Mercurial > repos > galaxy-australia > kmc

comparison kmc_tools_transform.xml @ 2:c97f8a687258 draft

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planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
author galaxy-australia
date Wed, 02 Oct 2024 08:34:43 +0000
parents c7fda6e88567
children
comparison
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1:c7fda6e88567 2:c97f8a687258
134 <tests> 134 <tests>
135 <test> 135 <test>
136 <!-- #1 test perform sort operation on KMC DB --> 136 <!-- #1 test perform sort operation on KMC DB -->
137 <param name="input_collection"> 137 <param name="input_collection">
138 <collection type="list"> 138 <collection type="list">
139 <element name="db.kmc_suf" value="db.kmc_suf"/> 139 <element name="db.kmc_pre" value="filtered_kmers1.kmc_pre"/>
140 <element name="db.kmc_pre" value="db.kmc_pre"/> 140 <element name="db.kmc_suf" value="filtered_kmers1.kmc_suf"/>
141 </collection> 141 </collection>
142 </param> 142 </param>
143 <conditional name="ops"> 143 <conditional name="ops">
144 <param name="transform_operation" value="sort"/> 144 <param name="transform_operation" value="sort"/>
145 </conditional> 145 </conditional>
158 </test> 158 </test>
159 <test> 159 <test>
160 <!-- #2 test Generate Histogram Table --> 160 <!-- #2 test Generate Histogram Table -->
161 <param name="input_collection"> 161 <param name="input_collection">
162 <collection type="list"> 162 <collection type="list">
163 <element name="db.kmc_suf" value="db.kmc_suf"/> 163 <element name="db.kmc_pre" value="filtered_kmers1.kmc_pre"/>
164 <element name="db.kmc_pre" value="db.kmc_pre"/> 164 <element name="db.kmc_suf" value="filtered_kmers1.kmc_suf"/>
165 </collection> 165 </collection>
166 </param> 166 </param>
167 <conditional name="ops"> 167 <conditional name="ops">
168 <param name="transform_operation" value="histogram"/> 168 <param name="transform_operation" value="histogram"/>
169 </conditional> 169 </conditional>
181 </test> 181 </test>
182 <test> 182 <test>
183 <!-- #3 test Generate dump Table --> 183 <!-- #3 test Generate dump Table -->
184 <param name="input_collection"> 184 <param name="input_collection">
185 <collection type="list"> 185 <collection type="list">
186 <element name="db.kmc_suf" value="db.kmc_suf"/> 186 <element name="db.kmc_pre" value="filtered_kmers1.kmc_pre"/>
187 <element name="db.kmc_pre" value="db.kmc_pre"/> 187 <element name="db.kmc_suf" value="filtered_kmers1.kmc_suf"/>
188 </collection> 188 </collection>
189 </param> 189 </param>
190 <conditional name="ops"> 190 <conditional name="ops">
191 <param name="transform_operation" value="dump"/> 191 <param name="transform_operation" value="dump"/>
192 </conditional> 192 </conditional>
204 </test> 204 </test>
205 <test> 205 <test>
206 <!-- #4 test perform reduce operation --> 206 <!-- #4 test perform reduce operation -->
207 <param name="input_collection"> 207 <param name="input_collection">
208 <collection type="list"> 208 <collection type="list">
209 <element name="db.kmc_suf" value="db.kmc_suf"/> 209 <element name="db.kmc_pre" value="filtered_kmers1.kmc_pre"/>
210 <element name="db.kmc_pre" value="db.kmc_pre"/> 210 <element name="db.kmc_suf" value="filtered_kmers1.kmc_suf"/>
211 </collection> 211 </collection>
212 </param> 212 </param>
213 <repeat name="operations"> 213 <repeat name="operations">
214 <conditional name="ops"> 214 <conditional name="ops">
215 <param name="transform_operation" value="reduce"/> 215 <param name="transform_operation" value="reduce"/>
235 <section name="input_opt"> 235 <section name="input_opt">
236 <param name="min_kmer_occurrence" value="4"/> 236 <param name="min_kmer_occurrence" value="4"/>
237 <param name="max_kmer_occurrence" value="40"/> 237 <param name="max_kmer_occurrence" value="40"/>
238 </section> 238 </section>
239 </repeat> 239 </repeat>
240 <output_collection name="kmc_db" type="list"> 240 <output_collection name="kmc_db" type="list">
241 <element name="reduce_1_db.kmc_suf" file="reduce_1_db.kmc_suf"/> 241 <element name="compact_3_db.kmc_pre" file="compact_3_db.kmc_pre"/>
242 <element name="reduce_1_db.kmc_pre" file="reduce_1_db.kmc_pre"/>
243 <element name="sort_2_db.kmc_suf" file="sort_2_db.kmc_suf"/>
244 <element name="sort_2_db.kmc_pre" file="sort_2_db.kmc_pre"/>
245 <element name="compact_3_db.kmc_suf" file="compact_3_db.kmc_suf"/> 242 <element name="compact_3_db.kmc_suf" file="compact_3_db.kmc_suf"/>
246 <element name="compact_3_db.kmc_pre" file="compact_3_db.kmc_pre"/> 243 <element name="reduce_1_db.kmc_pre" file="reduce_1_db.kmc_pre"/>
244 <element name="reduce_1_db.kmc_suf" file="reduce_1_db.kmc_suf"/>
245 <element name="sort_2_db.kmc_pre" file="sort_2_db.kmc_pre"/>
246 <element name="sort_2_db.kmc_suf" file="sort_2_db.kmc_suf"/>
247 </output_collection> 247 </output_collection>
248 </test> 248 </test>
249 </tests> 249 </tests>
250 <help><![CDATA[ 250 <help><![CDATA[
251 251