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comparison lotus2.xml @ 17:28f284a679ce draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
author earlhaminst
date Fri, 28 Oct 2022 12:22:34 +0000
parents 12599a8dd22f
children 6c22795e1be0
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16:12599a8dd22f 17:28f284a679ce
1 <tool id="lotus2" name="LotuS2" version="@VERSION@" profile="20.09"> 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@">2.19</token> 4 <token name="@VERSION@">2.21</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>
24 <param name="ref_fasta" type="data" format="@REF_FASTA_FORMATS@" label="Taxonomy reference sequences" help="In FASTA format" /> 24 <param name="ref_fasta" type="data" format="@REF_FASTA_FORMATS@" label="Taxonomy reference sequences" help="In FASTA format" />
25 <param argument="-tax4refDB" type="data" format="tabular" label="Taxonomy reference lineages" help="Tab-separated file with 2 columns mapping each FASTA header of the reference sequences to a GTDB-style taxonomy string" /> 25 <param argument="-tax4refDB" type="data" format="tabular" label="Taxonomy reference lineages" help="Tab-separated file with 2 columns mapping each FASTA header of the reference sequences to a GTDB-style taxonomy string" />
26 </when> 26 </when>
27 </conditional> 27 </conditional>
28 <param argument="-useBestBlastHitOnly" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Use the best Blast hit only" help="Do not use LCA (lowest common ancestor) to determine the most likely taxonomic level (not recommended)" /> 28 <param argument="-useBestBlastHitOnly" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Use the best Blast hit only" help="Do not use LCA (lowest common ancestor) to determine the most likely taxonomic level (not recommended)" />
29 </xml>
30 <xml name="id_macro">
31 <param argument="-id" type="float" min="0.9" max="1" value="" optional="true" label="Clustering threshold for OTUs (optional)" />
32 </xml> 29 </xml>
33 <xml name="ITSx_macro"> 30 <xml name="ITSx_macro">
34 <param argument="-ITSx" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use ITSx to only retain OTUs fitting to ITS1/ITS2 hmm models" /> 31 <param argument="-ITSx" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use ITSx to only retain OTUs fitting to ITS1/ITS2 hmm models" />
35 </xml> 32 </xml>
36 </macros> 33 </macros>
73 ln -s '$f.forward' 'input/${symlink_basename($f.forward.dataset)}' && 70 ln -s '$f.forward' 'input/${symlink_basename($f.forward.dataset)}' &&
74 ln -s '$f.reverse' 'input/${symlink_basename($f.reverse.dataset)}' && 71 ln -s '$f.reverse' 'input/${symlink_basename($f.reverse.dataset)}' &&
75 #end for 72 #end for
76 #end if 73 #end if
77 74
78 #if $tax_args.aligner_cond.taxAligner not in ('0', '3') and $tax_args.aligner_cond.refDB_cond.refDB == 'history': 75 #if $aligner_cond.taxAligner not in ('0', '3') and $aligner_cond.refDB_cond.refDB == 'history':
79 #set $ext = $tax_args.aligner_cond.refDB_cond.ref_fasta.ext 76 #set $ext = $aligner_cond.refDB_cond.ref_fasta.ext
80 #set $ref_fasta_symlink = $symlink_basename($tax_args.aligner_cond.refDB_cond.ref_fasta, strip_ext=True) + '.' + $ext 77 #set $ref_fasta_symlink = $symlink_basename($aligner_cond.refDB_cond.ref_fasta, strip_ext=True) + '.' + $ext
81 ln -s '$tax_args.aligner_cond.refDB_cond.ref_fasta' '$ref_fasta_symlink' && 78 ln -s '$aligner_cond.refDB_cond.ref_fasta' '$ref_fasta_symlink' &&
82 #end if 79 #end if
83 80
84 #if not $map: 81 #if not $map:
85 cat '$generated_mapping' && 82 cat '$generated_mapping' &&
86 #set map = $generated_mapping 83 #set map = $generated_mapping
90 -i input/ 87 -i input/
91 -o output 88 -o output
92 -tmpDir tmp_folder 89 -tmpDir tmp_folder
93 -threads "\${GALAXY_SLOTS:-1}" 90 -threads "\${GALAXY_SLOTS:-1}"
94 -map '$map' 91 -map '$map'
95 #if $sdmopt: 92 #if $other_opts.sdmopt:
96 -sdmopt '$sdmopt' 93 -sdmopt '$other_opts.sdmopt'
97 #end if 94 #end if
98 #if $platform != '': 95 #if $other_opts.platform != '':
99 -platform $platform 96 -platform $other_opts.platform
100 #end if 97 #end if
101 #if $barcode: 98 #if $other_opts.barcode:
102 -barcode '$barcode' 99 -barcode '$other_opts.barcode'
103 #end if 100 #end if
104 #if $forwardPrimer: 101 #if $forwardPrimer:
105 -forwardPrimer '$forwardPrimer' 102 -forwardPrimer '$forwardPrimer'
106 #end if 103 #end if
107 #if $reversePrimer: 104 #if $reversePrimer:
108 -reversePrimer '$reversePrimer' 105 -reversePrimer '$reversePrimer'
109 #end if 106 #end if
110 #if $offtarget_cond.offtargetDB != 'no': 107 #if $other_opts.offtarget_cond.offtargetDB != 'no':
111 -offtargetDB '$offtarget_cond.ref_file' 108 -offtargetDB '$other_opts.offtarget_cond.ref_file'
112 #end if 109 #end if
113 -useMini4map $useMini4map 110 -useMini4map $other_opts.useMini4map
114 111
115 -clustering $clu_args.clu_cond.clustering 112 -clustering $clu_cond.clustering
116 #if $clu_args.clu_cond.clustering in ('1', '3'): 113 #if $clu_cond.clustering in ('1', '3'):
117 #if str($clu_args.clu_cond.id): 114 #if str($clu_cond.id):
118 -id $clu_args.clu_cond.id 115 -id $clu_cond.id
119 #end if 116 #end if
120 #elif $clu_args.clu_cond.clustering == '2': 117 #elif $clu_cond.clustering == '2':
121 #if str($clu_args.clu_cond.swarm_distance): 118 #if str($clu_cond.swarm_distance):
122 -swarm_distance $clu_args.clu_cond.swarm_distance 119 -swarm_distance $clu_cond.swarm_distance
123 #end if 120 #end if
124 #end if 121 #end if
125 #if $clu_args.derepMin: 122 #if $clu_args.derepMin:
126 -derepMin '$clu_args.derepMin' 123 -derepMin '$clu_args.derepMin'
127 #end if 124 #end if
131 #end if 128 #end if
132 #if str($clu_args.chim_skew): 129 #if str($clu_args.chim_skew):
133 -chim_skew $clu_args.chim_skew 130 -chim_skew $clu_args.chim_skew
134 #end if 131 #end if
135 132
136 -taxAligner $tax_args.aligner_cond.taxAligner 133 -taxAligner $aligner_cond.taxAligner
137 #if $tax_args.aligner_cond.taxAligner == '0': 134 #if $aligner_cond.taxAligner == '0':
138 #if str($tax_args.aligner_cond.rdp_thr): 135 #if str($aligner_cond.rdp_thr):
139 -rdp_thr $tax_args.aligner_cond.rdp_thr 136 -rdp_thr $aligner_cond.rdp_thr
140 #end if 137 #end if
141 #elif $tax_args.aligner_cond.taxAligner == '3': 138 #elif $aligner_cond.taxAligner == '3':
142 #if str($tax_args.aligner_cond.utax_thr): 139 #if str($aligner_cond.utax_thr):
143 -utax_thr $tax_args.aligner_cond.utax_thr 140 -utax_thr $aligner_cond.utax_thr
144 #end if 141 #end if
145 #else: 142 #else:
146 #if $tax_args.aligner_cond.refDB_cond.refDB == 'cached': 143 #if $aligner_cond.refDB_cond.refDB == 'cached':
147 #if $tax_args.aligner_cond.refDB_cond.ref_db != '': 144 #if $aligner_cond.refDB_cond.ref_db != '':
148 -refDB $tax_args.aligner_cond.refDB_cond.ref_db 145 -refDB $aligner_cond.refDB_cond.ref_db
149 -greengenesSpecies $tax_args.aligner_cond.refDB_cond.greengenesSpecies 146 -greengenesSpecies $aligner_cond.refDB_cond.greengenesSpecies
150 #end if 147 #end if
151 #else: 148 #else:
152 -refDB '$ref_fasta_symlink' 149 -refDB '$ref_fasta_symlink'
153 -tax4refDB '$tax_args.aligner_cond.refDB_cond.tax4refDB' 150 -tax4refDB '$aligner_cond.refDB_cond.tax4refDB'
154 #end if 151 #end if
155 -useBestBlastHitOnly $tax_args.aligner_cond.useBestBlastHitOnly 152 -useBestBlastHitOnly $aligner_cond.useBestBlastHitOnly
156 #end if 153 #end if
157 #if $tax_args.amplicon_cond.amplicon_type != '': 154 #if $tax_args.amplicon_cond.amplicon_type != '':
158 -amplicon_type $tax_args.amplicon_cond.amplicon_type 155 -amplicon_type $tax_args.amplicon_cond.amplicon_type
159 #end if 156 #end if
160 #if $tax_args.amplicon_cond.amplicon_type in ('ITS', 'ITS1', 'ITS2'): 157 #if $tax_args.amplicon_cond.amplicon_type in ('ITS', 'ITS1', 'ITS2'):
219 <when value="paired_collection"> 216 <when value="paired_collection">
220 <param name="pair_input" type="data_collection" collection_type="list:paired" format="fastqsanger,fastqsanger.gz" label="List of paired reads" /> 217 <param name="pair_input" type="data_collection" collection_type="list:paired" format="fastqsanger,fastqsanger.gz" label="List of paired reads" />
221 </when> 218 </when>
222 </conditional> 219 </conditional>
223 <param argument="-map" type="data" format="tabular" optional="true" label="Mapping file (optional)" help="Needed to demultiplex the FASTQ files using sdm. If the FASTQ are already demultiplexed, this can be omitted." /> 220 <param argument="-map" type="data" format="tabular" optional="true" label="Mapping file (optional)" help="Needed to demultiplex the FASTQ files using sdm. If the FASTQ are already demultiplexed, this can be omitted." />
224 <param argument="-sdmopt" type="data" format="txt" optional="true" label="SDM option file (optional)" />
225 <param argument="-platform" type="select" label="Sequencing platform">
226 <option value="" selected="true">(Default)</option>
227 <option value="miSeq">miSeq</option>
228 <option value="hiSeq">hiSeq</option>
229 <option value="454">454</option>
230 <option value="PacBio">PacBio</option>
231 </param>
232 <param argument="-barcode" type="data" format="fastqsanger" optional="true" label="Barcode (MID) sequences (optional)" help="FASTQ file with barcodes (in the processed mi/hiSeq format), if provided by the sequencer" />
233 <param argument="-forwardPrimer" type="text" value="" label="Forward primer used to amplify DNA region (optional)" help="E.g. 16S primer fwd" /> 221 <param argument="-forwardPrimer" type="text" value="" label="Forward primer used to amplify DNA region (optional)" help="E.g. 16S primer fwd" />
234 <param argument="-reversePrimer" type="text" value="" label="Reverse primer used to amplify DNA region (optional)" help="E.g. 16S primer rev" /> 222 <param argument="-reversePrimer" type="text" value="" label="Reverse primer used to amplify DNA region (optional)" help="E.g. 16S primer rev" />
235 <conditional name="offtarget_cond"> 223 <conditional name="clu_cond">
236 <param argument="-offtargetDB" type="select" label="Remove likely contaminant OTUs/ASVs based on alignment to host genome" help="Useful for low-bacterial biomass samples to remove possible host genome contaminations"> 224 <param argument="-clustering" type="select" label="Clustering algorithm">
237 <option value="no" selected="true">Disabled</option> 225 <option value="7" selected="true">DADA2</option>
238 <option value="cached">Use a built-in genome</option> 226 <option value="2">swarm</option>
239 <option value="history">Use a genome from history</option> 227 <option value="3">CD-HIT</option>
240 </param> 228 <option value="8">VSEARCH</option>
241 <when value="no" /> 229 </param>
242 <when value="cached"> 230 <when value="2">
243 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list"> 231 <param argument="-swarm_distance" type="integer" min="1" value="1" optional="true" label="Clustering threshold for OTUs when using swarm clustering (optional)" />
244 <options from_data_table="all_fasta"> 232 </when>
245 <filter type="sort_by" column="2" /> 233 <when value="3">
246 <validator type="no_options" message="No reference genomes are available" /> 234 <param argument="-id" type="float" min="0.9" max="1" value="0.97" optional="true" label="Clustering threshold for OTUs" />
247 </options> 235 </when>
248 </param> 236 <when value="7">
249 </when> 237 </when>
250 <when value="history"> 238 <when value="8">
251 <param name="ref_file" type="data" format="fasta,fasta.gz" label="FASTA reference genome" />
252 </when> 239 </when>
253 </conditional> 240 </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" /> 241 <conditional name="aligner_cond">
255 <section name="clu_args" title="Clustering Options"> 242 <param argument="-taxAligner" type="select" label="Taxonomy aligner for taxonomic profiling of OTUs">
256 <conditional name="clu_cond"> 243 <option value="0" selected="true">RDPclassifier (max likelihood)</option>
257 <param argument="-clustering" type="select" label="Clustering algorithm"> 244 <!-- <option value="1">Blast LCA against custom reference database</option> -->
258 <option value="2">swarm</option> 245 <option value="2">LAMBDA, LCA against custom reference database</option>
259 <option value="3">cd-hit</option> 246 <!-- <option value="4">VSEARCH LCA against custom reference database</option> -->
260 <option value="6">unoise3</option> 247 </param>
261 <option value="7" selected="true">dada2</option> 248 <when value="0">
262 <option value="8">vsearch</option> 249 <param argument="-rdp_thr" type="float" min="0" max="1" value="0.8" optional="true" label="Confidence threshold for RDP (optional)"/>
263 </param> 250 </when>
264 <when value="2"> 251 <!-- <when value="1">
265 <param argument="-swarm_distance" type="integer" min="1" value="1" optional="true" label="Clustering threshold for OTUs when using swarm clustering (optional)" /> 252 <expand macro="refDB_macro" ref_fasta_formats="fasta" />
266 </when> 253 </when> -->
267 <when value="3"> 254 <when value="2">
268 <expand macro="id_macro" /> 255 <expand macro="refDB_macro" />
269 </when> 256 </when>
270 <when value="6"> 257 <!-- <when value="3">
271 </when> 258 <param argument="-utax_thr" type="float" min="0" max="1" value="0.8" optional="true" label="Confidence threshold for UTAX (optional)"/>
272 <when value="7"> 259 </when>
273 </when> 260 <when value="4">
274 <when value="8"> 261 <expand macro="refDB_macro" />
275 </when> 262 </when> -->
276 </conditional> 263 </conditional>
264 <section name="clu_args" title="Other Clustering Options">
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." /> 265 <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." />
278 <param argument="-deactivateChimeraCheck" type="select" label="Chimera check"> 266 <param argument="-deactivateChimeraCheck" type="select" label="Chimera check">
279 <option value="" selected="true">(Default)</option> 267 <option value="" selected="true">(Default)</option>
280 <option value="0">OTU chimera checks</option> 268 <option value="0">OTU chimera checks</option>
281 <option value="1">No chimera check at all</option> 269 <option value="1">No chimera check at all</option>
282 <option value="2">Disable deNovo chimera check</option> 270 <option value="2">Disable deNovo chimera check</option>
283 <option value="3">Disable ref based chimera check</option> 271 <option value="3">Disable ref based chimera check</option>
284 </param> 272 </param>
285 <param argument="-chim_skew" type="integer" min="0" value="" optional="true" label="Skew in chimeric fragment abundance" /> 273 <param argument="-chim_skew" type="integer" min="0" value="" optional="true" label="Skew in chimeric fragment abundance" />
286 </section> 274 </section>
287 <section name="tax_args" title="Taxonomy Options"> 275 <section name="tax_args" title="Other Taxonomy Options">
288 <conditional name="aligner_cond">
289 <param argument="-taxAligner" type="select" label="Taxonomy aligner for taxonomic profiling of OTUs">
290 <option value="0" selected="true">RDPclassifier (max likelihood)</option>
291 <!-- <option value="1">Blast LCA against custom reference database</option> -->
292 <option value="2">LAMBDA LCA against custom reference database</option>
293 <!-- <option value="4">VSEARCH LCA against custom reference database</option> -->
294 </param>
295 <when value="0">
296 <param argument="-rdp_thr" type="float" min="0" max="1" value="0.8" optional="true" label="Confidence threshold for RDP (optional)"/>
297 </when>
298 <!-- <when value="1">
299 <expand macro="refDB_macro" ref_fasta_formats="fasta" />
300 </when> -->
301 <when value="2">
302 <expand macro="refDB_macro" />
303 </when>
304 <!-- <when value="3">
305 <param argument="-utax_thr" type="float" min="0" max="1" value="0.8" optional="true" label="Confidence threshold for UTAX (optional)"/>
306 </when>
307 <when value="4">
308 <expand macro="refDB_macro" />
309 </when> -->
310 </conditional>
311 <conditional name="amplicon_cond"> 276 <conditional name="amplicon_cond">
312 <param argument="-amplicon_type" type="select" label="Amplicon type"> 277 <param argument="-amplicon_type" type="select" label="Amplicon type">
313 <option value="" selected="true">(Default)</option> 278 <option value="" selected="true">(Default)</option>
314 <option value="LSU">LSU Large subunit (23S/28S)</option> 279 <option value="LSU">LSU Large subunit (23S/28S)</option>
315 <option value="SSU">SSU small subunit (16S/18S)</option> 280 <option value="SSU">SSU small subunit (16S/18S)</option>
336 <option value="fungi">fungal 18S/23S/ITS annotation</option> 301 <option value="fungi">fungal 18S/23S/ITS annotation</option>
337 </param> 302 </param>
338 <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" /> 303 <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" />
339 <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)"/> 304 <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)"/>
340 <param argument="-LCA_frac" type="float" min="0" max="1" value="" optional="true" label="Minimum fraction of reads with identical taxonomy (optional)"/> 305 <param argument="-LCA_frac" type="float" min="0" max="1" value="" optional="true" label="Minimum fraction of reads with identical taxonomy (optional)"/>
341 <param argument="-lulu" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Use LULU to merge OTUs based on their occurrence" /> 306 <param argument="-lulu" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use LULU to merge OTUs based on their occurrence" />
342 <param argument="-buildPhylo" type="select" label="Build OTU phylogeny"> 307 <param argument="-buildPhylo" type="select" label="Build OTU phylogeny">
343 <option value="0">Disable</option> 308 <option value="0">Disable</option>
344 <option value="1" selected="true">Use fasttree2</option> 309 <option value="1" selected="true">Use fasttree2</option>
345 <option value="2">Use iqtree2</option> 310 <option value="2">Use iqtree2</option>
346 </param> 311 </param>
350 <add value="|" /> 315 <add value="|" />
351 <add value="$" /> 316 <add value="$" />
352 </valid> 317 </valid>
353 </sanitizer> 318 </sanitizer>
354 </param> 319 </param>
320 </section>
321 <section name="other_opts" title="Other options">
322 <param argument="-sdmopt" type="data" format="txt" optional="true" label="SDM option file (optional)" />
323 <param argument="-platform" type="select" label="Sequencing platform">
324 <option value="" selected="true">(Default)</option>
325 <option value="miSeq">miSeq</option>
326 <option value="hiSeq">hiSeq</option>
327 <option value="454">454</option>
328 <option value="PacBio">PacBio</option>
329 </param>
330 <param argument="-barcode" type="data" format="fastqsanger" optional="true" label="Barcode (MID) sequences (optional)" help="FASTQ file with barcodes (in the processed mi/hiSeq format), if provided by the sequencer" />
331 <conditional name="offtarget_cond">
332 <param argument="-offtargetDB" type="select" label="Remove likely contaminant OTUs/ASVs based on alignment to host genome" help="Useful for low-bacterial biomass samples to remove possible host genome contaminations">
333 <option value="no" selected="true">Disabled</option>
334 <option value="cached">Use a built-in genome</option>
335 <option value="history">Use a genome from history</option>
336 </param>
337 <when value="no" />
338 <when value="cached">
339 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
340 <options from_data_table="all_fasta">
341 <filter type="sort_by" column="2" />
342 <validator type="no_options" message="No reference genomes are available" />
343 </options>
344 </param>
345 </when>
346 <when value="history">
347 <param name="ref_file" type="data" format="fasta,fasta.gz" label="FASTA reference genome" />
348 </when>
349 </conditional>
350 <param argument="-useMini4map" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use minimap2 instead of VSEARCH to map back reads to OTUs" />
355 </section> 351 </section>
356 </inputs> 352 </inputs>
357 353
358 <outputs> 354 <outputs>
359 <data name="outputs" format="zip" label="${tool.name} on ${on_string}: Complete LotuS2 output" from_work_dir="output.zip" /> 355 <data name="outputs" format="zip" label="${tool.name} on ${on_string}: Complete LotuS2 output" from_work_dir="output.zip" />
368 <test> 364 <test>
369 <conditional name="inputs"> 365 <conditional name="inputs">
370 <param name="paired_or_single" value="single"/> 366 <param name="paired_or_single" value="single"/>
371 <param name="input" value="Anh_sample1.fastq.gz,Anh_sample2.fastq.gz" ftype="fastqsanger.gz"/> 367 <param name="input" value="Anh_sample1.fastq.gz,Anh_sample2.fastq.gz" ftype="fastqsanger.gz"/>
372 </conditional> 368 </conditional>
373 <param name="platform" value="454" /> 369 <conditional name="clu_cond">
370 <param name="clustering" value="3" />
371 </conditional>
374 <section name="clu_args"> 372 <section name="clu_args">
375 <conditional name="clu_cond">
376 <param name="clustering" value="3" />
377 </conditional>
378 <param name="derepMin" value="1" /> 373 <param name="derepMin" value="1" />
374 </section>
375 <section name="tax_args">
376 <param name="lulu" value="false" />
377 </section>
378 <section name="other_opts">
379 <param name="platform" value="454" />
379 </section> 380 </section>
380 <output name="otu" file="OTU.txt" compare="sim_size" /> 381 <output name="otu" file="OTU.txt" compare="sim_size" />
381 <output name="otu_fna" file="OTU.fna" compare="sim_size" /> 382 <output name="otu_fna" file="OTU.fna" compare="sim_size" />
382 <output name="mapping" file="mapping.txt" /> 383 <output name="mapping" file="mapping.txt" />
383 </test> 384 </test>
394 </element> 395 </element>
395 </collection> 396 </collection>
396 </param> 397 </param>
397 </conditional> 398 </conditional>
398 <param name="map" value="mapping_paired.txt" /> 399 <param name="map" value="mapping_paired.txt" />
399 <param name="platform" value="454" /> 400 <conditional name="clu_cond">
401 <param name="clustering" value="3" />
402 </conditional>
400 <section name="clu_args"> 403 <section name="clu_args">
401 <conditional name="clu_cond">
402 <param name="clustering" value="3" />
403 </conditional>
404 <param name="derepMin" value="1" /> 404 <param name="derepMin" value="1" />
405 </section>
406 <section name="tax_args">
407 <param name="lulu" value="false" />
408 </section>
409 <section name="other_opts">
410 <param name="platform" value="454" />
405 </section> 411 </section>
406 <output name="otu" file="OTU_paired.txt" compare="sim_size" /> 412 <output name="otu" file="OTU_paired.txt" compare="sim_size" />
407 <output name="otu_fna" file="OTU_paired.fna" compare="sim_size" /> 413 <output name="otu_fna" file="OTU_paired.fna" compare="sim_size" />
408 </test> 414 </test>
409 </tests> 415 </tests>
410 416
411 <help><![CDATA[ 417 <help><![CDATA[
412 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. 418 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.
413 419
414 Documentation can be found at `<http://lotus2.earlham.ac.uk/>`_. 420 .. class:: infomark
421
422 The full LotuS2 **documentation** can be found at `<http://lotus2.earlham.ac.uk/>`_.
415 ]]></help> 423 ]]></help>
416 <citations> 424 <citations>
417 <citation type="doi">10.1101/2021.12.24.474111</citation> 425 <citation type="doi">10.1186/s40168-022-01365-1</citation>
426 <citation type="doi">10.1186/s40168-021-01012-1</citation>
418 </citations> 427 </citations>
419 </tool> 428 </tool>