lotus2: lotus2.xml annotate

annotate lotus2.xml @ 23:469095a58c15 draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 33e0b986cfdef97a2ba8d473e7c5e4a40ce3bc08

author	earlhaminst
date	Wed, 22 Nov 2023 18:16:11 +0000
parents	ceb2cb800298
children	fede743a9002

rev	line source
22 ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4 earlhaminst parents: 21 diff changeset	1 <tool id="lotus2" name="LotuS2" version="@VERSION@+galaxy0" 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>
22 ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4 earlhaminst parents: 21 diff changeset	4 <token name="@VERSION@">2.28.1</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>
22 ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4 earlhaminst parents: 21 diff changeset	14 <option value="KSGP">Bacteria, Archaea, Eukaryotes SSU (KSGP)</option>
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	15 <option value="SLV">Silva LSU (23/28S) or SSU (16/18S) (SLV)</option>
22 ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4 earlhaminst parents: 21 diff changeset	16 <option value="GG2">GreenGenes2 SSU (GG2)</option>
ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4 earlhaminst parents: 21 diff changeset	17 <option value="UNITE">ITS fungi specific (UNITE)</option>
ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4 earlhaminst parents: 21 diff changeset	18 <option value="PR2">LSU spezialized on Ocean environmentas (PR2)</option>
ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4 earlhaminst parents: 21 diff changeset	19 <option value="beetax">Bee gut specific SSU (beetax)</option>
ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4 earlhaminst parents: 21 diff changeset	20 <option value="HITdb">Human gut specific SSU (HITdb)</option>
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	21 </param>
22 ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4 earlhaminst parents: 21 diff changeset	22 <param argument="-greengenesSpecies" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Create greengenes output labels instead of OTU" help="To be used with greengenes specific programs such as BugBase." />
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	23 </when>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	24 <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	25 <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	26 <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	27 </when>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	28 </conditional>
2 cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	29 <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	30 </xml>
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	31 <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	32 <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	33 </xml>
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	34 </macros>
21 fa84bba02a62 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 1632994d621dd37cd96792b152f4fe3f8e85b90c earlhaminst parents: 20 diff changeset	35 <xrefs>
fa84bba02a62 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 1632994d621dd37cd96792b152f4fe3f8e85b90c earlhaminst parents: 20 diff changeset	36 <xref type="bio.tools">lotus2</xref>
fa84bba02a62 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 1632994d621dd37cd96792b152f4fe3f8e85b90c earlhaminst parents: 20 diff changeset	37 </xrefs>
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	38 <requirements>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	39 <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	40 </requirements>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	41 <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	42 <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	43 #import re
22 ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4 earlhaminst parents: 21 diff changeset	44
ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4 earlhaminst parents: 21 diff changeset	45 LOTUS2_DIR=\$(dirname "\$(realpath "\$(which lotus2)")") &&
ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4 earlhaminst parents: 21 diff changeset	46 if [ ! -e "\$LOTUS2_DIR/DB" ]; then
ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4 earlhaminst parents: 21 diff changeset	47 {
ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4 earlhaminst parents: 21 diff changeset	48 echo "LotuS2 databases missing in \$LOTUS2_DIR, these needs to be installed with:" &&
ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4 earlhaminst parents: 21 diff changeset	49 echo "perl autoInstall.pl -condaDBinstall" &&
ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4 earlhaminst parents: 21 diff changeset	50 echo "We currently recommend to use a conda environment instead of a biocontainer to prevent this problem.";
ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4 earlhaminst parents: 21 diff changeset	51 } >&2 &&
ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4 earlhaminst parents: 21 diff changeset	52 exit 1;
ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4 earlhaminst parents: 21 diff changeset	53 fi &&
ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4 earlhaminst parents: 21 diff changeset	54
12 3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a" earlhaminst parents: 11 diff changeset	55 #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	56 #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	57 #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	58 #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	59 #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	60 #end if
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a" earlhaminst parents: 11 diff changeset	61 #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	62 #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	63 #else:
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a" earlhaminst parents: 11 diff changeset	64 #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	65 #end if
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a" earlhaminst parents: 11 diff changeset	66 #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	67 #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	68 #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	69 #break
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a" earlhaminst parents: 11 diff changeset	70 #end if
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a" earlhaminst parents: 11 diff changeset	71 #end for
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a" earlhaminst parents: 11 diff changeset	72 #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	73 ${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	74 #end def
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	75
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	76 mkdir input
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	77 &&
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	78 #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	79 #for $f in $inputs.input:
11 8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	80 ln -s '$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	81 #end for
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	82 #else:
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	83 #for $f in $inputs.pair_input:
11 8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	84 ln -s '$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	85 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	86 #end for
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	87 #end if
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	88
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	89 #if $aligner_cond.taxAligner not in ('0', '3') and $aligner_cond.refDB_cond.refDB == 'history':
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	90 #set $ext = $aligner_cond.refDB_cond.ref_fasta.ext
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	91 #set $ref_fasta_symlink = $symlink_basename($aligner_cond.refDB_cond.ref_fasta, strip_ext=True) + '.' + $ext
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	92 ln -s '$aligner_cond.refDB_cond.ref_fasta' '$ref_fasta_symlink' &&
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	93 #end if
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	94
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	95 #if not $map:
11 8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	96 cat '$generated_mapping' &&
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	97 #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	98 #end if
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	99
18 6c22795e1be0 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit afdb7dbe3283ee64d3aa2277efe505c7341575d8 earlhaminst parents: 17 diff changeset	100 set +e &&
6c22795e1be0 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit afdb7dbe3283ee64d3aa2277efe505c7341575d8 earlhaminst parents: 17 diff changeset	101
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	102 lotus2
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	103 -i input/
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	104 -o output
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	105 -tmpDir tmp_folder
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	106 -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	107 -map '$map'
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	108 #if $other_opts.sdmopt:
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	109 -sdmopt '$other_opts.sdmopt'
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	110 #end if
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	111 #if $other_opts.platform != '':
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	112 -platform $other_opts.platform
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	113 #end if
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	114 #if $other_opts.barcode:
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	115 -barcode '$other_opts.barcode'
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	116 #end if
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	117 #if $forwardPrimer:
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	118 -forwardPrimer '$forwardPrimer'
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	119 #end if
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	120 #if $reversePrimer:
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	121 -reversePrimer '$reversePrimer'
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	122 #end if
23 469095a58c15 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 33e0b986cfdef97a2ba8d473e7c5e4a40ce3bc08 earlhaminst parents: 22 diff changeset	123 #if $other_opts.offtarget_cond.offtargetDB == 'cached':
469095a58c15 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 33e0b986cfdef97a2ba8d473e7c5e4a40ce3bc08 earlhaminst parents: 22 diff changeset	124 -offtargetDB '$other_opts.offtarget_cond.ref_file.fields.path'
469095a58c15 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 33e0b986cfdef97a2ba8d473e7c5e4a40ce3bc08 earlhaminst parents: 22 diff changeset	125 #elif $other_opts.offtarget_cond.offtargetDB == 'history':
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	126 -offtargetDB '$other_opts.offtarget_cond.ref_file'
2 cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	127 #end if
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	128 -useMini4map $other_opts.useMini4map
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	129
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	130 -clustering $clu_cond.clustering
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	131 #if $clu_cond.clustering in ('1', '3'):
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	132 #if str($clu_cond.id):
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	133 -id $clu_cond.id
10 6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	134 #end if
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	135 #elif $clu_cond.clustering == '2':
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	136 #if str($clu_cond.swarm_distance):
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	137 -swarm_distance $clu_cond.swarm_distance
10 6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	138 #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	139 #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	140 #if $clu_args.derepMin:
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24" earlhaminst parents: 0 diff changeset	141 -derepMin '$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	142 #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	143
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	144 #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	145 -deactivateChimeraCheck $clu_args.deactivateChimeraCheck
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	146 #end if
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	147 #if str($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	148 -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	149 #end if
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	150
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	151 -taxAligner $aligner_cond.taxAligner
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	152 #if $aligner_cond.taxAligner == '0':
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	153 #if str($aligner_cond.rdp_thr):
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	154 -rdp_thr $aligner_cond.rdp_thr
10 6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	155 #end if
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	156 #elif $aligner_cond.taxAligner == '3':
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	157 #if str($aligner_cond.utax_thr):
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	158 -utax_thr $aligner_cond.utax_thr
10 6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	159 #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	160 #else:
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	161 #if $aligner_cond.refDB_cond.refDB == 'cached':
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	162 #if $aligner_cond.refDB_cond.ref_db != '':
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	163 -refDB $aligner_cond.refDB_cond.ref_db
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	164 -greengenesSpecies $aligner_cond.refDB_cond.greengenesSpecies
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	165 #end if
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	166 #else:
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	167 -refDB '$ref_fasta_symlink'
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	168 -tax4refDB '$aligner_cond.refDB_cond.tax4refDB'
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	169 #end if
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	170 -useBestBlastHitOnly $aligner_cond.useBestBlastHitOnly
1 85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24" earlhaminst parents: 0 diff changeset	171 #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	172 #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	173 -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	174 #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	175 #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	176 -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	177 #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	178
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	179 #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	180 -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	181 #end if
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	182 -keepUnclassified $tax_args.keepUnclassified
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	183 #if str($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	184 -LCA_cover $tax_args.LCA_cover
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	185 #end if
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	186 #if str($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	187 -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	188 #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	189 -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	190 -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	191 #if $tax_args.taxExcludeGrep:
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	192 -taxExcludeGrep '$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	193 #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	194 ; EXIT_VALUE=\$? ;
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	195
7 692832801d70 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 81334bedc488edc36581c015b5a4c06926ec236c" earlhaminst parents: 6 diff changeset	196 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	197 &&
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24" earlhaminst parents: 0 diff changeset	198 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	199 ]]></command>
11 8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	200 <configfiles>
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	201 <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	202 #import re
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	203 #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	204 #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	205 ${fn}#slurp
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	206 #end def
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	207 #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	208 #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	209 #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	210 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	211 #end for
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	212 #else:
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	213 #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	214 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	215 #end for
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	216 #end if
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	217 ]]></configfile>
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea" earlhaminst parents: 10 diff changeset	218 </configfiles>
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	219 <inputs>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	220 <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	221 <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	222 <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	223 <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	224 </param>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	225 <when value="single">
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	226 <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	227 </when>
2 cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	228 <!--
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	229 <when value="paired">
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	230 <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	231 <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	232 </when>
2 cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	233 -->
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	234 <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	235 <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	236 </when>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	237 </conditional>
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	238 <param argument="-map" type="data" format="tabular" optional="true" label="Mapping file (optional)" help="Needed to demultiplex the FASTQ files using sdm. If the FASTQ are already demultiplexed, this can be omitted." />
10 6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" earlhaminst parents: 9 diff changeset	239 <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	240 <param argument="-reversePrimer" type="text" value="" label="Reverse primer used to amplify DNA region (optional)" help="E.g. 16S primer rev" />
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	241 <conditional name="clu_cond">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	242 <param argument="-clustering" type="select" label="Clustering algorithm">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	243 <option value="7" selected="true">DADA2</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	244 <option value="2">swarm</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	245 <option value="3">CD-HIT</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	246 <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	247 </param>
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	248 <when value="2">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	249 <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	250 </when>
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	251 <when value="3">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	252 <param argument="-id" type="float" min="0.9" max="1" value="0.97" optional="true" label="Clustering threshold for OTUs" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	253 </when>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	254 <when value="7">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	255 </when>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	256 <when value="8">
2 cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	257 </when>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	258 </conditional>
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	259 <conditional name="aligner_cond">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	260 <param argument="-taxAligner" type="select" label="Taxonomy aligner for taxonomic profiling of OTUs">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	261 <option value="0" selected="true">RDPclassifier (max likelihood)</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	262 <!-- <option value="1">Blast LCA against custom reference database</option> -->
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	263 <option value="2">LAMBDA, LCA against custom reference database</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	264 <!-- <option value="4">VSEARCH LCA against custom reference database</option> -->
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	265 </param>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	266 <when value="0">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	267 <param argument="-rdp_thr" type="float" min="0" max="1" value="0.8" optional="true" label="Confidence threshold for RDP (optional)"/>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	268 </when>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	269 <!-- <when value="1">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	270 <expand macro="refDB_macro" ref_fasta_formats="fasta" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	271 </when> -->
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	272 <when value="2">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	273 <expand macro="refDB_macro" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	274 </when>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	275 <!-- <when value="3">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	276 <param argument="-utax_thr" type="float" min="0" max="1" value="0.8" optional="true" label="Confidence threshold for UTAX (optional)"/>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	277 </when>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	278 <when value="4">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	279 <expand macro="refDB_macro" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	280 </when> -->
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	281 </conditional>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	282 <section name="clu_args" title="Other Clustering Options">
20 1d660ee0b1c8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e532d288f092df22f32805cea50583fe16a1070f earlhaminst parents: 19 diff changeset	283 <param argument="-derepMin" type="text" value="" label="Minimum size of dereplicated raw reads (optional)" help="E.g. 4:1,4:2,3:3 . See https://lotus2.earlham.ac.uk/images/Derep_options.pdf for how to specify this parameter. If not specified, LotuS2 will select an appropriate default for the chosen clustering algorithm." />
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	284 <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	285 <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	286 <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	287 <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	288 <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	289 <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	290 </param>
6 fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" earlhaminst parents: 5 diff changeset	291 <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	292 </section>
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	293 <section name="tax_args" title="Other Taxonomy Options">
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	294 <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	295 <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	296 <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	297 <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	298 <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	299 <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	300 <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	301 <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	302 </param>
8 0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c" earlhaminst parents: 7 diff changeset	303 <when value="" />
0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c" earlhaminst parents: 7 diff changeset	304 <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	305 <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	306 <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	307 <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	308 </when>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	309 <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	310 <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	311 </when>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	312 <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	313 <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	314 </when>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	315 </conditional>
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	316 <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	317 <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	318 <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	319 <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	320 </param>
22 ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4 earlhaminst parents: 21 diff changeset	321 <param argument="-keepUnclassified" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Keep unclassified OTUs" help="Includes unclassified OTUs (no Phylum assignment) 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	322 <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	323 <param argument="-LCA_frac" type="float" min="0" max="1" value="" optional="true" label="Minimum fraction of reads with identical taxonomy (optional)"/>
20 1d660ee0b1c8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e532d288f092df22f32805cea50583fe16a1070f earlhaminst parents: 19 diff changeset	324 <param argument="-lulu" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use LULU to merge OTUs based on their occurrence" />
2 cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	325 <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	326 <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	327 <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	328 <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	329 </param>
15 6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	330 <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	331 <sanitizer>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	332 <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	333 <add value="\|" />
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	334 <add value="$" />
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	335 </valid>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	336 </sanitizer>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	337 </param>
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	338 </section>
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	339 <section name="other_opts" title="Other options">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	340 <param argument="-sdmopt" type="data" format="txt" optional="true" label="SDM option file (optional)" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	341 <param argument="-platform" type="select" label="Sequencing platform">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	342 <option value="" selected="true">(Default)</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	343 <option value="miSeq">miSeq</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	344 <option value="hiSeq">hiSeq</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	345 <option value="454">454</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	346 <option value="PacBio">PacBio</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	347 </param>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	348 <param argument="-barcode" type="data" format="fastqsanger" optional="true" label="Barcode (MID) sequences (optional)" help="FASTQ file with barcodes (in the processed mi/hiSeq format), if provided by the sequencer" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	349 <conditional name="offtarget_cond">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	350 <param argument="-offtargetDB" type="select" label="Remove likely contaminant OTUs/ASVs based on alignment to host genome" help="Useful for low-bacterial biomass samples to remove possible host genome contaminations">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	351 <option value="no" selected="true">Disabled</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	352 <option value="cached">Use a built-in genome</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	353 <option value="history">Use a genome from history</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	354 </param>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	355 <when value="no" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	356 <when value="cached">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	357 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	358 <options from_data_table="all_fasta">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	359 <filter type="sort_by" column="2" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	360 <validator type="no_options" message="No reference genomes are available" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	361 </options>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	362 </param>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	363 </when>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	364 <when value="history">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	365 <param name="ref_file" type="data" format="fasta,fasta.gz" label="FASTA reference genome" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	366 </when>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	367 </conditional>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	368 <param argument="-useMini4map" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use minimap2 instead of VSEARCH to map back reads to OTUs" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	369 </section>
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	370 </inputs>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	371
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	372 <outputs>
7 692832801d70 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 81334bedc488edc36581c015b5a4c06926ec236c" earlhaminst parents: 6 diff changeset	373 <data name="outputs" format="zip" label="${tool.name} on ${on_string}: Complete LotuS2 output" from_work_dir="output.zip" />
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	374 <data name="otu" format="tabular" label="${tool.name} on ${on_string}: OTU abundance matrix" from_work_dir="output/OTU.txt" />
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	375 <data name="otu_fna" format="fasta" label="${tool.name} on ${on_string}: FASTA-formatted extended OTU seed sequences" from_work_dir="output/OTU.fna" />
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	376 <data name="OTUphylo_nwk" format="newick" label="${tool.name} on ${on_string}: Newick-formatted phylogenetic tree between sequences" from_work_dir="output/OTUphylo.nwk" />
2 cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466" earlhaminst parents: 1 diff changeset	377 <data name="mapping" format="tabular" label="${tool.name} on ${on_string}: mapping file" from_work_dir="output/primary/in.map" />
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	378 <data name="runlog" format="txt" label="${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	379 </outputs>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	380
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	381 <tests>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	382 <test>
15 6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	383 <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	384 <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	385 <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	386 </conditional>
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	387 <conditional name="clu_cond">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	388 <param name="clustering" value="3" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	389 </conditional>
15 6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	390 <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	391 <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	392 </section>
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	393 <section name="tax_args">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	394 <param name="lulu" value="false" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	395 </section>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	396 <section name="other_opts">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	397 <param name="platform" value="454" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	398 </section>
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	399 <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	400 <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	401 <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	402 </test>
4 59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" earlhaminst parents: 3 diff changeset	403 <test>
15 6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	404 <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	405 <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	406 <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	407 <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	408 <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	409 <collection type="paired">
20 1d660ee0b1c8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e532d288f092df22f32805cea50583fe16a1070f earlhaminst parents: 19 diff changeset	410 <element name="forward" value="Arabidopsis_R1.fastqsanger.gz" ftype="fastqsanger.gz" />
1d660ee0b1c8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e532d288f092df22f32805cea50583fe16a1070f earlhaminst parents: 19 diff changeset	411 <element name="reverse" value="Arabidopsis_R2.fastqsanger.gz" ftype="fastqsanger.gz" />
15 6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	412 </collection>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	413 </element>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	414 </collection>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	415 </param>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda" earlhaminst parents: 14 diff changeset	416 </conditional>
20 1d660ee0b1c8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e532d288f092df22f32805cea50583fe16a1070f earlhaminst parents: 19 diff changeset	417 <param name="map" value="mapping_paired.txt" ftype="tabular" />
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	418 <section name="tax_args">
20 1d660ee0b1c8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e532d288f092df22f32805cea50583fe16a1070f earlhaminst parents: 19 diff changeset	419 <param name="lulu" value="true" />
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	420 </section>
8 0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c" earlhaminst parents: 7 diff changeset	421 <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	422 <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	423 </test>
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	424 </tests>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	425
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	426 <help><![CDATA[
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	427 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	428
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	429 .. class:: infomark
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	430
20 1d660ee0b1c8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e532d288f092df22f32805cea50583fe16a1070f earlhaminst parents: 19 diff changeset	431 The full LotuS2 documentation can be found at `<https://lotus2.earlham.ac.uk/>`_.
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	432 ]]></help>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	433 <citations>
17 28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	434 <citation type="doi">10.1186/s40168-022-01365-1</citation>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd earlhaminst parents: 16 diff changeset	435 <citation type="doi">10.1186/s40168-021-01012-1</citation>
0 478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	436 </citations>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" earlhaminst parents: diff changeset	437 </tool>

Mercurial > repos > earlhaminst > lotus2

annotate lotus2.xml @ 23:469095a58c15 draft