lotus2: lotus2.xml annotate

annotate lotus2.xml @ 20:1d660ee0b1c8 draft

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

rev	line source
19 a3d31a68f291 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 3d69a14f20c8088412cf3729814be721b0db778c earlhaminst parents: 18 diff changeset	1 <tool id="lotus2" name="LotuS2" version="@VERSION@+galaxy2" profile="20.09">
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	2 <description>fast OTU processing pipeline</description>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	3 <macros>
20 1d660ee0b1c8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e532d288f092df22f32805cea50583fe16a1070f earlhaminst parents: 19 diff changeset	4 <token name="@VERSION@">2.23</token>
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	5 <xml name="refDB_macro" token_ref_fasta_formats="fasta,fasta.gz">
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	6 <conditional name="refDB_cond">
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	7 <param argument="-refDB" type="select" label="Taxonomy reference database">
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	8 <option value="cached">Use a built-in taxonomy database</option>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	9 <option value="history">Use a taxonomy from history</option>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	10 </param>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	11 <when value="cached">
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	12 <param argument="-ref_db" type="select" label="Using reference database" help="Select database from the list">
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	13 <option value="" selected="true">(Default)</option>
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	14 <option value="SLV">Silva LSU (23/28S) or SSU (16/18S) (SLV)</option>
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	15 <option value="GG">Greengenes (GG)</option>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	16 <option value="UNITE">ITS focused on fungi (UNITE)</option>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	17 <option value="PR2">SSU focused on Protists (PR2)</option>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	18 <option value="beetax">Bee gut specific database and tax names (beetax)</option>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	19 <option value="HITdb">Human gut microbiota (HITdb)</option>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	20 </param>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	21 <param argument="-greengenesSpecies" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Create greengenes output labels instead of OTU" />
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	22 </when>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	23 <when value="history">
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	24 <param name="ref_fasta" type="data" format="@REF_FASTA_FORMATS@" label="Taxonomy reference sequences" help="In FASTA format" />
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	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" />
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	26 </when>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	27 </conditional>
2 cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	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)" />
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	29 </xml>
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	30 <xml name="ITSx_macro">
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	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" />
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	32 </xml>
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	33 </macros>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	34 <requirements>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	35 <requirement type="package" version="@VERSION@">lotus2</requirement>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	36 </requirements>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	37 <version_command>lotus2 --version</version_command>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	38 <command detect_errors="exit_code"><![CDATA[
2 cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	39 #import os.path
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	40 #import re
12 3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a" earlhaminst parents: 11 diff changeset	41 #def symlink_basename($f, strip_ext=False):
11 8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	42 #set $fn = re.sub('[^\w\-_.]', '_', $f.name)
12 3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a" earlhaminst parents: 11 diff changeset	43 #if strip_ext:
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a" earlhaminst parents: 11 diff changeset	44 #if $fn.endswith('.gz'):
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a" earlhaminst parents: 11 diff changeset	45 #set $fn = $fn[:-3]
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a" earlhaminst parents: 11 diff changeset	46 #end if
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a" earlhaminst parents: 11 diff changeset	47 #if $f.ext.startswith('fasta'):
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a" earlhaminst parents: 11 diff changeset	48 #set $exts_to_drop = ('.fa', '.fasta', '.fna')
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a" earlhaminst parents: 11 diff changeset	49 #else:
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a" earlhaminst parents: 11 diff changeset	50 #set $exts_to_drop = []
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a" earlhaminst parents: 11 diff changeset	51 #end if
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a" earlhaminst parents: 11 diff changeset	52 #for $ext in $exts_to_drop:
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a" earlhaminst parents: 11 diff changeset	53 #if $fn.endswith($ext):
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a" earlhaminst parents: 11 diff changeset	54 #set $fn = $fn[:-len($ext)]
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a" earlhaminst parents: 11 diff changeset	55 #break
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a" earlhaminst parents: 11 diff changeset	56 #end if
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a" earlhaminst parents: 11 diff changeset	57 #end for
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a" earlhaminst parents: 11 diff changeset	58 #end if
11 8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	59 ${fn}#slurp
2 cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	60 #end def
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	61
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	62 mkdir input
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	63 &&
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	64 #if $inputs.paired_or_single == 'single':
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	65 #for $f in $inputs.input:
11 8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	66 ln -s '$f' 'input/${symlink_basename($f)}' &&
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	67 #end for
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	68 #else:
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	69 #for $f in $inputs.pair_input:
11 8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	70 ln -s '$f.forward' 'input/${symlink_basename($f.forward.dataset)}' &&
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	71 ln -s '$f.reverse' 'input/${symlink_basename($f.reverse.dataset)}' &&
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	72 #end for
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	73 #end if
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	74
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	75 #if $aligner_cond.taxAligner not in ('0', '3') and $aligner_cond.refDB_cond.refDB == 'history':
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	76 #set $ext = $aligner_cond.refDB_cond.ref_fasta.ext
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	77 #set $ref_fasta_symlink = $symlink_basename($aligner_cond.refDB_cond.ref_fasta, strip_ext=True) + '.' + $ext
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	78 ln -s '$aligner_cond.refDB_cond.ref_fasta' '$ref_fasta_symlink' &&
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	79 #end if
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	80
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	81 #if not $map:
11 8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	82 cat '$generated_mapping' &&
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	83 #set map = $generated_mapping
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	84 #end if
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	85
18 6c22795e1be0 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit afdb7dbe3283ee64d3aa2277efe505c7341575d8 earlhaminst parents: 17 diff changeset	86 set +e &&
6c22795e1be0 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit afdb7dbe3283ee64d3aa2277efe505c7341575d8 earlhaminst parents: 17 diff changeset	87
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	88 lotus2
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	89 -i input/
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	90 -o output
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	91 -tmpDir tmp_folder
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	92 -threads "\${GALAXY_SLOTS:-1}"
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	93 -map '$map'
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	94 #if $other_opts.sdmopt:
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	95 -sdmopt '$other_opts.sdmopt'
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	96 #end if
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	97 #if $other_opts.platform != '':
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	98 -platform $other_opts.platform
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	99 #end if
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	100 #if $other_opts.barcode:
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	101 -barcode '$other_opts.barcode'
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	102 #end if
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	103 #if $forwardPrimer:
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	104 -forwardPrimer '$forwardPrimer'
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	105 #end if
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	106 #if $reversePrimer:
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	107 -reversePrimer '$reversePrimer'
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	108 #end if
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	109 #if $other_opts.offtarget_cond.offtargetDB != 'no':
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	110 -offtargetDB '$other_opts.offtarget_cond.ref_file'
2 cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	111 #end if
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	112 -useMini4map $other_opts.useMini4map
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	113
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	114 -clustering $clu_cond.clustering
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	115 #if $clu_cond.clustering in ('1', '3'):
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	116 #if str($clu_cond.id):
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	117 -id $clu_cond.id
10 6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	118 #end if
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	119 #elif $clu_cond.clustering == '2':
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	120 #if str($clu_cond.swarm_distance):
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	121 -swarm_distance $clu_cond.swarm_distance
10 6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	122 #end if
2 cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	123 #end if
1 85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24" earlhaminst parents: 0 diff changeset	124 #if $clu_args.derepMin:
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24" earlhaminst parents: 0 diff changeset	125 -derepMin '$clu_args.derepMin'
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24" earlhaminst parents: 0 diff changeset	126 #end if
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	127
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	128 #if $clu_args.deactivateChimeraCheck != '':
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	129 -deactivateChimeraCheck $clu_args.deactivateChimeraCheck
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	130 #end if
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	131 #if str($clu_args.chim_skew):
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	132 -chim_skew $clu_args.chim_skew
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	133 #end if
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	134
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	135 -taxAligner $aligner_cond.taxAligner
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	136 #if $aligner_cond.taxAligner == '0':
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	137 #if str($aligner_cond.rdp_thr):
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	138 -rdp_thr $aligner_cond.rdp_thr
10 6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	139 #end if
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	140 #elif $aligner_cond.taxAligner == '3':
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	141 #if str($aligner_cond.utax_thr):
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	142 -utax_thr $aligner_cond.utax_thr
10 6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	143 #end if
1 85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24" earlhaminst parents: 0 diff changeset	144 #else:
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	145 #if $aligner_cond.refDB_cond.refDB == 'cached':
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	146 #if $aligner_cond.refDB_cond.ref_db != '':
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	147 -refDB $aligner_cond.refDB_cond.ref_db
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	148 -greengenesSpecies $aligner_cond.refDB_cond.greengenesSpecies
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	149 #end if
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	150 #else:
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	151 -refDB '$ref_fasta_symlink'
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	152 -tax4refDB '$aligner_cond.refDB_cond.tax4refDB'
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	153 #end if
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	154 -useBestBlastHitOnly $aligner_cond.useBestBlastHitOnly
1 85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24" earlhaminst parents: 0 diff changeset	155 #end if
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	156 #if $tax_args.amplicon_cond.amplicon_type != '':
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	157 -amplicon_type $tax_args.amplicon_cond.amplicon_type
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	158 #end if
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	159 #if $tax_args.amplicon_cond.amplicon_type in ('ITS', 'ITS1', 'ITS2'):
9 82ff4f47436a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 540400ccedbc8a88d00e021b645d35ac72e8098b" earlhaminst parents: 8 diff changeset	160 -ITSx $tax_args.amplicon_cond.ITSx
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	161 #end if
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	162
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	163 #if $tax_args.tax_group != '':
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	164 -tax_group $tax_args.tax_group
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	165 #end if
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	166 -keepUnclassified $tax_args.keepUnclassified
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	167 #if str($tax_args.LCA_cover):
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	168 -LCA_cover $tax_args.LCA_cover
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	169 #end if
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	170 #if str($tax_args.LCA_frac):
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	171 -LCA_frac $tax_args.LCA_frac
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	172 #end if
2 cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	173 -lulu $tax_args.lulu
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	174 -buildPhylo $tax_args.buildPhylo
15 6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	175 #if $tax_args.taxExcludeGrep:
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	176 -taxExcludeGrep '$tax_args.taxExcludeGrep'
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	177 #end if
1 85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24" earlhaminst parents: 0 diff changeset	178 ; EXIT_VALUE=\$? ;
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	179
7 692832801d70 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 81334bedc488edc36581c015b5a4c06926ec236c" earlhaminst parents: 6 diff changeset	180 zip -8 -r -v output.zip output/
1 85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24" earlhaminst parents: 0 diff changeset	181 &&
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24" earlhaminst parents: 0 diff changeset	182 exit \$EXIT_VALUE
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	183 ]]></command>
11 8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	184 <configfiles>
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	185 <configfile name="generated_mapping"><![CDATA[#slurp
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	186 #import re
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	187 #def symlink_basename($f):
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	188 #set $fn = re.sub('[^\w\-_.]', '_', $f.name)
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	189 ${fn}#slurp
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	190 #end def
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	191 #SampleID fastqFile SequencingRun
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	192 #if $inputs.paired_or_single == 'single':
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	193 #for $i, $f in enumerate($inputs.input):
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	194 SMPL${i} ${symlink_basename($f)} a
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	195 #end for
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	196 #else:
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	197 #for $i, $f in enumerate($inputs.pair_input):
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	198 SMPL${i} ${symlink_basename($f.forward.dataset)},${symlink_basename($f.reverse.dataset)} a
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	199 #end for
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	200 #end if
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	201 ]]></configfile>
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	202 </configfiles>
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	203 <inputs>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	204 <conditional name="inputs">
8 0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c" earlhaminst parents: 7 diff changeset	205 <param name="paired_or_single" type="select" label="Single- or Paired-end data?">
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	206 <option value="single" selected="true">Single-end</option>
8 0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c" earlhaminst parents: 7 diff changeset	207 <option value="paired_collection">Paired-end list</option>
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	208 </param>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	209 <when value="single">
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	210 <param name="input" type="data" format="fastqsanger,fastqsanger.gz" multiple="true" label="Single-end reads" />
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	211 </when>
2 cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	212 <!--
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	213 <when value="paired">
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	214 <param name="left_input" type="data" format="fastqsanger,fastqsanger.gz" multiple="true" label="Left/Forward strand reads" />
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	215 <param name="right_input" type="data" format="fastqsanger,fastqsanger.gz" multiple="true" label="Right/Reverse strand reads" />
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	216 </when>
2 cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	217 -->
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	218 <when value="paired_collection">
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	219 <param name="pair_input" type="data_collection" collection_type="list:paired" format="fastqsanger,fastqsanger.gz" label="List of paired reads" />
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	220 </when>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	221 </conditional>
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	222 <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." />
10 6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	223 <param argument="-forwardPrimer" type="text" value="" label="Forward primer used to amplify DNA region (optional)" help="E.g. 16S primer fwd" />
6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	224 <param argument="-reversePrimer" type="text" value="" label="Reverse primer used to amplify DNA region (optional)" help="E.g. 16S primer rev" />
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	225 <conditional name="clu_cond">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	226 <param argument="-clustering" type="select" label="Clustering algorithm">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	227 <option value="7" selected="true">DADA2</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	228 <option value="2">swarm</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	229 <option value="3">CD-HIT</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	230 <option value="8">VSEARCH</option>
2 cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	231 </param>
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	232 <when value="2">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	233 <param argument="-swarm_distance" type="integer" min="1" value="1" optional="true" label="Clustering threshold for OTUs when using swarm clustering (optional)" />
2 cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	234 </when>
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	235 <when value="3">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	236 <param argument="-id" type="float" min="0.9" max="1" value="0.97" optional="true" label="Clustering threshold for OTUs" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	237 </when>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	238 <when value="7">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	239 </when>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	240 <when value="8">
2 cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	241 </when>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	242 </conditional>
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	243 <conditional name="aligner_cond">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	244 <param argument="-taxAligner" type="select" label="Taxonomy aligner for taxonomic profiling of OTUs">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	245 <option value="0" selected="true">RDPclassifier (max likelihood)</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	246 <!-- <option value="1">Blast LCA against custom reference database</option> -->
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	247 <option value="2">LAMBDA, LCA against custom reference database</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	248 <!-- <option value="4">VSEARCH LCA against custom reference database</option> -->
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	249 </param>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	250 <when value="0">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	251 <param argument="-rdp_thr" type="float" min="0" max="1" value="0.8" optional="true" label="Confidence threshold for RDP (optional)"/>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	252 </when>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	253 <!-- <when value="1">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	254 <expand macro="refDB_macro" ref_fasta_formats="fasta" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	255 </when> -->
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	256 <when value="2">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	257 <expand macro="refDB_macro" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	258 </when>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	259 <!-- <when value="3">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	260 <param argument="-utax_thr" type="float" min="0" max="1" value="0.8" optional="true" label="Confidence threshold for UTAX (optional)"/>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	261 </when>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	262 <when value="4">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	263 <expand macro="refDB_macro" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	264 </when> -->
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	265 </conditional>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	266 <section name="clu_args" title="Other Clustering Options">
20 1d660ee0b1c8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e532d288f092df22f32805cea50583fe16a1070f earlhaminst parents: 19 diff changeset	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." />
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	268 <param argument="-deactivateChimeraCheck" type="select" label="Chimera check">
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	269 <option value="" selected="true">(Default)</option>
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	270 <option value="0">OTU chimera checks</option>
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	271 <option value="1">No chimera check at all</option>
2 cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	272 <option value="2">Disable deNovo chimera check</option>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	273 <option value="3">Disable ref based chimera check</option>
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	274 </param>
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	275 <param argument="-chim_skew" type="integer" min="0" value="" optional="true" label="Skew in chimeric fragment abundance" />
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	276 </section>
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	277 <section name="tax_args" title="Other Taxonomy Options">
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	278 <conditional name="amplicon_cond">
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	279 <param argument="-amplicon_type" type="select" label="Amplicon type">
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	280 <option value="" selected="true">(Default)</option>
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	281 <option value="LSU">LSU Large subunit (23S/28S)</option>
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	282 <option value="SSU">SSU small subunit (16S/18S)</option>
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	283 <option value="ITS">ITS internal transcribed spacer</option>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	284 <option value="ITS1">ITS1</option>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	285 <option value="ITS2">ITS2</option>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	286 </param>
8 0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c" earlhaminst parents: 7 diff changeset	287 <when value="" />
0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c" earlhaminst parents: 7 diff changeset	288 <when value="LSU" />
0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c" earlhaminst parents: 7 diff changeset	289 <when value="SSU" />
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	290 <when value="ITS">
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	291 <expand macro="ITSx_macro" />
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	292 </when>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	293 <when value="ITS1">
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	294 <expand macro="ITSx_macro" />
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	295 </when>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	296 <when value="ITS2">
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	297 <expand macro="ITSx_macro" />
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	298 </when>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	299 </conditional>
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	300 <param argument="-tax_group" type="select" label="Tax group">
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	301 <option value="" selected="true">(Default)</option>
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	302 <option value="bacteria">bacterial 16S rDNA annnotation</option>
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	303 <option value="fungi">fungal 18S/23S/ITS annotation</option>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	304 </param>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	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" />
10 6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	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)"/>
6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	307 <param argument="-LCA_frac" type="float" min="0" max="1" value="" optional="true" label="Minimum fraction of reads with identical taxonomy (optional)"/>
20 1d660ee0b1c8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e532d288f092df22f32805cea50583fe16a1070f earlhaminst parents: 19 diff changeset	308 <param argument="-lulu" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use LULU to merge OTUs based on their occurrence" />
2 cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	309 <param argument="-buildPhylo" type="select" label="Build OTU phylogeny">
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	310 <option value="0">Disable</option>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	311 <option value="1" selected="true">Use fasttree2</option>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	312 <option value="2">Use iqtree2</option>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	313 </param>
15 6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	314 <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">
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	315 <sanitizer>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	316 <valid initial="default">
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	317 <add value="\|" />
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	318 <add value="$" />
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	319 </valid>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	320 </sanitizer>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	321 </param>
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	322 </section>
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	323 <section name="other_opts" title="Other options">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	324 <param argument="-sdmopt" type="data" format="txt" optional="true" label="SDM option file (optional)" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	325 <param argument="-platform" type="select" label="Sequencing platform">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	326 <option value="" selected="true">(Default)</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	327 <option value="miSeq">miSeq</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	328 <option value="hiSeq">hiSeq</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	329 <option value="454">454</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	330 <option value="PacBio">PacBio</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	331 </param>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	332 <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" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	333 <conditional name="offtarget_cond">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	334 <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">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	335 <option value="no" selected="true">Disabled</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	336 <option value="cached">Use a built-in genome</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	337 <option value="history">Use a genome from history</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	338 </param>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	339 <when value="no" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	340 <when value="cached">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	341 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	342 <options from_data_table="all_fasta">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	343 <filter type="sort_by" column="2" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	344 <validator type="no_options" message="No reference genomes are available" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	345 </options>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	346 </param>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	347 </when>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	348 <when value="history">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	349 <param name="ref_file" type="data" format="fasta,fasta.gz" label="FASTA reference genome" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	350 </when>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	351 </conditional>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	352 <param argument="-useMini4map" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use minimap2 instead of VSEARCH to map back reads to OTUs" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	353 </section>
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	354 </inputs>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	355
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	356 <outputs>
7 692832801d70 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 81334bedc488edc36581c015b5a4c06926ec236c" earlhaminst parents: 6 diff changeset	357 <data name="outputs" format="zip" label="${tool.name} on ${on_string}: Complete LotuS2 output" from_work_dir="output.zip" />
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	358 <data name="otu" format="tabular" label="${tool.name} on ${on_string}: OTU abundance matrix" from_work_dir="output/OTU.txt" />
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	359 <data name="otu_fna" format="fasta" label="${tool.name} on ${on_string}: FASTA-formatted extended OTU seed sequences" from_work_dir="output/OTU.fna" />
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	360 <data name="OTUphylo_nwk" format="newick" label="${tool.name} on ${on_string}: Newick-formatted phylogenetic tree between sequences" from_work_dir="output/OTUphylo.nwk" />
2 cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	361 <data name="mapping" format="tabular" label="${tool.name} on ${on_string}: mapping file" from_work_dir="output/primary/in.map" />
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	362 <data name="runlog" format="txt" label="${tool.name} on ${on_string}: main log file" from_work_dir="output/LotuSLogS/LotuS_run.log" />
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	363 </outputs>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	364
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	365 <tests>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	366 <test>
15 6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	367 <conditional name="inputs">
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	368 <param name="paired_or_single" value="single"/>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	369 <param name="input" value="Anh_sample1.fastq.gz,Anh_sample2.fastq.gz" ftype="fastqsanger.gz"/>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	370 </conditional>
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	371 <conditional name="clu_cond">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	372 <param name="clustering" value="3" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	373 </conditional>
15 6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	374 <section name="clu_args">
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	375 <param name="derepMin" value="1" />
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	376 </section>
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	377 <section name="tax_args">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	378 <param name="lulu" value="false" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	379 </section>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	380 <section name="other_opts">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	381 <param name="platform" value="454" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	382 </section>
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	383 <output name="otu" file="OTU.txt" compare="sim_size" />
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	384 <output name="otu_fna" file="OTU.fna" compare="sim_size" />
2 cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	385 <output name="mapping" file="mapping.txt" />
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	386 </test>
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	387 <test>
15 6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	388 <conditional name="inputs">
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	389 <param name="paired_or_single" value="paired_collection"/>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	390 <param name="pair_input">
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	391 <collection type="list:paired">
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	392 <element name="Anh_sample">
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	393 <collection type="paired">
20 1d660ee0b1c8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e532d288f092df22f32805cea50583fe16a1070f earlhaminst parents: 19 diff changeset	394 <element name="forward" value="Arabidopsis_R1.fastqsanger.gz" ftype="fastqsanger.gz" />
1d660ee0b1c8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e532d288f092df22f32805cea50583fe16a1070f earlhaminst parents: 19 diff changeset	395 <element name="reverse" value="Arabidopsis_R2.fastqsanger.gz" ftype="fastqsanger.gz" />
15 6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	396 </collection>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	397 </element>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	398 </collection>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	399 </param>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	400 </conditional>
20 1d660ee0b1c8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e532d288f092df22f32805cea50583fe16a1070f earlhaminst parents: 19 diff changeset	401 <param name="map" value="mapping_paired.txt" ftype="tabular" />
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	402 <section name="tax_args">
20 1d660ee0b1c8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e532d288f092df22f32805cea50583fe16a1070f earlhaminst parents: 19 diff changeset	403 <param name="lulu" value="true" />
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	404 </section>
8 0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c" earlhaminst parents: 7 diff changeset	405 <output name="otu" file="OTU_paired.txt" compare="sim_size" />
0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c" earlhaminst parents: 7 diff changeset	406 <output name="otu_fna" file="OTU_paired.fna" compare="sim_size" />
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	407 </test>
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	408 </tests>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	409
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	410 <help><![CDATA[
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	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.
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	412
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	413 .. class:: infomark
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	414
20 1d660ee0b1c8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e532d288f092df22f32805cea50583fe16a1070f earlhaminst parents: 19 diff changeset	415 The full LotuS2 documentation can be found at `<https://lotus2.earlham.ac.uk/>`_.
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	416 ]]></help>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	417 <citations>
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	418 <citation type="doi">10.1186/s40168-022-01365-1</citation>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	419 <citation type="doi">10.1186/s40168-021-01012-1</citation>
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	420 </citations>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	421 </tool>

Mercurial > repos > earlhaminst > lotus2

annotate lotus2.xml @ 20:1d660ee0b1c8 draft