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comparison lotus2.xml @ 20:1d660ee0b1c8 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e532d288f092df22f32805cea50583fe16a1070f
author earlhaminst
date Sat, 03 Dec 2022 16:37:26 +0000
parents a3d31a68f291
children fa84bba02a62
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19:a3d31a68f291 20:1d660ee0b1c8
1 <tool id="lotus2" name="LotuS2" version="@VERSION@+galaxy2" profile="20.09"> 1 <tool id="lotus2" name="LotuS2" version="@VERSION@+galaxy2" 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@">2.21</token> 4 <token name="@VERSION@">2.23</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>
262 <when value="4"> 262 <when value="4">
263 <expand macro="refDB_macro" /> 263 <expand macro="refDB_macro" />
264 </when> --> 264 </when> -->
265 </conditional> 265 </conditional>
266 <section name="clu_args" title="Other Clustering Options"> 266 <section name="clu_args" title="Other Clustering Options">
267 <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." /> 267 <param argument="-derepMin" type="text" value="" label="Minimum size of dereplicated raw reads (optional)" help="E.g. 4:1,4:2,3:3 . See https://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." />
268 <param argument="-deactivateChimeraCheck" type="select" label="Chimera check"> 268 <param argument="-deactivateChimeraCheck" type="select" label="Chimera check">
269 <option value="" selected="true">(Default)</option> 269 <option value="" selected="true">(Default)</option>
270 <option value="0">OTU chimera checks</option> 270 <option value="0">OTU chimera checks</option>
271 <option value="1">No chimera check at all</option> 271 <option value="1">No chimera check at all</option>
272 <option value="2">Disable deNovo chimera check</option> 272 <option value="2">Disable deNovo chimera check</option>
303 <option value="fungi">fungal 18S/23S/ITS annotation</option> 303 <option value="fungi">fungal 18S/23S/ITS annotation</option>
304 </param> 304 </param>
305 <param argument="-keepUnclassified" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Keep unclassified OTUs" help="Includes unclassified OTUs (i.e. no match in RDP/Blast database) in OTU and taxa abundance matrix calculations" /> 305 <param argument="-keepUnclassified" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Keep unclassified OTUs" help="Includes unclassified OTUs (i.e. no match in RDP/Blast database) in OTU and taxa abundance matrix calculations" />
306 <param argument="-LCA_cover" type="float" min="0" max="1" value="" optional="true" label="Minimum horizontal coverage of an OTU sequence against ref DB (optional)"/> 306 <param argument="-LCA_cover" type="float" min="0" max="1" value="" optional="true" label="Minimum horizontal coverage of an OTU sequence against ref DB (optional)"/>
307 <param argument="-LCA_frac" type="float" min="0" max="1" value="" optional="true" label="Minimum fraction of reads with identical taxonomy (optional)"/> 307 <param argument="-LCA_frac" type="float" min="0" max="1" value="" optional="true" label="Minimum fraction of reads with identical taxonomy (optional)"/>
308 <param argument="-lulu" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Use LULU to merge OTUs based on their occurrence" /> 308 <param argument="-lulu" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use LULU to merge OTUs based on their occurrence" />
309 <param argument="-buildPhylo" type="select" label="Build OTU phylogeny"> 309 <param argument="-buildPhylo" type="select" label="Build OTU phylogeny">
310 <option value="0">Disable</option> 310 <option value="0">Disable</option>
311 <option value="1" selected="true">Use fasttree2</option> 311 <option value="1" selected="true">Use fasttree2</option>
312 <option value="2">Use iqtree2</option> 312 <option value="2">Use iqtree2</option>
313 </param> 313 </param>
389 <param name="paired_or_single" value="paired_collection"/> 389 <param name="paired_or_single" value="paired_collection"/>
390 <param name="pair_input"> 390 <param name="pair_input">
391 <collection type="list:paired"> 391 <collection type="list:paired">
392 <element name="Anh_sample"> 392 <element name="Anh_sample">
393 <collection type="paired"> 393 <collection type="paired">
394 <element name="forward" value="Anh_sample1.fastq.gz" ftype="fastqsanger.gz" /> 394 <element name="forward" value="Arabidopsis_R1.fastqsanger.gz" ftype="fastqsanger.gz" />
395 <element name="reverse" value="Anh_sample2.fastq.gz" ftype="fastqsanger.gz" /> 395 <element name="reverse" value="Arabidopsis_R2.fastqsanger.gz" ftype="fastqsanger.gz" />
396 </collection> 396 </collection>
397 </element> 397 </element>
398 </collection> 398 </collection>
399 </param> 399 </param>
400 </conditional> 400 </conditional>
401 <param name="map" value="mapping_paired.txt" /> 401 <param name="map" value="mapping_paired.txt" ftype="tabular" />
402 <conditional name="clu_cond">
403 <param name="clustering" value="3" />
404 </conditional>
405 <section name="clu_args">
406 <param name="derepMin" value="1" />
407 </section>
408 <section name="tax_args"> 402 <section name="tax_args">
409 <param name="lulu" value="false" /> 403 <param name="lulu" value="true" />
410 </section>
411 <section name="other_opts">
412 <param name="platform" value="454" />
413 </section> 404 </section>
414 <output name="otu" file="OTU_paired.txt" compare="sim_size" /> 405 <output name="otu" file="OTU_paired.txt" compare="sim_size" />
415 <output name="otu_fna" file="OTU_paired.fna" compare="sim_size" /> 406 <output name="otu_fna" file="OTU_paired.fna" compare="sim_size" />
416 </test> 407 </test>
417 </tests> 408 </tests>
419 <help><![CDATA[ 410 <help><![CDATA[
420 If you have separate FASTA and quality files, these can be combined in a FASTQ file using the "Combine FASTA and QUAL into FASTQ" tool. 411 If you have separate FASTA and quality files, these can be combined in a FASTQ file using the "Combine FASTA and QUAL into FASTQ" tool.
421 412
422 .. class:: infomark 413 .. class:: infomark
423 414
424 The full LotuS2 **documentation** can be found at `<http://lotus2.earlham.ac.uk/>`_. 415 The full LotuS2 **documentation** can be found at `<https://lotus2.earlham.ac.uk/>`_.
425 ]]></help> 416 ]]></help>
426 <citations> 417 <citations>
427 <citation type="doi">10.1186/s40168-022-01365-1</citation> 418 <citation type="doi">10.1186/s40168-022-01365-1</citation>
428 <citation type="doi">10.1186/s40168-021-01012-1</citation> 419 <citation type="doi">10.1186/s40168-021-01012-1</citation>
429 </citations> 420 </citations>