lotus2: lotus2.xml annotate

annotate lotus2.xml @ 16:12599a8dd22f draft

"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8353999a2b618f31ae43544ae9faa99ff02039e2"

author	earlhaminst
date	Tue, 22 Mar 2022 13:45:18 +0000
parents	6e9fd3e0dcbb
children	28f284a679ce

rev	line source
15 6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	1 <tool id="lotus2" name="LotuS2" version="@VERSION@" 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>
15 6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	4 <token name="@VERSION@">2.19</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>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	30 <xml name="id_macro">
10 6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	31 <param argument="-id" type="float" min="0.9" max="1" value="" optional="true" label="Clustering threshold for OTUs (optional)" />
1 85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24" earlhaminst parents: 0 diff changeset	32 </xml>
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	33 <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	34 <param argument="-ITSx" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use ITSx to only retain OTUs fitting to ITS1/ITS2 hmm models" />
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	35 </xml>
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	36 </macros>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	37 <requirements>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	38 <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	39 </requirements>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	40 <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	41 <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	42 #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	43 #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	44 #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	45 #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	46 #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	47 #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	48 #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	49 #end if
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a" earlhaminst parents: 11 diff changeset	50 #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	51 #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	52 #else:
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a" earlhaminst parents: 11 diff changeset	53 #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	54 #end if
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a" earlhaminst parents: 11 diff changeset	55 #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	56 #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	57 #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	58 #break
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a" earlhaminst parents: 11 diff changeset	59 #end if
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a" earlhaminst parents: 11 diff changeset	60 #end for
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a" earlhaminst parents: 11 diff changeset	61 #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	62 ${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	63 #end def
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	64
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	65 mkdir input
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	66 &&
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	67 #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	68 #for $f in $inputs.input:
11 8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	69 ln -s '$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	70 #end for
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	71 #else:
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	72 #for $f in $inputs.pair_input:
11 8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	73 ln -s '$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	74 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	75 #end for
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	76 #end if
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	77
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	78 #if $tax_args.aligner_cond.taxAligner not in ('0', '3') and $tax_args.aligner_cond.refDB_cond.refDB == 'history':
8 0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c" earlhaminst parents: 7 diff changeset	79 #set $ext = $tax_args.aligner_cond.refDB_cond.ref_fasta.ext
12 3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a" earlhaminst parents: 11 diff changeset	80 #set $ref_fasta_symlink = $symlink_basename($tax_args.aligner_cond.refDB_cond.ref_fasta, strip_ext=True) + '.' + $ext
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	81 ln -s '$tax_args.aligner_cond.refDB_cond.ref_fasta' '$ref_fasta_symlink' &&
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	82 #end if
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	83
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	84 #if not $map:
11 8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	85 cat '$generated_mapping' &&
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	86 #set map = $generated_mapping
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	87 #end if
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	88
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	89 lotus2
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	90 -i input/
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	91 -o output
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	92 -tmpDir tmp_folder
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	93 -threads "\${GALAXY_SLOTS:-1}"
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	94 -map '$map'
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	95 #if $sdmopt:
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	96 -sdmopt '$sdmopt'
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	97 #end if
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	98 #if $platform != '':
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	99 -platform $platform
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	100 #end if
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	101 #if $barcode:
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	102 -barcode '$barcode'
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	103 #end if
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	104 #if $forwardPrimer:
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	105 -forwardPrimer '$forwardPrimer'
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	106 #end if
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	107 #if $reversePrimer:
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	108 -reversePrimer '$reversePrimer'
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	109 #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	110 #if $offtarget_cond.offtargetDB != 'no':
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	111 -offtargetDB '$offtarget_cond.ref_file'
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	112 #end if
15 6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	113 -useMini4map $useMini4map
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	114
2 cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	115 -clustering $clu_args.clu_cond.clustering
10 6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	116 #if $clu_args.clu_cond.clustering in ('1', '3'):
6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	117 #if str($clu_args.clu_cond.id):
6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	118 -id $clu_args.clu_cond.id
6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	119 #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	120 #elif $clu_args.clu_cond.clustering == '2':
10 6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	121 #if str($clu_args.clu_cond.swarm_distance):
6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	122 -swarm_distance $clu_args.clu_cond.swarm_distance
6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	123 #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	124 #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	125 #if $clu_args.derepMin:
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24" earlhaminst parents: 0 diff changeset	126 -derepMin '$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	127 #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	128
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	129 #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	130 -deactivateChimeraCheck $clu_args.deactivateChimeraCheck
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	131 #end if
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	132 #if str($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	133 -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	134 #end if
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	135
1 85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24" earlhaminst parents: 0 diff changeset	136 -taxAligner $tax_args.aligner_cond.taxAligner
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24" earlhaminst parents: 0 diff changeset	137 #if $tax_args.aligner_cond.taxAligner == '0':
10 6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	138 #if str($tax_args.aligner_cond.rdp_thr):
6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	139 -rdp_thr $tax_args.aligner_cond.rdp_thr
6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	140 #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	141 #elif $tax_args.aligner_cond.taxAligner == '3':
10 6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	142 #if str($tax_args.aligner_cond.utax_thr):
6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	143 -utax_thr $tax_args.aligner_cond.utax_thr
6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	144 #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	145 #else:
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	146 #if $tax_args.aligner_cond.refDB_cond.refDB == 'cached':
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	147 #if $tax_args.aligner_cond.refDB_cond.ref_db != '':
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	148 -refDB $tax_args.aligner_cond.refDB_cond.ref_db
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	149 -greengenesSpecies $tax_args.aligner_cond.refDB_cond.greengenesSpecies
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	150 #end if
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	151 #else:
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	152 -refDB '$ref_fasta_symlink'
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	153 -tax4refDB '$tax_args.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	154 #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	155 -useBestBlastHitOnly $tax_args.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	156 #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	157 #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	158 -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	159 #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	160 #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	161 -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	162 #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	163
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	164 #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	165 -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	166 #end if
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	167 -keepUnclassified $tax_args.keepUnclassified
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	168 #if str($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	169 -LCA_cover $tax_args.LCA_cover
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	170 #end if
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	171 #if str($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	172 -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	173 #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	174 -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	175 -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	176 #if $tax_args.taxExcludeGrep:
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	177 -taxExcludeGrep '$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	178 #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	179 ; EXIT_VALUE=\$? ;
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	180
7 692832801d70 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 81334bedc488edc36581c015b5a4c06926ec236c" earlhaminst parents: 6 diff changeset	181 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	182 &&
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24" earlhaminst parents: 0 diff changeset	183 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	184 ]]></command>
11 8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	185 <configfiles>
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	186 <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	187 #import re
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	188 #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	189 #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	190 ${fn}#slurp
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	191 #end def
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	192 #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	193 #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	194 #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	195 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	196 #end for
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	197 #else:
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	198 #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	199 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	200 #end for
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	201 #end if
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	202 ]]></configfile>
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	203 </configfiles>
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	204 <inputs>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	205 <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	206 <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	207 <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	208 <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	209 </param>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	210 <when value="single">
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	211 <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	212 </when>
2 cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	213 <!--
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	214 <when value="paired">
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	215 <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	216 <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	217 </when>
2 cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	218 -->
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	219 <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	220 <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	221 </when>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	222 </conditional>
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	223 <param argument="-map" type="data" format="tabular" optional="true" label="Mapping file (optional)" help="Needed to demultiplex the FASTQ files using sdm. If the FASTQ are already demultiplexed, this can be omitted." />
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	224 <param argument="-sdmopt" type="data" format="txt" optional="true" label="SDM option file (optional)" />
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	225 <param argument="-platform" type="select" label="Sequencing platform">
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	226 <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	227 <option value="miSeq">miSeq</option>
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	228 <option value="hiSeq">hiSeq</option>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	229 <option value="454">454</option>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	230 <option value="PacBio">PacBio</option>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	231 </param>
1 85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24" earlhaminst parents: 0 diff changeset	232 <param argument="-barcode" type="data" format="fastqsanger" optional="true" label="Barcode (MID) sequences (optional)" help="FASTQ file with barcodes (in the processed mi/hiSeq format), if provided by the sequencer" />
10 6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	233 <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	234 <param argument="-reversePrimer" type="text" value="" label="Reverse primer used to amplify DNA region (optional)" help="E.g. 16S primer rev" />
2 cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	235 <conditional name="offtarget_cond">
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	236 <param argument="-offtargetDB" type="select" label="Remove likely contaminant OTUs/ASVs based on alignment to host genome" help="Useful for low-bacterial biomass samples to remove possible host genome contaminations">
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	237 <option value="no" selected="true">Disabled</option>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	238 <option value="cached">Use a built-in genome</option>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	239 <option value="history">Use a genome from history</option>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	240 </param>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	241 <when value="no" />
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	242 <when value="cached">
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	243 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	244 <options from_data_table="all_fasta">
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	245 <filter type="sort_by" column="2" />
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	246 <validator type="no_options" message="No reference genomes are available" />
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	247 </options>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	248 </param>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	249 </when>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	250 <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	251 <param name="ref_file" type="data" format="fasta,fasta.gz" label="FASTA reference genome" />
2 cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	252 </when>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	253 </conditional>
15 6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	254 <param argument="-useMini4map" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use minimap2 instead of VSEARCH to map back reads to OTUs" />
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	255 <section name="clu_args" title="Clustering Options">
2 cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	256 <conditional name="clu_cond">
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	257 <param argument="-clustering" type="select" label="Clustering algorithm">
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	258 <option value="2">swarm</option>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	259 <option value="3">cd-hit</option>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	260 <option value="6">unoise3</option>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	261 <option value="7" selected="true">dada2</option>
15 6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	262 <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	263 </param>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	264 <when value="2">
10 6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	265 <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	266 </when>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	267 <when value="3">
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	268 <expand macro="id_macro" />
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	269 </when>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	270 <when value="6">
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	271 </when>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	272 <when value="7">
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	273 </when>
15 6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	274 <when value="8">
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	275 </when>
2 cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	276 </conditional>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	277 <param argument="-derepMin" type="text" value="" label="Minimum size of dereplicated raw reads (optional)" help="E.g. 4:1,4:2,3:3 . See http://lotus2.earlham.ac.uk/images/Derep_options.pdf for how to specify this parameter. If not specified, LotuS2 will select an appropriate default for the chosen clustering algorithm." />
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	278 <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	279 <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	280 <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	281 <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	282 <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	283 <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	284 </param>
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	285 <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	286 </section>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	287 <section name="tax_args" title="Taxonomy Options">
1 85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24" earlhaminst parents: 0 diff changeset	288 <conditional name="aligner_cond">
2 cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	289 <param argument="-taxAligner" type="select" label="Taxonomy aligner for taxonomic profiling of OTUs">
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	290 <option value="0" selected="true">RDPclassifier (max likelihood)</option>
10 6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	291 <!-- <option value="1">Blast LCA against custom reference database</option> -->
2 cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	292 <option value="2">LAMBDA LCA against custom reference database</option>
10 6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	293 <!-- <option value="4">VSEARCH LCA against custom reference database</option> -->
1 85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24" earlhaminst parents: 0 diff changeset	294 </param>
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24" earlhaminst parents: 0 diff changeset	295 <when value="0">
10 6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	296 <param argument="-rdp_thr" type="float" min="0" max="1" value="0.8" optional="true" label="Confidence threshold for RDP (optional)"/>
1 85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24" earlhaminst parents: 0 diff changeset	297 </when>
15 6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	298 <!-- <when value="1">
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	299 <expand macro="refDB_macro" ref_fasta_formats="fasta" />
15 6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	300 </when> -->
1 85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24" earlhaminst parents: 0 diff changeset	301 <when value="2">
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24" earlhaminst parents: 0 diff changeset	302 <expand macro="refDB_macro" />
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24" earlhaminst parents: 0 diff changeset	303 </when>
15 6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	304 <!-- <when value="3">
10 6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	305 <param argument="-utax_thr" type="float" min="0" max="1" value="0.8" optional="true" label="Confidence threshold for UTAX (optional)"/>
1 85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24" earlhaminst parents: 0 diff changeset	306 </when>
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24" earlhaminst parents: 0 diff changeset	307 <when value="4">
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24" earlhaminst parents: 0 diff changeset	308 <expand macro="refDB_macro" />
15 6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	309 </when> -->
1 85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24" earlhaminst parents: 0 diff changeset	310 </conditional>
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	311 <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	312 <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	313 <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	314 <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	315 <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	316 <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	317 <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	318 <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	319 </param>
8 0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c" earlhaminst parents: 7 diff changeset	320 <when value="" />
0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c" earlhaminst parents: 7 diff changeset	321 <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	322 <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	323 <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	324 <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	325 </when>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	326 <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	327 <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	328 </when>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	329 <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	330 <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	331 </when>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	332 </conditional>
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	333 <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	334 <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	335 <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	336 <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	337 </param>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	338 <param argument="-keepUnclassified" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Keep unclassified OTUs" help="Includes unclassified OTUs (i.e. no match in RDP/Blast database) in OTU and taxa abundance matrix calculations" />
10 6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	339 <param argument="-LCA_cover" type="float" min="0" max="1" value="" optional="true" label="Minimum horizontal coverage of an OTU sequence against ref DB (optional)"/>
6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	340 <param argument="-LCA_frac" type="float" min="0" max="1" value="" optional="true" label="Minimum fraction of reads with identical taxonomy (optional)"/>
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	341 <param argument="-lulu" type="boolean" truevalue="1" falsevalue="0" checked="false" 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	342 <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	343 <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	344 <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	345 <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	346 </param>
15 6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	347 <param argument="-taxExcludeGrep" type="text" value="" label="Taxonomic groups to exclude, as a regular expression" help="OTUs matching this regular expression will be assigned as unknown, and by default removed">
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	348 <sanitizer>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	349 <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	350 <add value="\|" />
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	351 <add value="$" />
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	352 </valid>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	353 </sanitizer>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	354 </param>
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	355 </section>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	356 </inputs>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	357
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	358 <outputs>
7 692832801d70 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 81334bedc488edc36581c015b5a4c06926ec236c" earlhaminst parents: 6 diff changeset	359 <data name="outputs" format="zip" label="${tool.name} on ${on_string}: Complete LotuS2 output" from_work_dir="output.zip" />
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	360 <data name="otu" format="tabular" label="${tool.name} on ${on_string}: OTU abundance matrix" from_work_dir="output/OTU.txt" />
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	361 <data name="otu_fna" format="fasta" label="${tool.name} on ${on_string}: FASTA-formatted extended OTU seed sequences" from_work_dir="output/OTU.fna" />
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	362 <data name="OTUphylo_nwk" format="newick" label="${tool.name} on ${on_string}: Newick-formatted phylogenetic tree between sequences" from_work_dir="output/OTUphylo.nwk" />
2 cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	363 <data name="mapping" format="tabular" label="${tool.name} on ${on_string}: mapping file" from_work_dir="output/primary/in.map" />
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	364 <data name="runlog" format="txt" label="${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	365 </outputs>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	366
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	367 <tests>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	368 <test>
15 6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	369 <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	370 <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	371 <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	372 </conditional>
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	373 <param name="platform" value="454" />
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 <conditional name="clu_cond">
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	376 <param name="clustering" value="3" />
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	377 </conditional>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	378 <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	379 </section>
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	380 <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	381 <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	382 <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	383 </test>
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	384 <test>
15 6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	385 <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	386 <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	387 <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	388 <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	389 <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	390 <collection type="paired">
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	391 <element name="forward" value="Anh_sample1.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	392 <element name="reverse" value="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	393 </collection>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	394 </element>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	395 </collection>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	396 </param>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	397 </conditional>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	398 <param name="map" value="mapping_paired.txt" />
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	399 <param name="platform" value="454" />
15 6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	400 <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	401 <conditional name="clu_cond">
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	402 <param name="clustering" value="3" />
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	403 </conditional>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	404 <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	405 </section>
8 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" 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	407 <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	408 </test>
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	409 </tests>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	410
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	411 <help><![CDATA[
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	412 If you have separate FASTA and quality files, these can be combined in a FASTQ file using the "Combine FASTA and QUAL into FASTQ" tool.
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	413
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	414 Documentation can be found at `<http://lotus2.earlham.ac.uk/>`_.
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	415 ]]></help>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	416 <citations>
16 12599a8dd22f "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8353999a2b618f31ae43544ae9faa99ff02039e2" earlhaminst parents: 15 diff changeset	417 <citation type="doi">10.1101/2021.12.24.474111</citation>
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	418 </citations>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	419 </tool>

Mercurial > repos > earlhaminst > lotus2

annotate lotus2.xml @ 16:12599a8dd22f draft