annotate lotus2.xml @ 8:0fddee8b1f7e draft

"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c"
author earlhaminst
date Tue, 08 Jun 2021 02:17:42 +0000
parents 692832801d70
children 82ff4f47436a
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692832801d70 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 81334bedc488edc36581c015b5a4c06926ec236c"
earlhaminst
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1 <tool id="lotus2" name="LotuS2" version="@VERSION@+galaxy1" profile="20.01">
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478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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2 <description>fast OTU processing pipeline</description>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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3 <macros>
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earlhaminst
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4 <token name="@VERSION@">2.07</token>
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
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5 <xml name="refDB_macro" token_ref_fasta_formats="fasta,fasta.gz">
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59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
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6 <conditional name="refDB_cond">
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
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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"
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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"
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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
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10 </param>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
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11 <when value="cached">
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fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
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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"
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13 <option value="" selected="true">(Default)</option>
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
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14 <option value="SLV">Silva LSU (23/28S) or SSU (16/18S) (SLV)</option>
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59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
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15 <option value="GG">Greengenes (GG)</option>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
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16 <option value="UNITE">ITS focused on fungi (UNITE)</option>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
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17 <option value="PR2">SSU focused on Protists (PR2)</option>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
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18 <option value="beetax">Bee gut specific database and tax names (beetax)</option>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
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19 <option value="HITdb">Human gut microbiota (HITdb)</option>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
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20 </param>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
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21 <param argument="-greengenesSpecies" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Create greengenes output labels instead of OTU" />
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
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22 </when>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
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23 <when value="history">
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fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
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24 <param name="ref_fasta" type="data" format="@REF_FASTA_FORMATS@" label="Taxonomy reference sequences" help="In FASTA format" />
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59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
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25 <param argument="-tax4refDB" type="data" format="tabular" label="Taxonomy reference lineages" help="Tab-separated file with 2 columns mapping each FASTA header of the reference sequences to a GTDB-style taxonomy string" />
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
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26 </when>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
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27 </conditional>
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cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
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28 <param argument="-useBestBlastHitOnly" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Use the best Blast hit only" help="Do not use LCA (lowest common ancestor) to determine the most likely taxonomic level (not recommended)" />
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
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29 </xml>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
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30 <xml name="id_macro">
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fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
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31 <param argument="-id" type="float" min="0.9" max="1" value="" optional="true" label="Clustering threshold for OTUs" />
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85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
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32 </xml>
4
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
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33 <xml name="ITSx_macro">
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
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34 <param argument="-ITSx" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use ITSx to only retain OTUs fitting to ITS1/ITS2 hmm models" />
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
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35 </xml>
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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36 </macros>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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37 <requirements>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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38 <requirement type="package" version="@VERSION@">lotus2</requirement>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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39 </requirements>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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40 <version_command>lotus2 --version</version_command>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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41 <command detect_errors="exit_code"><![CDATA[
2
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
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42 #import os.path
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
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43 #import re
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0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c"
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44 #def symlink_basename($f, $f_ext):
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fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
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45 #set $fn = re.sub('[^\w\-_.]', '_', $f.element_identifier)
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
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46 #if $fn.endswith('.gz'):
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
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47 #set $fn = $fn[:-3]
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cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
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48 #end if
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0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c"
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49 #if $f_ext.startswith('fastq'):
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fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
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50 #set $exts_to_drop = ('.fq', '.fastq', '.fastqsanger')
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0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c"
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51 #elif $f_ext.startswith('fasta'):
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fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
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52 #set $exts_to_drop = ('.fa', '.fasta', '.fna')
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
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53 #else
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
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54 #set $exts_to_drop = []
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
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55 #end if
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
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56 #for $ext in $exts_to_drop:
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
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57 #if $fn.endswith($ext):
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
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58 #set $fn = $fn[:-len($ext)]
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cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
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59 #break
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
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60 #end if
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
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61 #end for
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
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62 $fn#slurp
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
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63 #end def
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
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64
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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65 mkdir input
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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66 &&
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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67 #if $inputs.paired_or_single == 'single':
6
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
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68 #for $f in $inputs.input:
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
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69 #set $ext = $f.ext.replace('sanger', '')
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0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c"
earlhaminst
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70 ln -s '$f' 'input/${symlink_basename($f, $ext)}.${ext}' &&
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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71 #end for
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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72 #elif $inputs.paired_or_single == 'paired':
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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73 #for i, f in enumerate($inputs.left_input):
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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74 #set ext = $f.ext.replace('sanger', '')
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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75 ln -s '$f' 'input/input${i}.1.${ext}' &&
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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76 #end for
6
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
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77 #for $i, $f in enumerate($inputs.right_input):
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
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78 #set $ext = $f.ext.replace('sanger', '')
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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parents:
diff changeset
79 ln -s '$f' 'input/input${i}.2.${ext}' &&
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
80 #end for
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
81 #else:
6
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
82 #for $f in $inputs.pair_input:
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
83 #set $ext = $f.forward.ext.replace('sanger', '')
8
0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c"
earlhaminst
parents: 7
diff changeset
84 ln -s '$f.forward' 'input/${symlink_basename($f, $ext)}.1.${ext}' &&
6
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
85 #set $ext = $f.reverse.ext.replace('sanger', '')
8
0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c"
earlhaminst
parents: 7
diff changeset
86 ln -s '$f.reverse' 'input/${symlink_basename($f, $ext)}.2.${ext}' &&
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
87 #end for
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
88 #end if
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
89
6
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
90 #if $tax_args.aligner_cond.taxAligner not in ('0', '3') and $tax_args.aligner_cond.refDB_cond.refDB == 'history':
8
0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c"
earlhaminst
parents: 7
diff changeset
91 #set $ext = $tax_args.aligner_cond.refDB_cond.ref_fasta.ext
0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c"
earlhaminst
parents: 7
diff changeset
92 #set $ref_fasta_symlink = $symlink_basename($tax_args.aligner_cond.refDB_cond.ref_fasta, $ext) + '.' + $ext
6
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
93 ln -s '$tax_args.aligner_cond.refDB_cond.ref_fasta' '$ref_fasta_symlink' &&
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
94 #end if
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
95
4
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
parents: 3
diff changeset
96 #if not $map:
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
parents: 3
diff changeset
97 lotus2 -create_map mapping.txt -i input/ &&
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
parents: 3
diff changeset
98 cat mapping.txt &&
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
parents: 3
diff changeset
99 #set map = 'mapping.txt'
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
parents: 3
diff changeset
100 #end if
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
101
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'
6
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
108 #if $sdmopt:
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
109 -sdmopt '$sdmopt'
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
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
111 #if $platform != '':
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
112 -platform $platform
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
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
114 #if $barcode:
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
115 -barcode '$barcode'
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
2
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
123 #if $offtarget_cond.offtargetDB != 'no':
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
124 -offtargetDB '$offtarget_cond.ref_file'
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
125 #end if
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
126
2
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
127 -clustering $clu_args.clu_cond.clustering
6
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
128 #if $clu_args.clu_cond.clustering in ('1', '3') and str($clu_args.clu_cond.id):
2
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
129 -id $clu_args.clu_cond.id
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
130 #elif $clu_args.clu_cond.clustering == '2':
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
131 -swarm_distance $clu_args.clu_cond.swarm_distance
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
132 #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
133 #if $clu_args.derepMin:
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
134 -derepMin '$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
135 #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
136
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
137 #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
138 -deactivateChimeraCheck $clu_args.deactivateChimeraCheck
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
139 #end if
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
140 #if str($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
141 -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
142 #end if
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
143
1
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
144 -taxAligner $tax_args.aligner_cond.taxAligner
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
145 #if $tax_args.aligner_cond.taxAligner == '0':
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
146 -rdp_thr $tax_args.aligner_cond.rdp_thr
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
147 #elif $tax_args.aligner_cond.taxAligner == '3':
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
148 -utax_thr $tax_args.aligner_cond.utax_thr
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
149 #else:
4
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
parents: 3
diff changeset
150 #if $tax_args.aligner_cond.refDB_cond.refDB == 'cached':
6
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
151 #if $tax_args.aligner_cond.refDB_cond.ref_db != '':
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
152 -refDB $tax_args.aligner_cond.refDB_cond.ref_db
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
153 -greengenesSpecies $tax_args.aligner_cond.refDB_cond.greengenesSpecies
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
154 #end if
4
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
parents: 3
diff changeset
155 #else:
6
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
156 -refDB '$ref_fasta_symlink'
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
157 -tax4refDB '$tax_args.aligner_cond.refDB_cond.tax4refDB'
4
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
parents: 3
diff changeset
158 #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
159 -useBestBlastHitOnly $tax_args.aligner_cond.useBestBlastHitOnly
1
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
160 #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
161 #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
162 -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
163 #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
164 #if $tax_args.amplicon_cond.amplicon_type in ('ITS', 'ITS1', 'ITS2'):
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
parents: 3
diff changeset
165 -ITSx $tax_args.amplicon_cond.ITSx_macro
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
parents: 3
diff changeset
166 #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
167
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
168 #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
169 -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
170 #end if
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
171 -keepUnclassified $tax_args.keepUnclassified
6
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
172 #if str($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
173 -LCA_cover $tax_args.LCA_cover
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
174 #end if
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
175 #if str($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
176 -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
177 #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
178 -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
179 -buildPhylo $tax_args.buildPhylo
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
180
1
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
181 ; EXIT_VALUE=\$? ;
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
182
7
692832801d70 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 81334bedc488edc36581c015b5a4c06926ec236c"
earlhaminst
parents: 6
diff changeset
183 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
184 &&
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
185 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
186 ]]></command>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
187
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
188 <inputs>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
189 <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
190 <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
191 <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
192 <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
193 </param>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
194 <when value="single">
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
195 <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
196 </when>
2
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
197 <!--
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
198 <when value="paired">
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
199 <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
200 <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
201 </when>
2
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
202 -->
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
203 <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
204 <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
205 </when>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
206 </conditional>
4
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
parents: 3
diff changeset
207 <param argument="-map" type="data" format="tabular" optional="true" label="Mapping file (optional)" help="Needed to demultiplex the FASTQ files using sdm. If the FASTQ are already demultiplexed, this can be omitted." />
6
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
208 <param argument="-sdmopt" type="data" format="txt" optional="true" label="SDM option file (optional)" />
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
209 <param argument="-platform" type="select" label="Sequencing platform">
6
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
210 <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
211 <option value="miSeq">miSeq</option>
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
212 <option value="hiSeq">hiSeq</option>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
213 <option value="454">454</option>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
214 <option value="PacBio">PacBio</option>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
215 </param>
1
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
216 <param argument="-barcode" type="data" format="fastqsanger" optional="true" label="Barcode (MID) sequences (optional)" help="FASTQ file with barcodes (in the processed mi/hiSeq format), if provided by the sequencer" />
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
217 <param argument="-forwardPrimer" type="text" value="" label="Forward primer used to amplify DNA region" help="E.g. 16S primer fwd" />
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
218 <param argument="-reversePrimer" type="text" value="" label="Reverse primer used to amplify DNA region" help="E.g. 16S primer rev" />
2
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
219 <conditional name="offtarget_cond">
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
220 <param argument="-offtargetDB" type="select" label="Remove likely contaminant OTUs/ASVs based on alignment to host genome" help="Useful for low-bacterial biomass samples to remove possible host genome contaminations">
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
221 <option value="no" selected="true">Disabled</option>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
222 <option value="cached">Use a built-in genome</option>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
223 <option value="history">Use a genome from history</option>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
224 </param>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
225 <when value="no" />
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
226 <when value="cached">
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
227 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
228 <options from_data_table="all_fasta">
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
229 <filter type="sort_by" column="2" />
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
230 <validator type="no_options" message="No reference genomes are available" />
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
231 </options>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
232 </param>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
233 </when>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
234 <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
235 <param name="ref_file" type="data" format="fasta,fasta.gz" label="FASTA reference genome" />
2
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
236 </when>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
237 </conditional>
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
238 <section name="clu_args" title="Clustering Options">
2
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
239 <conditional name="clu_cond">
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
240 <param argument="-clustering" type="select" label="Clustering algorithm">
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
241 <option value="1">UPARSE</option>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
242 <option value="2">swarm</option>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
243 <option value="3">cd-hit</option>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
244 <option value="6">unoise3</option>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
245 <option value="7" selected="true">dada2</option>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
246 </param>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
247 <when value="1">
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
248 <expand macro="id_macro" />
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
249 </when>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
250 <when value="2">
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
251 <param argument="-swarm_distance" type="integer" min="1" value="1" label="Clustering threshold for OTUs when using swarm clustering" />
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
252 </when>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
253 <when value="3">
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
254 <expand macro="id_macro" />
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
255 </when>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
256 <when value="6">
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
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 <when value="7">
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
259 </when>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
260 </conditional>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
261 <param argument="-derepMin" type="text" value="" label="Minimum size of dereplicated raw reads (optional)" help="E.g. 4:1,4:2,3:3 . See http://lotus2.earlham.ac.uk/images/Derep_options.pdf for how to specify this parameter. If not specified, LotuS2 will select an appropriate default for the chosen clustering algorithm." />
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
262 <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
263 <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
264 <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
265 <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
266 <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
267 <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
268 </param>
6
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
269 <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
270 </section>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
271 <section name="tax_args" title="Taxonomy Options">
1
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
272 <conditional name="aligner_cond">
2
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
273 <param argument="-taxAligner" type="select" label="Taxonomy aligner for taxonomic profiling of OTUs">
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
274 <option value="0" selected="true">RDPclassifier (max likelihood)</option>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
275 <option value="1">Blast LCA against custom reference database</option>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
276 <option value="2">LAMBDA LCA against custom reference database</option>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
277 <option value="3">UTAX likelihood corrected</option>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
278 <option value="4">VSEARCH LCA against custom reference database</option>
1
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
279 </param>
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
280 <when value="0">
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
281 <param argument="-rdp_thr" type="float" min="0" max="1" value="0.8" label="Confidence threshold for RDP"/>
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
282 </when>
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
283 <when value="1">
6
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
284 <expand macro="refDB_macro" ref_fasta_formats="fasta" />
1
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
285 </when>
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
286 <when value="2">
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
287 <expand macro="refDB_macro" />
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
288 </when>
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
289 <when value="3">
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
290 <param argument="-utax_thr" type="float" min="0" max="1" value="0.8" label="Confidence threshold for UTAX"/>
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
291 </when>
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
292 <when value="4">
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
293 <expand macro="refDB_macro" />
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
294 </when>
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
295 </conditional>
4
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
parents: 3
diff changeset
296 <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
297 <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
298 <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
299 <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
300 <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
301 <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
302 <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
303 <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
304 </param>
8
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="" />
0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c"
earlhaminst
parents: 7
diff changeset
306 <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
307 <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
308 <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
309 <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
310 </when>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
parents: 3
diff changeset
311 <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
312 <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
313 </when>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
parents: 3
diff changeset
314 <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
315 <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
316 </when>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
parents: 3
diff changeset
317 </conditional>
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
318 <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
319 <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
320 <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
321 <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
322 </param>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
323 <param argument="-keepUnclassified" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Keep unclassified OTUs" help="Includes unclassified OTUs (i.e. no match in RDP/Blast database) in OTU and taxa abundance matrix calculations" />
6
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
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parents: 5
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324 <param argument="-LCA_cover" type="float" min="0" max="1" value="" optional="true" label="Minimum horizontal coverage of an OTU sequence against ref DB"/>
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
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325 <param argument="-LCA_frac" type="float" min="0" max="1" value="" optional="true" label="Minimum fraction of reads with identical taxonomy"/>
4
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
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326 <param argument="-lulu" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Use LULU to merge OTUs based on their occurrence" />
2
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
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parents: 1
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327 <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"
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parents: 1
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328 <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
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329 <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
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330 <option value="2">Use iqtree2</option>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
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parents: 1
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331 </param>
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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332 </section>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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diff changeset
333 </inputs>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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334
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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diff changeset
335 <outputs>
7
692832801d70 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 81334bedc488edc36581c015b5a4c06926ec236c"
earlhaminst
parents: 6
diff changeset
336 <data name="outputs" format="zip" label="${tool.name} on ${on_string}: Complete LotuS2 output" from_work_dir="output.zip" />
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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337 <data name="otu" format="tabular" label="${tool.name} on ${on_string}: OTU abundance matrix" from_work_dir="output/OTU.txt" />
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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338 <data name="otu_fna" format="fasta" label="${tool.name} on ${on_string}: FASTA-formatted extended OTU seed sequences" from_work_dir="output/OTU.fna" />
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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diff changeset
339 <data name="OTUphylo_nwk" format="newick" label="${tool.name} on ${on_string}: Newick-formatted phylogenetic tree between sequences" from_work_dir="output/OTUphylo.nwk" />
2
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
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340 <data name="mapping" format="tabular" label="${tool.name} on ${on_string}: mapping file" from_work_dir="output/primary/in.map" />
4
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
parents: 3
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341 <data name="runlog" format="txt" label="${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
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diff changeset
342 </outputs>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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diff changeset
343
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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diff changeset
344 <tests>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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diff changeset
345 <test>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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diff changeset
346 <param name="paired_or_single" value="single"/>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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diff changeset
347 <param name="input" value="Anh_sample1.fastq.gz,Anh_sample2.fastq.gz" ftype="fastqsanger.gz"/>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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diff changeset
348 <param name="platform" value="454" />
1
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
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349 <param name="clustering" value="3" />
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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diff changeset
350 <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
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diff changeset
351 <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
352 <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
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diff changeset
353 </test>
4
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
parents: 3
diff changeset
354 <test>
8
0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c"
earlhaminst
parents: 7
diff changeset
355 <param name="paired_or_single" value="paired_collection"/>
0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c"
earlhaminst
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diff changeset
356 <param name="pair_input">
0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c"
earlhaminst
parents: 7
diff changeset
357 <collection type="list:paired">
0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c"
earlhaminst
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diff changeset
358 <element name="Anh_sample">
0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c"
earlhaminst
parents: 7
diff changeset
359 <collection type="paired">
0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c"
earlhaminst
parents: 7
diff changeset
360 <element name="forward" value="Anh_sample1.fastq.gz" ftype="fastqsanger.gz" />
0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c"
earlhaminst
parents: 7
diff changeset
361 <element name="reverse" value="Anh_sample2.fastq.gz" ftype="fastqsanger.gz" />
0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c"
earlhaminst
parents: 7
diff changeset
362 </collection>
0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c"
earlhaminst
parents: 7
diff changeset
363 </element>
0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c"
earlhaminst
parents: 7
diff changeset
364 </collection>
0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c"
earlhaminst
parents: 7
diff changeset
365 </param>
0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c"
earlhaminst
parents: 7
diff changeset
366 <param name="mapping" value="mapping_paired.txt" />
4
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
parents: 3
diff changeset
367 <param name="platform" value="454" />
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
parents: 3
diff changeset
368 <param name="clustering" value="3" />
8
0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c"
earlhaminst
parents: 7
diff changeset
369 <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
370 <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
371 </test>
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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diff changeset
372 </tests>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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diff changeset
373
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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diff changeset
374 <help><![CDATA[
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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diff changeset
375 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"
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diff changeset
376
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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diff changeset
377 Documentation can be found at `<http://lotus2.earlham.ac.uk/>`_.
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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diff changeset
378 ]]></help>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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diff changeset
379 <citations>
1
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
380 <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"
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381 </citations>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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382 </tool>