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comparison lotus2.xml @ 10:6d55d9464719 draft

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"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330"
author earlhaminst
date Tue, 08 Jun 2021 17:21:29 +0000
parents 82ff4f47436a
children 8f732780e0f3
comparison
equal deleted inserted replaced
9:82ff4f47436a 10:6d55d9464719
1 <tool id="lotus2" name="LotuS2" version="@VERSION@+galaxy1" profile="20.01"> 1 <tool id="lotus2" name="LotuS2" version="@VERSION@+galaxy2" profile="20.01">
2 <description>fast OTU processing pipeline</description> 2 <description>fast OTU processing pipeline</description>
3 <macros> 3 <macros>
4 <token name="@VERSION@">2.07</token> 4 <token name="@VERSION@">2.07</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">
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> 29 </xml>
30 <xml name="id_macro"> 30 <xml name="id_macro">
31 <param argument="-id" type="float" min="0.9" max="1" value="" optional="true" label="Clustering threshold for OTUs" /> 31 <param argument="-id" type="float" min="0.9" max="1" value="" optional="true" label="Clustering threshold for OTUs (optional)" />
32 </xml> 32 </xml>
33 <xml name="ITSx_macro"> 33 <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" /> 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" />
35 </xml> 35 </xml>
36 </macros> 36 </macros>
123 #if $offtarget_cond.offtargetDB != 'no': 123 #if $offtarget_cond.offtargetDB != 'no':
124 -offtargetDB '$offtarget_cond.ref_file' 124 -offtargetDB '$offtarget_cond.ref_file'
125 #end if 125 #end if
126 126
127 -clustering $clu_args.clu_cond.clustering 127 -clustering $clu_args.clu_cond.clustering
128 #if $clu_args.clu_cond.clustering in ('1', '3') and str($clu_args.clu_cond.id): 128 #if $clu_args.clu_cond.clustering in ('1', '3'):
129 -id $clu_args.clu_cond.id 129 #if str($clu_args.clu_cond.id):
130 -id $clu_args.clu_cond.id
131 #end if
130 #elif $clu_args.clu_cond.clustering == '2': 132 #elif $clu_args.clu_cond.clustering == '2':
131 -swarm_distance $clu_args.clu_cond.swarm_distance 133 #if str($clu_args.clu_cond.swarm_distance):
134 -swarm_distance $clu_args.clu_cond.swarm_distance
135 #end if
132 #end if 136 #end if
133 #if $clu_args.derepMin: 137 #if $clu_args.derepMin:
134 -derepMin '$clu_args.derepMin' 138 -derepMin '$clu_args.derepMin'
135 #end if 139 #end if
136 140
141 -chim_skew $clu_args.chim_skew 145 -chim_skew $clu_args.chim_skew
142 #end if 146 #end if
143 147
144 -taxAligner $tax_args.aligner_cond.taxAligner 148 -taxAligner $tax_args.aligner_cond.taxAligner
145 #if $tax_args.aligner_cond.taxAligner == '0': 149 #if $tax_args.aligner_cond.taxAligner == '0':
146 -rdp_thr $tax_args.aligner_cond.rdp_thr 150 #if str($tax_args.aligner_cond.rdp_thr):
151 -rdp_thr $tax_args.aligner_cond.rdp_thr
152 #end if
147 #elif $tax_args.aligner_cond.taxAligner == '3': 153 #elif $tax_args.aligner_cond.taxAligner == '3':
148 -utax_thr $tax_args.aligner_cond.utax_thr 154 #if str($tax_args.aligner_cond.utax_thr):
155 -utax_thr $tax_args.aligner_cond.utax_thr
156 #end if
149 #else: 157 #else:
150 #if $tax_args.aligner_cond.refDB_cond.refDB == 'cached': 158 #if $tax_args.aligner_cond.refDB_cond.refDB == 'cached':
151 #if $tax_args.aligner_cond.refDB_cond.ref_db != '': 159 #if $tax_args.aligner_cond.refDB_cond.ref_db != '':
152 -refDB $tax_args.aligner_cond.refDB_cond.ref_db 160 -refDB $tax_args.aligner_cond.refDB_cond.ref_db
153 -greengenesSpecies $tax_args.aligner_cond.refDB_cond.greengenesSpecies 161 -greengenesSpecies $tax_args.aligner_cond.refDB_cond.greengenesSpecies
212 <option value="hiSeq">hiSeq</option> 220 <option value="hiSeq">hiSeq</option>
213 <option value="454">454</option> 221 <option value="454">454</option>
214 <option value="PacBio">PacBio</option> 222 <option value="PacBio">PacBio</option>
215 </param> 223 </param>
216 <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" /> 224 <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" />
217 <param argument="-forwardPrimer" type="text" value="" label="Forward primer used to amplify DNA region" help="E.g. 16S primer fwd" /> 225 <param argument="-forwardPrimer" type="text" value="" label="Forward primer used to amplify DNA region (optional)" help="E.g. 16S primer fwd" />
218 <param argument="-reversePrimer" type="text" value="" label="Reverse primer used to amplify DNA region" help="E.g. 16S primer rev" /> 226 <param argument="-reversePrimer" type="text" value="" label="Reverse primer used to amplify DNA region (optional)" help="E.g. 16S primer rev" />
219 <conditional name="offtarget_cond"> 227 <conditional name="offtarget_cond">
220 <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"> 228 <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">
221 <option value="no" selected="true">Disabled</option> 229 <option value="no" selected="true">Disabled</option>
222 <option value="cached">Use a built-in genome</option> 230 <option value="cached">Use a built-in genome</option>
223 <option value="history">Use a genome from history</option> 231 <option value="history">Use a genome from history</option>
246 </param> 254 </param>
247 <when value="1"> 255 <when value="1">
248 <expand macro="id_macro" /> 256 <expand macro="id_macro" />
249 </when> 257 </when>
250 <when value="2"> 258 <when value="2">
251 <param argument="-swarm_distance" type="integer" min="1" value="1" label="Clustering threshold for OTUs when using swarm clustering" /> 259 <param argument="-swarm_distance" type="integer" min="1" value="1" optional="true" label="Clustering threshold for OTUs when using swarm clustering (optional)" />
252 </when> 260 </when>
253 <when value="3"> 261 <when value="3">
254 <expand macro="id_macro" /> 262 <expand macro="id_macro" />
255 </when> 263 </when>
256 <when value="6"> 264 <when value="6">
270 </section> 278 </section>
271 <section name="tax_args" title="Taxonomy Options"> 279 <section name="tax_args" title="Taxonomy Options">
272 <conditional name="aligner_cond"> 280 <conditional name="aligner_cond">
273 <param argument="-taxAligner" type="select" label="Taxonomy aligner for taxonomic profiling of OTUs"> 281 <param argument="-taxAligner" type="select" label="Taxonomy aligner for taxonomic profiling of OTUs">
274 <option value="0" selected="true">RDPclassifier (max likelihood)</option> 282 <option value="0" selected="true">RDPclassifier (max likelihood)</option>
275 <option value="1">Blast LCA against custom reference database</option> 283 <!-- <option value="1">Blast LCA against custom reference database</option> -->
276 <option value="2">LAMBDA LCA against custom reference database</option> 284 <option value="2">LAMBDA LCA against custom reference database</option>
277 <option value="3">UTAX likelihood corrected</option> 285 <!-- <option value="4">VSEARCH LCA against custom reference database</option> -->
278 <option value="4">VSEARCH LCA against custom reference database</option>
279 </param> 286 </param>
280 <when value="0"> 287 <when value="0">
281 <param argument="-rdp_thr" type="float" min="0" max="1" value="0.8" label="Confidence threshold for RDP"/> 288 <param argument="-rdp_thr" type="float" min="0" max="1" value="0.8" optional="true" label="Confidence threshold for RDP (optional)"/>
282 </when> 289 </when>
283 <when value="1"> 290 <when value="1">
284 <expand macro="refDB_macro" ref_fasta_formats="fasta" /> 291 <expand macro="refDB_macro" ref_fasta_formats="fasta" />
285 </when> 292 </when>
286 <when value="2"> 293 <when value="2">
287 <expand macro="refDB_macro" /> 294 <expand macro="refDB_macro" />
288 </when> 295 </when>
289 <when value="3"> 296 <when value="3">
290 <param argument="-utax_thr" type="float" min="0" max="1" value="0.8" label="Confidence threshold for UTAX"/> 297 <param argument="-utax_thr" type="float" min="0" max="1" value="0.8" optional="true" label="Confidence threshold for UTAX (optional)"/>
291 </when> 298 </when>
292 <when value="4"> 299 <when value="4">
293 <expand macro="refDB_macro" /> 300 <expand macro="refDB_macro" />
294 </when> 301 </when>
295 </conditional> 302 </conditional>
319 <option value="" selected="true">(Default)</option> 326 <option value="" selected="true">(Default)</option>
320 <option value="bacteria">bacterial 16S rDNA annnotation</option> 327 <option value="bacteria">bacterial 16S rDNA annnotation</option>
321 <option value="fungi">fungal 18S/23S/ITS annotation</option> 328 <option value="fungi">fungal 18S/23S/ITS annotation</option>
322 </param> 329 </param>
323 <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" /> 330 <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" />
324 <param argument="-LCA_cover" type="float" min="0" max="1" value="" optional="true" label="Minimum horizontal coverage of an OTU sequence against ref DB"/> 331 <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)"/>
325 <param argument="-LCA_frac" type="float" min="0" max="1" value="" optional="true" label="Minimum fraction of reads with identical taxonomy"/> 332 <param argument="-LCA_frac" type="float" min="0" max="1" value="" optional="true" label="Minimum fraction of reads with identical taxonomy (optional)"/>
326 <param argument="-lulu" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Use LULU to merge OTUs based on their occurrence" /> 333 <param argument="-lulu" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Use LULU to merge OTUs based on their occurrence" />
327 <param argument="-buildPhylo" type="select" label="Build OTU phylogeny"> 334 <param argument="-buildPhylo" type="select" label="Build OTU phylogeny">
328 <option value="0">Disable</option> 335 <option value="0">Disable</option>
329 <option value="1" selected="true">Use fasttree2</option> 336 <option value="1" selected="true">Use fasttree2</option>
330 <option value="2">Use iqtree2</option> 337 <option value="2">Use iqtree2</option>