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comparison lotus2.xml @ 15:6e9fd3e0dcbb draft

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"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda"
author earlhaminst
date Fri, 11 Feb 2022 19:48:19 +0000
parents 30340f534fbe
children 12599a8dd22f
comparison
equal deleted inserted replaced
14:30340f534fbe 15:6e9fd3e0dcbb
1 <tool id="lotus2" name="LotuS2" version="@VERSION@" profile="20.01"> 1 <tool id="lotus2" name="LotuS2" version="@VERSION@" profile="20.09">
2 <description>fast OTU processing pipeline</description> 2 <description>fast OTU processing pipeline</description>
3 <macros> 3 <macros>
4 <token name="@VERSION@">2.09.2</token> 4 <token name="@VERSION@">2.19</token>
5 <xml name="refDB_macro" token_ref_fasta_formats="fasta,fasta.gz"> 5 <xml name="refDB_macro" token_ref_fasta_formats="fasta,fasta.gz">
6 <conditional name="refDB_cond"> 6 <conditional name="refDB_cond">
7 <param argument="-refDB" type="select" label="Taxonomy reference database"> 7 <param argument="-refDB" type="select" label="Taxonomy reference database">
8 <option value="cached">Use a built-in taxonomy database</option> 8 <option value="cached">Use a built-in taxonomy database</option>
9 <option value="history">Use a taxonomy from history</option> 9 <option value="history">Use a taxonomy from history</option>
108 -reversePrimer '$reversePrimer' 108 -reversePrimer '$reversePrimer'
109 #end if 109 #end if
110 #if $offtarget_cond.offtargetDB != 'no': 110 #if $offtarget_cond.offtargetDB != 'no':
111 -offtargetDB '$offtarget_cond.ref_file' 111 -offtargetDB '$offtarget_cond.ref_file'
112 #end if 112 #end if
113 -useMini4map $useMini4map
113 114
114 -clustering $clu_args.clu_cond.clustering 115 -clustering $clu_args.clu_cond.clustering
115 #if $clu_args.clu_cond.clustering in ('1', '3'): 116 #if $clu_args.clu_cond.clustering in ('1', '3'):
116 #if str($clu_args.clu_cond.id): 117 #if str($clu_args.clu_cond.id):
117 -id $clu_args.clu_cond.id 118 -id $clu_args.clu_cond.id
170 #if str($tax_args.LCA_frac): 171 #if str($tax_args.LCA_frac):
171 -LCA_frac $tax_args.LCA_frac 172 -LCA_frac $tax_args.LCA_frac
172 #end if 173 #end if
173 -lulu $tax_args.lulu 174 -lulu $tax_args.lulu
174 -buildPhylo $tax_args.buildPhylo 175 -buildPhylo $tax_args.buildPhylo
175 176 #if $tax_args.taxExcludeGrep:
177 -taxExcludeGrep '$tax_args.taxExcludeGrep'
178 #end if
176 ; EXIT_VALUE=\$? ; 179 ; EXIT_VALUE=\$? ;
177 180
178 zip -8 -r -v output.zip output/ 181 zip -8 -r -v output.zip output/
179 && 182 &&
180 exit \$EXIT_VALUE 183 exit \$EXIT_VALUE
246 </when> 249 </when>
247 <when value="history"> 250 <when value="history">
248 <param name="ref_file" type="data" format="fasta,fasta.gz" label="FASTA reference genome" /> 251 <param name="ref_file" type="data" format="fasta,fasta.gz" label="FASTA reference genome" />
249 </when> 252 </when>
250 </conditional> 253 </conditional>
254 <param argument="-useMini4map" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use minimap2 instead of VSEARCH to map back reads to OTUs" />
251 <section name="clu_args" title="Clustering Options"> 255 <section name="clu_args" title="Clustering Options">
252 <conditional name="clu_cond"> 256 <conditional name="clu_cond">
253 <param argument="-clustering" type="select" label="Clustering algorithm"> 257 <param argument="-clustering" type="select" label="Clustering algorithm">
254 <option value="1">UPARSE</option>
255 <option value="2">swarm</option> 258 <option value="2">swarm</option>
256 <option value="3">cd-hit</option> 259 <option value="3">cd-hit</option>
257 <option value="6">unoise3</option> 260 <option value="6">unoise3</option>
258 <option value="7" selected="true">dada2</option> 261 <option value="7" selected="true">dada2</option>
259 </param> 262 <option value="8">vsearch</option>
260 <when value="1"> 263 </param>
261 <expand macro="id_macro" />
262 </when>
263 <when value="2"> 264 <when value="2">
264 <param argument="-swarm_distance" type="integer" min="1" value="1" optional="true" label="Clustering threshold for OTUs when using swarm clustering (optional)" /> 265 <param argument="-swarm_distance" type="integer" min="1" value="1" optional="true" label="Clustering threshold for OTUs when using swarm clustering (optional)" />
265 </when> 266 </when>
266 <when value="3"> 267 <when value="3">
267 <expand macro="id_macro" /> 268 <expand macro="id_macro" />
268 </when> 269 </when>
269 <when value="6"> 270 <when value="6">
270 </when> 271 </when>
271 <when value="7"> 272 <when value="7">
273 </when>
274 <when value="8">
272 </when> 275 </when>
273 </conditional> 276 </conditional>
274 <param argument="-derepMin" type="text" value="" label="Minimum size of dereplicated raw reads (optional)" help="E.g. 4:1,4:2,3:3 . See http://lotus2.earlham.ac.uk/images/Derep_options.pdf for how to specify this parameter. If not specified, LotuS2 will select an appropriate default for the chosen clustering algorithm." /> 277 <param argument="-derepMin" type="text" value="" label="Minimum size of dereplicated raw reads (optional)" help="E.g. 4:1,4:2,3:3 . See http://lotus2.earlham.ac.uk/images/Derep_options.pdf for how to specify this parameter. If not specified, LotuS2 will select an appropriate default for the chosen clustering algorithm." />
275 <param argument="-deactivateChimeraCheck" type="select" label="Chimera check"> 278 <param argument="-deactivateChimeraCheck" type="select" label="Chimera check">
276 <option value="" selected="true">(Default)</option> 279 <option value="" selected="true">(Default)</option>
290 <!-- <option value="4">VSEARCH LCA against custom reference database</option> --> 293 <!-- <option value="4">VSEARCH LCA against custom reference database</option> -->
291 </param> 294 </param>
292 <when value="0"> 295 <when value="0">
293 <param argument="-rdp_thr" type="float" min="0" max="1" value="0.8" optional="true" label="Confidence threshold for RDP (optional)"/> 296 <param argument="-rdp_thr" type="float" min="0" max="1" value="0.8" optional="true" label="Confidence threshold for RDP (optional)"/>
294 </when> 297 </when>
295 <when value="1"> 298 <!-- <when value="1">
296 <expand macro="refDB_macro" ref_fasta_formats="fasta" /> 299 <expand macro="refDB_macro" ref_fasta_formats="fasta" />
297 </when> 300 </when> -->
298 <when value="2"> 301 <when value="2">
299 <expand macro="refDB_macro" /> 302 <expand macro="refDB_macro" />
300 </when> 303 </when>
301 <when value="3"> 304 <!-- <when value="3">
302 <param argument="-utax_thr" type="float" min="0" max="1" value="0.8" optional="true" label="Confidence threshold for UTAX (optional)"/> 305 <param argument="-utax_thr" type="float" min="0" max="1" value="0.8" optional="true" label="Confidence threshold for UTAX (optional)"/>
303 </when> 306 </when>
304 <when value="4"> 307 <when value="4">
305 <expand macro="refDB_macro" /> 308 <expand macro="refDB_macro" />
306 </when> 309 </when> -->
307 </conditional> 310 </conditional>
308 <conditional name="amplicon_cond"> 311 <conditional name="amplicon_cond">
309 <param argument="-amplicon_type" type="select" label="Amplicon type"> 312 <param argument="-amplicon_type" type="select" label="Amplicon type">
310 <option value="" selected="true">(Default)</option> 313 <option value="" selected="true">(Default)</option>
311 <option value="LSU">LSU Large subunit (23S/28S)</option> 314 <option value="LSU">LSU Large subunit (23S/28S)</option>
339 <param argument="-buildPhylo" type="select" label="Build OTU phylogeny"> 342 <param argument="-buildPhylo" type="select" label="Build OTU phylogeny">
340 <option value="0">Disable</option> 343 <option value="0">Disable</option>
341 <option value="1" selected="true">Use fasttree2</option> 344 <option value="1" selected="true">Use fasttree2</option>
342 <option value="2">Use iqtree2</option> 345 <option value="2">Use iqtree2</option>
343 </param> 346 </param>
347 <param argument="-taxExcludeGrep" type="text" value="" label="Taxonomic groups to exclude, as a regular expression" help="OTUs matching this regular expression will be assigned as unknown, and by default removed">
348 <sanitizer>
349 <valid initial="default">
350 <add value="|" />
351 <add value="$" />
352 </valid>
353 </sanitizer>
354 </param>
344 </section> 355 </section>
345 </inputs> 356 </inputs>
346 357
347 <outputs> 358 <outputs>
348 <data name="outputs" format="zip" label="${tool.name} on ${on_string}: Complete LotuS2 output" from_work_dir="output.zip" /> 359 <data name="outputs" format="zip" label="${tool.name} on ${on_string}: Complete LotuS2 output" from_work_dir="output.zip" />
353 <data name="runlog" format="txt" label="${tool.name} on ${on_string}: main log file" from_work_dir="output/LotuSLogS/LotuS_run.log" /> 364 <data name="runlog" format="txt" label="${tool.name} on ${on_string}: main log file" from_work_dir="output/LotuSLogS/LotuS_run.log" />
354 </outputs> 365 </outputs>
355 366
356 <tests> 367 <tests>
357 <test> 368 <test>
358 <param name="paired_or_single" value="single"/> 369 <conditional name="inputs">
359 <param name="input" value="Anh_sample1.fastq.gz,Anh_sample2.fastq.gz" ftype="fastqsanger.gz"/> 370 <param name="paired_or_single" value="single"/>
371 <param name="input" value="Anh_sample1.fastq.gz,Anh_sample2.fastq.gz" ftype="fastqsanger.gz"/>
372 </conditional>
360 <param name="platform" value="454" /> 373 <param name="platform" value="454" />
361 <param name="clustering" value="3" /> 374 <section name="clu_args">
375 <conditional name="clu_cond">
376 <param name="clustering" value="3" />
377 </conditional>
378 <param name="derepMin" value="1" />
379 </section>
362 <output name="otu" file="OTU.txt" compare="sim_size" /> 380 <output name="otu" file="OTU.txt" compare="sim_size" />
363 <output name="otu_fna" file="OTU.fna" compare="sim_size" /> 381 <output name="otu_fna" file="OTU.fna" compare="sim_size" />
364 <output name="mapping" file="mapping.txt" /> 382 <output name="mapping" file="mapping.txt" />
365 </test> 383 </test>
366 <test> 384 <test>
367 <param name="paired_or_single" value="paired_collection"/> 385 <conditional name="inputs">
368 <param name="pair_input"> 386 <param name="paired_or_single" value="paired_collection"/>
369 <collection type="list:paired"> 387 <param name="pair_input">
370 <element name="Anh_sample"> 388 <collection type="list:paired">
371 <collection type="paired"> 389 <element name="Anh_sample">
372 <element name="forward" value="Anh_sample1.fastq.gz" ftype="fastqsanger.gz" /> 390 <collection type="paired">
373 <element name="reverse" value="Anh_sample2.fastq.gz" ftype="fastqsanger.gz" /> 391 <element name="forward" value="Anh_sample1.fastq.gz" ftype="fastqsanger.gz" />
374 </collection> 392 <element name="reverse" value="Anh_sample2.fastq.gz" ftype="fastqsanger.gz" />
375 </element> 393 </collection>
376 </collection> 394 </element>
377 </param> 395 </collection>
378 <param name="mapping" value="mapping_paired.txt" /> 396 </param>
397 </conditional>
398 <param name="map" value="mapping_paired.txt" />
379 <param name="platform" value="454" /> 399 <param name="platform" value="454" />
380 <param name="clustering" value="3" /> 400 <section name="clu_args">
401 <conditional name="clu_cond">
402 <param name="clustering" value="3" />
403 </conditional>
404 <param name="derepMin" value="1" />
405 </section>
381 <output name="otu" file="OTU_paired.txt" compare="sim_size" /> 406 <output name="otu" file="OTU_paired.txt" compare="sim_size" />
382 <output name="otu_fna" file="OTU_paired.fna" compare="sim_size" /> 407 <output name="otu_fna" file="OTU_paired.fna" compare="sim_size" />
383 </test> 408 </test>
384 </tests> 409 </tests>
385 410