Mercurial > repos > galaxy-australia > kmc

comparison kmc_tools_simple.xml @ 2:c97f8a687258 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
equal deleted inserted replaced
1:c7fda6e88567 2:c97f8a687258
1 <tool id="kmc_simple" name="KMC simple" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="kmc_simple" name="KMC simple" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>simple operations for two input kmer sets</description> 2 <description>simple operations for two input kmer sets</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
3 <xrefs> 6 <xrefs>
4 <xref type='bio.tools'>kmc</xref> 7 <xref type='bio.tools'>kmc</xref>
5 </xrefs> 8 </xrefs>
6 <macros>
7 <import>macros.xml</import>
8 </macros>
9 <expand macro="requirements" /> 9 <expand macro="requirements" />
10 <expand macro="stdio" /> 10 <expand macro="stdio" />
11 <expand macro="version_command" /> 11 <expand macro="version_command" />
12 <command><![CDATA[ 12 <command><![CDATA[
13 mkdir outdir && 13 mkdir outdir &&
220 <tests> 220 <tests>
221 <test> 221 <test>
222 <!-- #1 test with default parameters --> 222 <!-- #1 test with default parameters -->
223 <param name="input_collection_one"> 223 <param name="input_collection_one">
224 <collection type="list"> 224 <collection type="list">
225 <element name="kmers_one.kmc_suf" value="kmers_one.kmc_suf"/> 225 <element name="kmers_one.kmc_pre" value="filtered_kmers1.kmc_pre"/>
226 <element name="kmers_one.kmc_pre" value="kmers_one.kmc_pre"/> 226 <element name="kmers_one.kmc_suf" value="filtered_kmers1.kmc_suf"/>
227 </collection> 227 </collection>
228 </param> 228 </param>
229 <param name="input_collection_two"> 229 <param name="input_collection_two">
230 <collection type="list"> 230 <collection type="list">
231 <element name="kmers_two.kmc_suf" value="kmers_two.kmc_suf"/> 231 <element name="kmers_two.kmc_pre" value="filtered_kmers2.kmc_pre"/>
232 <element name="kmers_two.kmc_pre" value="kmers_two.kmc_pre"/> 232 <element name="kmers_two.kmc_suf" value="filtered_kmers2.kmc_suf"/>
233 </collection> 233 </collection>
234 </param> 234 </param>
235 <conditional name="input_options_cond"> 235 <conditional name="input_options_cond">
236 <param name="input_param" value="None"/> 236 <param name="input_param" value="None"/>
237 </conditional> 237 </conditional>
238 <param name="select_operation" value="intersect" /> 238 <param name="select_operation" value="intersect" />
239 <section name="add_output_params"> 239 <section name="add_output_params">
240 <param name="oc" value="max"/> 240 <param name="oc" value="max"/>
241 </section> 241 </section>
242 <output_collection name="kmc_db" type="list"> 242 <output_collection name="kmc_db" type="list">
243 <element name="intersect_max_db.kmc_pre" file="intersect_max_db.kmc_pre"/>
243 <element name="intersect_max_db.kmc_suf" file="intersect_max_db.kmc_suf"/> 244 <element name="intersect_max_db.kmc_suf" file="intersect_max_db.kmc_suf"/>
244 <element name="intersect_max_db.kmc_pre" file="intersect_max_db.kmc_pre"/>
245 </output_collection> 245 </output_collection>
246 </test> 246 </test>
247 <test> 247 <test>
248 <!-- #2 test with input parameters for KMC DB one only --> 248 <!-- #2 test with input parameters for KMC DB one only -->
249 <param name="input_collection_one"> 249 <param name="input_collection_one">
250 <collection type="list"> 250 <collection type="list">
251 <element name="kmers_one.kmc_suf" value="kmers_one.kmc_suf"/> 251 <element name="kmers_one.kmc_pre" value="filtered_kmers1.kmc_pre"/>
252 <element name="kmers_one.kmc_pre" value="kmers_one.kmc_pre"/> 252 <element name="kmers_one.kmc_suf" value="filtered_kmers1.kmc_suf"/>
253 </collection> 253 </collection>
254 </param> 254 </param>
255 <param name="input_collection_two"> 255 <param name="input_collection_two">
256 <collection type="list"> 256 <collection type="list">
257 <element name="kmers_two.kmc_suf" value="kmers_two.kmc_suf"/> 257 <element name="kmers_two.kmc_pre" value="filtered_kmers2.kmc_pre"/>
258 <element name="kmers_two.kmc_pre" value="kmers_two.kmc_pre"/> 258 <element name="kmers_two.kmc_suf" value="filtered_kmers2.kmc_suf"/>
259 </collection> 259 </collection>
260 </param> 260 </param>
261 <conditional name="input_options_cond"> 261 <conditional name="input_options_cond">
262 <param name="input_param" value="kmc_one_params"/> 262 <param name="input_param" value="kmc_one_params"/>
263 </conditional> 263 </conditional>
268 </section> 268 </section>
269 <section name="add_output_params"> 269 <section name="add_output_params">
270 <param name="oc" value="min"/> 270 <param name="oc" value="min"/>
271 </section> 271 </section>
272 <output_collection name="kmc_db" type="list"> 272 <output_collection name="kmc_db" type="list">
273 <element name="intersect_min_db.kmc_pre" file="intersect_min_db.kmc_pre"/>
273 <element name="intersect_min_db.kmc_suf" file="intersect_min_db.kmc_suf"/> 274 <element name="intersect_min_db.kmc_suf" file="intersect_min_db.kmc_suf"/>
274 <element name="intersect_min_db.kmc_pre" file="intersect_min_db.kmc_pre"/>
275 </output_collection> 275 </output_collection>
276 </test> 276 </test>
277 <test> 277 <test>
278 <!-- #3 test with input parameters for KMC DB two only --> 278 <!-- #3 test with input parameters for KMC DB two only -->
279 <param name="input_collection_one"> 279 <param name="input_collection_one">
280 <collection type="list"> 280 <collection type="list">
281 <element name="kmers_one.kmc_suf" value="kmers_one.kmc_suf"/> 281 <element name="kmers_one.kmc_pre" value="filtered_kmers1.kmc_pre"/>
282 <element name="kmers_one.kmc_pre" value="kmers_one.kmc_pre"/> 282 <element name="kmers_one.kmc_suf" value="filtered_kmers1.kmc_suf"/>
283 </collection> 283 </collection>
284 </param> 284 </param>
285 <param name="input_collection_two"> 285 <param name="input_collection_two">
286 <collection type="list"> 286 <collection type="list">
287 <element name="kmers_two.kmc_suf" value="kmers_two.kmc_suf"/> 287 <element name="kmers_two.kmc_pre" value="filtered_kmers2.kmc_pre"/>
288 <element name="kmers_two.kmc_pre" value="kmers_two.kmc_pre"/> 288 <element name="kmers_two.kmc_suf" value="filtered_kmers2.kmc_pre"/>
289 </collection> 289 </collection>
290 </param> 290 </param>
291 <conditional name="input_options_cond"> 291 <conditional name="input_options_cond">
292 <param name="input_param" value="kmc_two_params"/> 292 <param name="input_param" value="kmc_two_params"/>
293 </conditional> 293 </conditional>
294 <param name="select_operation" value="union" /> 294 <param name="select_operation" value="union" />
295 <section name="kmc_db_two_param"> 295 <section name="kmc_db_two_param">
296 <param name="min_kmer_occurrence" value="3"/> 296 <param name="min_kmer_occurrence" value="3"/>
297 <param name="max_kmer_occurrence" value="30"/> 297 <param name="max_kmer_occurrence" value="30"/>
298 </section>
299 <section name="add_output_params">
300 <param name="oc" value="sum"/>
298 </section> 301 </section>
299 <output_collection name="kmc_db" type="list"> 302 <output_collection name="kmc_db" type="list">
300 <element name="union_db.kmc_suf" file="union_db.kmc_suf"/> 303 <element name="union_sum_db.kmc_pre" file="union_sum_db.kmc_pre"/>
301 <element name="union_db.kmc_pre" file="union_db.kmc_pre"/> 304 <element name="union_sum_db.kmc_suf" file="union_sum_db.kmc_suf"/>
302 </output_collection> 305 </output_collection>
303 </test> 306 </test>
304 <test> 307 <test>
305 <!-- #4 test with input parameters for both KMC DB --> 308 <!-- #4 test with input parameters for both KMC DB -->
306 <param name="input_collection_one"> 309 <param name="input_collection_one">
307 <collection type="list"> 310 <collection type="list">
308 <element name="kmers_one.kmc_suf" value="kmers_one.kmc_suf"/> 311 <element name="kmers_one.kmc_pre" value="filtered_kmers1.kmc_pre"/>
309 <element name="kmers_one.kmc_pre" value="kmers_one.kmc_pre"/> 312 <element name="kmers_one.kmc_suf" value="filtered_kmers1.kmc_pre"/>
310 </collection> 313 </collection>
311 </param> 314 </param>
312 <param name="input_collection_two"> 315 <param name="input_collection_two">
313 <collection type="list"> 316 <collection type="list">
314 <element name="kmers_two.kmc_suf" value="kmers_two.kmc_suf"/> 317 <element name="kmers_two.kmc_pre" value="filtered_kmers2.kmc_pre"/>
315 <element name="kmers_two.kmc_pre" value="kmers_two.kmc_pre"/> 318 <element name="kmers_two.kmc_suf" value="filtered_kmers2.kmc_suf"/>
316 </collection> 319 </collection>
317 </param> 320 </param>
318 <conditional name="input_options_cond"> 321 <conditional name="input_options_cond">
319 <param name="input_param" value="both_kmc_params"/> 322 <param name="input_param" value="both_kmc_params"/>
320 </conditional> 323 </conditional>
321 <param name="select_operation" value="counters_subtract" /> 324 <param name="select_operation" value="counters_subtract" />
322 <section name="both_db_one_param"> 325 <section name="both_db_one_param">
326 <param name="min_kmer_occurrence" value="1"/>
327 <param name="max_kmer_occurrence" value="10"/>
328 </section>
329 <section name="both_db_two_param">
323 <param name="min_kmer_occurrence" value="2"/> 330 <param name="min_kmer_occurrence" value="2"/>
324 <param name="max_kmer_occurrence" value="20"/> 331 <param name="max_kmer_occurrence" value="20"/>
325 </section>
326 <section name="both_db_two_param">
327 <param name="min_kmer_occurrence" value="3"/>
328 <param name="max_kmer_occurrence" value="30"/>
329 </section> 332 </section>
330 <section name="add_output_params"> 333 <section name="add_output_params">
331 <param name="oc" value="sum"/> 334 <param name="oc" value="sum"/>
332 </section> 335 </section>
333 <output_collection name="kmc_db" type="list"> 336 <output_collection name="kmc_db" type="list">
337 <element name="counters_subtract_sum_db.kmc_pre" file="counters_subtract_sum_db.kmc_pre"/>
334 <element name="counters_subtract_sum_db.kmc_suf" file="counters_subtract_sum_db.kmc_suf"/> 338 <element name="counters_subtract_sum_db.kmc_suf" file="counters_subtract_sum_db.kmc_suf"/>
335 <element name="counters_subtract_sum_db.kmc_pre" file="counters_subtract_sum_db.kmc_pre"/>
336 </output_collection> 339 </output_collection>
337 </test> 340 </test>
338 </tests> 341 </tests>
339 <help><![CDATA[ 342 <help><![CDATA[
340 343