/>
152 </output_collection> 153 </output_collection>
154 <param name="savelog" value="true"/>
153 <expand macro="logfile-test"/> 155 <expand macro="logfile-test"/>
154 </test> 156 </test>
155 <test><!-- test with list and group file --> 157 <test><!-- test with list and group file -->
156 <param name="intype" value="in_listgroup"/> 158 <param name="intype" value="in_listgroup"/>
157 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 159 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
158 <param name="group" value="amazon.groups" ftype="mothur.groups"/> 160 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
159 <output_collection name="sharedseqs" count="35"> 161 <output_collection name="sharedseqs" count="35">
160 <element name="0.41.unique.forest_pasture" md5="ceb32c3dc2c99055efdaa6ef6aaed7f0" ftype="tabular"/> 162 <element name="0.41.unique.forest_pasture" md5="ceb32c3dc2c99055efdaa6ef6aaed7f0" ftype="tabular"/>
161 </output_collection> 163 </output_collection>
164 <param name="savelog" value="true"/>
162 <expand macro="logfile-test"/> 165 <expand macro="logfile-test"/>
163 </test> 166 </test>
164 <test><!-- test with shared seqs and subset of labels --> 167 <test><!-- test with shared seqs and subset of labels -->
165 <param name="intype" value="in_shared"/> 168 <param name="intype" value="in_shared"/>
166 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 169 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
168 <param name="groups" value="forest,pasture"/> 171 <param name="groups" value="forest,pasture"/>
169 <param name="label" value="0.03,0.33,0.41"/> 172 <param name="label" value="0.03,0.33,0.41"/>
170 <output_collection name="sharedseqs" count="3"> 173 <output_collection name="sharedseqs" count="3">
171 <element name="0.41.forest_pasture" md5="e07fe8acfa12d6f61a9efee88d91be54" ftype="tabular"/> 174 <element name="0.41.forest_pasture" md5="e07fe8acfa12d6f61a9efee88d91be54" ftype="tabular"/>
172 </output_collection> 175 </output_collection>
176 <param name="savelog" value="true"/>
173 <expand macro="logfile-test"/> 177 <expand macro="logfile-test"/>
174 </test> 178 </test>
175 <test><!-- test with unique seqs and subset of groups --> 179 <test><!-- test with unique seqs and subset of groups -->
176 <param name="intype" value="in_shared"/> 180 <param name="intype" value="in_shared"/>
177 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 181 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
178 <param name="selection" value="unique"/> 182 <param name="selection" value="unique"/>
179 <param name="groups" value="pasture"/> 183 <param name="groups" value="pasture"/>
180 <output_collection name="sharedseqs" count="34"> 184 <output_collection name="sharedseqs" count="34">
181 <element name="0.41.unique.pasture" md5="f4735f56d96d13cd603ca0b11c4bc231" ftype="tabular"/> 185 <element name="0.41.unique.pasture" md5="f4735f56d96d13cd603ca0b11c4bc231" ftype="tabular"/>
182 </output_collection> 186 </output_collection>
187 <param name="savelog" value="true"/>
183 <expand macro="logfile-test"/> 188 <expand macro="logfile-test"/>
184 </test> 189 </test>
185 <test><!-- test with accnos output --> 190 <test><!-- test with accnos output -->
186 <param name="intype" value="in_shared"/> 191 <param name="intype" value="in_shared"/>
187 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 192 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
188 <param name="output" value="accnos"/> 193 <param name="output" value="accnos"/>
189 <output_collection name="sharedaccnos" count="35"> 194 <output_collection name="sharedaccnos" count="35">
190 <element name="0.41.unique.forest_pasture" md5="0e0dcf8a91c03e1cc6adbf2593addf20" ftype="mothur.accnos"/> 195 <element name="0.41.unique.forest_pasture" md5="0e0dcf8a91c03e1cc6adbf2593addf20" ftype="mothur.accnos"/>
191 </output_collection> 196 </output_collection>
197 <param name="savelog" value="true"/>
192 <expand macro="logfile-test"/> 198 <expand macro="logfile-test"/>
193 </test> 199 </test>
194 <test><!-- test with fasta input and output --> 200 <test><!-- test with fasta input and output -->
195 <param name="intype" value="in_listgroup"/> 201 <param name="intype" value="in_listgroup"/>
196 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 202 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
200 <element name="0.41.unique.forest_pasture" md5="ceb32c3dc2c99055efdaa6ef6aaed7f0" ftype="tabular"/> 206 <element name="0.41.unique.forest_pasture" md5="ceb32c3dc2c99055efdaa6ef6aaed7f0" ftype="tabular"/>
201 </output_collection> 207 </output_collection>
202 <output_collection name="sharedfastas" count="35"> 208 <output_collection name="sharedfastas" count="35">
203 <element name="0.41.unique.forest_pasture" md5="fd4265d7c139d2d3acf8e19e6337ee28" ftype="fasta"/> 209 <element name="0.41.unique.forest_pasture" md5="fd4265d7c139d2d3acf8e19e6337ee28" ftype="fasta"/>
204 </output_collection> 210 </output_collection>
211 <param name="savelog" value="true"/>
205 <expand macro="logfile-test"/> 212 <expand macro="logfile-test"/>
206 </test> 213 </test>
207 </tests> 214 </tests>
208 <help><![CDATA[ 215 <help><![CDATA[
209 216