annotate lotus2.xml @ 24:fede743a9002 draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 726bde1eab1d49de8d7fab629b0efd1c1f965d8a
author earlhaminst
date Mon, 11 Dec 2023 20:09:58 +0000
parents 469095a58c15
children eb7baf1f72ca
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ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4
earlhaminst
parents: 21
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1 <tool id="lotus2" name="LotuS2" version="@VERSION@+galaxy0" profile="20.09">
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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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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fede743a9002 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 726bde1eab1d49de8d7fab629b0efd1c1f965d8a
earlhaminst
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4 <token name="@VERSION@">2.30</token>
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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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5 <xml name="refDB_macro" token_ref_fasta_formats="fasta,fasta.gz">
4
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
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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"
earlhaminst
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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"
earlhaminst
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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"
earlhaminst
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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">
6
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"
earlhaminst
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13 <option value="" selected="true">(Default)</option>
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ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4
earlhaminst
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14 <option value="KSGP">Bacteria, Archaea, Eukaryotes SSU (KSGP)</option>
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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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15 <option value="SLV">Silva LSU (23/28S) or SSU (16/18S) (SLV)</option>
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ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4
earlhaminst
parents: 21
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16 <option value="GG2">GreenGenes2 SSU (GG2)</option>
ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4
earlhaminst
parents: 21
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17 <option value="UNITE">ITS fungi specific (UNITE)</option>
ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4
earlhaminst
parents: 21
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18 <option value="PR2">LSU spezialized on Ocean environmentas (PR2)</option>
ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4
earlhaminst
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19 <option value="beetax">Bee gut specific SSU (beetax)</option>
ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4
earlhaminst
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20 <option value="HITdb">Human gut specific SSU (HITdb)</option>
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59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
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21 </param>
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ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4
earlhaminst
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22 <param argument="-greengenesSpecies" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Create greengenes output labels instead of OTU" help="To be used with greengenes specific programs such as BugBase." />
4
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
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23 </when>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
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24 <when value="history">
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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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25 <param name="ref_fasta" type="data" format="@REF_FASTA_FORMATS@" label="Taxonomy reference sequences" help="In FASTA format" />
4
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
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26 <param argument="-tax4refDB" type="data" format="tabular" label="Taxonomy reference lineages" help="Tab-separated file with 2 columns mapping each FASTA header of the reference sequences to a GTDB-style taxonomy string" />
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
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27 </when>
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
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28 </conditional>
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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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29 <param argument="-useBestBlastHitOnly" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Use the best Blast hit only" help="Do not use LCA (lowest common ancestor) to determine the most likely taxonomic level (not recommended)" />
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
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30 </xml>
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59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
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31 <xml name="ITSx_macro">
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
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32 <param argument="-ITSx" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use ITSx to only retain OTUs fitting to ITS1/ITS2 hmm models" />
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
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33 </xml>
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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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34 </macros>
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fa84bba02a62 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 1632994d621dd37cd96792b152f4fe3f8e85b90c
earlhaminst
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35 <xrefs>
fa84bba02a62 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 1632994d621dd37cd96792b152f4fe3f8e85b90c
earlhaminst
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36 <xref type="bio.tools">lotus2</xref>
fa84bba02a62 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 1632994d621dd37cd96792b152f4fe3f8e85b90c
earlhaminst
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37 </xrefs>
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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38 <requirements>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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39 <requirement type="package" version="@VERSION@">lotus2</requirement>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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40 </requirements>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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41 <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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42 <command detect_errors="exit_code"><![CDATA[
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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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43 #import re
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ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4
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44
ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4
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45 LOTUS2_DIR=\$(dirname "\$(realpath "\$(which lotus2)")") &&
ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4
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46 if [ ! -e "\$LOTUS2_DIR/DB" ]; then
ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4
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47 {
ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4
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48 echo "LotuS2 databases missing in \$LOTUS2_DIR, these needs to be installed with:" &&
ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4
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49 echo "perl autoInstall.pl -condaDBinstall" &&
ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4
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50 echo "We currently recommend to use a conda environment instead of a biocontainer to prevent this problem.";
ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4
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51 } >&2 &&
ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4
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52 exit 1;
ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4
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53 fi &&
ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4
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54
12
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a"
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55 #def symlink_basename($f, strip_ext=False):
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8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea"
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56 #set $fn = re.sub('[^\w\-_.]', '_', $f.name)
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3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a"
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57 #if strip_ext:
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a"
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58 #if $fn.endswith('.gz'):
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a"
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59 #set $fn = $fn[:-3]
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a"
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60 #end if
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a"
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61 #if $f.ext.startswith('fasta'):
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a"
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62 #set $exts_to_drop = ('.fa', '.fasta', '.fna')
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a"
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63 #else:
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a"
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64 #set $exts_to_drop = []
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a"
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65 #end if
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a"
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66 #for $ext in $exts_to_drop:
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a"
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67 #if $fn.endswith($ext):
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a"
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68 #set $fn = $fn[:-len($ext)]
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a"
earlhaminst
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69 #break
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a"
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70 #end if
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a"
earlhaminst
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71 #end for
3f3ee496acec "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a"
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72 #end if
11
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea"
earlhaminst
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73 ${fn}#slurp
2
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
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74 #end def
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
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75
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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76 mkdir input
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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77 &&
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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78 #if $inputs.paired_or_single == 'single':
6
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
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79 #for $f in $inputs.input:
11
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea"
earlhaminst
parents: 10
diff changeset
80 ln -s '$f' 'input/${symlink_basename($f)}' &&
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
81 #end for
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
82 #else:
6
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
83 #for $f in $inputs.pair_input:
11
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea"
earlhaminst
parents: 10
diff changeset
84 ln -s '$f.forward' 'input/${symlink_basename($f.forward.dataset)}' &&
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea"
earlhaminst
parents: 10
diff changeset
85 ln -s '$f.reverse' 'input/${symlink_basename($f.reverse.dataset)}' &&
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
86 #end for
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
87 #end if
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
88
17
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
89 #if $aligner_cond.taxAligner not in ('0', '3') and $aligner_cond.refDB_cond.refDB == 'history':
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
90 #set $ext = $aligner_cond.refDB_cond.ref_fasta.ext
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
91 #set $ref_fasta_symlink = $symlink_basename($aligner_cond.refDB_cond.ref_fasta, strip_ext=True) + '.' + $ext
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
92 ln -s '$aligner_cond.refDB_cond.ref_fasta' '$ref_fasta_symlink' &&
6
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
93 #end if
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
94
4
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
parents: 3
diff changeset
95 #if not $map:
11
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea"
earlhaminst
parents: 10
diff changeset
96 cat '$generated_mapping' &&
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea"
earlhaminst
parents: 10
diff changeset
97 #set map = $generated_mapping
4
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
parents: 3
diff changeset
98 #end if
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
99
18
6c22795e1be0 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit afdb7dbe3283ee64d3aa2277efe505c7341575d8
earlhaminst
parents: 17
diff changeset
100 set +e &&
6c22795e1be0 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit afdb7dbe3283ee64d3aa2277efe505c7341575d8
earlhaminst
parents: 17
diff changeset
101
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
102 lotus2
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
103 -i input/
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
104 -o output
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
105 -tmpDir tmp_folder
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
106 -threads "\${GALAXY_SLOTS:-1}"
4
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
parents: 3
diff changeset
107 -map '$map'
17
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
108 #if $other_opts.sdmopt:
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
109 -sdmopt '$other_opts.sdmopt'
6
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
110 #end if
17
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
111 #if $other_opts.platform != '':
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
112 -platform $other_opts.platform
6
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
113 #end if
17
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
114 #if $other_opts.barcode:
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
115 -barcode '$other_opts.barcode'
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
116 #end if
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
117 #if $forwardPrimer:
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
118 -forwardPrimer '$forwardPrimer'
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
119 #end if
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
120 #if $reversePrimer:
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
121 -reversePrimer '$reversePrimer'
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
122 #end if
23
469095a58c15 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 33e0b986cfdef97a2ba8d473e7c5e4a40ce3bc08
earlhaminst
parents: 22
diff changeset
123 #if $other_opts.offtarget_cond.offtargetDB == 'cached':
469095a58c15 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 33e0b986cfdef97a2ba8d473e7c5e4a40ce3bc08
earlhaminst
parents: 22
diff changeset
124 -offtargetDB '$other_opts.offtarget_cond.ref_file.fields.path'
469095a58c15 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 33e0b986cfdef97a2ba8d473e7c5e4a40ce3bc08
earlhaminst
parents: 22
diff changeset
125 #elif $other_opts.offtarget_cond.offtargetDB == 'history':
17
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
126 -offtargetDB '$other_opts.offtarget_cond.ref_file'
2
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
127 #end if
17
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
128 -useMini4map $other_opts.useMini4map
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
129
17
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
130 -clustering $clu_cond.clustering
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
131 #if $clu_cond.clustering in ('1', '3'):
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
132 #if str($clu_cond.id):
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
133 -id $clu_cond.id
10
6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330"
earlhaminst
parents: 9
diff changeset
134 #end if
17
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
135 #elif $clu_cond.clustering == '2':
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
136 #if str($clu_cond.swarm_distance):
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
137 -swarm_distance $clu_cond.swarm_distance
10
6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330"
earlhaminst
parents: 9
diff changeset
138 #end if
2
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
139 #end if
1
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
140 #if $clu_args.derepMin:
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
141 -derepMin '$clu_args.derepMin'
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
142 #end if
6
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
143
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
144 #if $clu_args.deactivateChimeraCheck != '':
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
145 -deactivateChimeraCheck $clu_args.deactivateChimeraCheck
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
146 #end if
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
147 #if str($clu_args.chim_skew):
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
148 -chim_skew $clu_args.chim_skew
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
149 #end if
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
150
17
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
151 -taxAligner $aligner_cond.taxAligner
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
152 #if $aligner_cond.taxAligner == '0':
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
153 #if str($aligner_cond.rdp_thr):
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
154 -rdp_thr $aligner_cond.rdp_thr
10
6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330"
earlhaminst
parents: 9
diff changeset
155 #end if
17
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
156 #elif $aligner_cond.taxAligner == '3':
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
157 #if str($aligner_cond.utax_thr):
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
158 -utax_thr $aligner_cond.utax_thr
10
6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330"
earlhaminst
parents: 9
diff changeset
159 #end if
1
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
160 #else:
17
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
161 #if $aligner_cond.refDB_cond.refDB == 'cached':
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
162 #if $aligner_cond.refDB_cond.ref_db != '':
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
163 -refDB $aligner_cond.refDB_cond.ref_db
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
164 -greengenesSpecies $aligner_cond.refDB_cond.greengenesSpecies
6
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
165 #end if
4
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
parents: 3
diff changeset
166 #else:
6
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
167 -refDB '$ref_fasta_symlink'
17
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
168 -tax4refDB '$aligner_cond.refDB_cond.tax4refDB'
4
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
parents: 3
diff changeset
169 #end if
17
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
170 -useBestBlastHitOnly $aligner_cond.useBestBlastHitOnly
1
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
171 #end if
6
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
172 #if $tax_args.amplicon_cond.amplicon_type != '':
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
173 -amplicon_type $tax_args.amplicon_cond.amplicon_type
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
174 #end if
4
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
parents: 3
diff changeset
175 #if $tax_args.amplicon_cond.amplicon_type in ('ITS', 'ITS1', 'ITS2'):
9
82ff4f47436a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 540400ccedbc8a88d00e021b645d35ac72e8098b"
earlhaminst
parents: 8
diff changeset
176 -ITSx $tax_args.amplicon_cond.ITSx
4
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
parents: 3
diff changeset
177 #end if
6
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
178
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
179 #if $tax_args.tax_group != '':
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
180 -tax_group $tax_args.tax_group
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
181 #end if
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
182 -keepUnclassified $tax_args.keepUnclassified
6
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
183 #if str($tax_args.LCA_cover):
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
184 -LCA_cover $tax_args.LCA_cover
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
185 #end if
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
186 #if str($tax_args.LCA_frac):
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
187 -LCA_frac $tax_args.LCA_frac
fc78d02657a9 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
earlhaminst
parents: 5
diff changeset
188 #end if
2
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
189 -lulu $tax_args.lulu
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
190 -buildPhylo $tax_args.buildPhylo
15
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda"
earlhaminst
parents: 14
diff changeset
191 #if $tax_args.taxExcludeGrep:
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda"
earlhaminst
parents: 14
diff changeset
192 -taxExcludeGrep '$tax_args.taxExcludeGrep'
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda"
earlhaminst
parents: 14
diff changeset
193 #end if
1
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
194 ; EXIT_VALUE=\$? ;
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
195
7
692832801d70 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 81334bedc488edc36581c015b5a4c06926ec236c"
earlhaminst
parents: 6
diff changeset
196 zip -8 -r -v output.zip output/
1
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
197 &&
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
198 exit \$EXIT_VALUE
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
199 ]]></command>
11
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea"
earlhaminst
parents: 10
diff changeset
200 <configfiles>
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea"
earlhaminst
parents: 10
diff changeset
201 <configfile name="generated_mapping"><![CDATA[#slurp
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea"
earlhaminst
parents: 10
diff changeset
202 #import re
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea"
earlhaminst
parents: 10
diff changeset
203 #def symlink_basename($f):
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea"
earlhaminst
parents: 10
diff changeset
204 #set $fn = re.sub('[^\w\-_.]', '_', $f.name)
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea"
earlhaminst
parents: 10
diff changeset
205 ${fn}#slurp
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea"
earlhaminst
parents: 10
diff changeset
206 #end def
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea"
earlhaminst
parents: 10
diff changeset
207 #SampleID fastqFile SequencingRun
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea"
earlhaminst
parents: 10
diff changeset
208 #if $inputs.paired_or_single == 'single':
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea"
earlhaminst
parents: 10
diff changeset
209 #for $i, $f in enumerate($inputs.input):
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea"
earlhaminst
parents: 10
diff changeset
210 SMPL${i} ${symlink_basename($f)} a
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea"
earlhaminst
parents: 10
diff changeset
211 #end for
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea"
earlhaminst
parents: 10
diff changeset
212 #else:
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea"
earlhaminst
parents: 10
diff changeset
213 #for $i, $f in enumerate($inputs.pair_input):
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea"
earlhaminst
parents: 10
diff changeset
214 SMPL${i} ${symlink_basename($f.forward.dataset)},${symlink_basename($f.reverse.dataset)} a
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea"
earlhaminst
parents: 10
diff changeset
215 #end for
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea"
earlhaminst
parents: 10
diff changeset
216 #end if
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea"
earlhaminst
parents: 10
diff changeset
217 ]]></configfile>
8f732780e0f3 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea"
earlhaminst
parents: 10
diff changeset
218 </configfiles>
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
219 <inputs>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
220 <conditional name="inputs">
8
0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c"
earlhaminst
parents: 7
diff changeset
221 <param name="paired_or_single" type="select" label="Single- or Paired-end data?">
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
222 <option value="single" selected="true">Single-end</option>
8
0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c"
earlhaminst
parents: 7
diff changeset
223 <option value="paired_collection">Paired-end list</option>
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
224 </param>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
225 <when value="single">
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
226 <param name="input" type="data" format="fastqsanger,fastqsanger.gz" multiple="true" label="Single-end reads" />
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
227 </when>
2
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
228 <!--
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
229 <when value="paired">
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
230 <param name="left_input" type="data" format="fastqsanger,fastqsanger.gz" multiple="true" label="Left/Forward strand reads" />
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
231 <param name="right_input" type="data" format="fastqsanger,fastqsanger.gz" multiple="true" label="Right/Reverse strand reads" />
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
232 </when>
2
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
233 -->
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
234 <when value="paired_collection">
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
235 <param name="pair_input" type="data_collection" collection_type="list:paired" format="fastqsanger,fastqsanger.gz" label="List of paired reads" />
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
236 </when>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
237 </conditional>
4
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
parents: 3
diff changeset
238 <param argument="-map" type="data" format="tabular" optional="true" label="Mapping file (optional)" help="Needed to demultiplex the FASTQ files using sdm. If the FASTQ are already demultiplexed, this can be omitted." />
10
6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330"
earlhaminst
parents: 9
diff changeset
239 <param argument="-forwardPrimer" type="text" value="" label="Forward primer used to amplify DNA region (optional)" help="E.g. 16S primer fwd" />
6d55d9464719 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330"
earlhaminst
parents: 9
diff changeset
240 <param argument="-reversePrimer" type="text" value="" label="Reverse primer used to amplify DNA region (optional)" help="E.g. 16S primer rev" />
17
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
241 <conditional name="clu_cond">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
242 <param argument="-clustering" type="select" label="Clustering algorithm">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
243 <option value="7" selected="true">DADA2</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
244 <option value="2">swarm</option>
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245 <option value="3">CD-HIT</option>
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246 <option value="8">VSEARCH</option>
2
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247 </param>
17
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248 <when value="2">
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249 <param argument="-swarm_distance" type="integer" min="1" value="1" optional="true" label="Clustering threshold for OTUs when using swarm clustering (optional)" />
2
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parents: 1
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250 </when>
17
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251 <when value="3">
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252 <param argument="-id" type="float" min="0.9" max="1" value="0.97" optional="true" label="Clustering threshold for OTUs" />
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253 </when>
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254 <when value="7">
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255 </when>
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256 <when value="8">
2
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257 </when>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
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258 </conditional>
17
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259 <conditional name="aligner_cond">
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260 <param argument="-taxAligner" type="select" label="Taxonomy aligner for taxonomic profiling of OTUs">
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261 <option value="0" selected="true">RDPclassifier (max likelihood)</option>
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262 <!-- <option value="1">Blast LCA against custom reference database</option> -->
24
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263 <option value="2">Lambda, LCA against custom reference database</option>
17
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264 <!-- <option value="4">VSEARCH LCA against custom reference database</option> -->
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265 </param>
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266 <when value="0">
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267 <param argument="-rdp_thr" type="float" min="0" max="1" value="0.8" optional="true" label="Confidence threshold for RDP (optional)"/>
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268 </when>
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269 <!-- <when value="1">
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270 <expand macro="refDB_macro" ref_fasta_formats="fasta" />
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271 </when> -->
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272 <when value="2">
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273 <expand macro="refDB_macro" />
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274 </when>
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275 <!-- <when value="3">
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276 <param argument="-utax_thr" type="float" min="0" max="1" value="0.8" optional="true" label="Confidence threshold for UTAX (optional)"/>
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277 </when>
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278 <when value="4">
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279 <expand macro="refDB_macro" />
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280 </when> -->
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281 </conditional>
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282 <section name="clu_args" title="Other Clustering Options">
20
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283 <param argument="-derepMin" type="text" value="" label="Minimum size of dereplicated raw reads (optional)" help="E.g. 4:1,4:2,3:3 . See https://lotus2.earlham.ac.uk/images/Derep_options.pdf for how to specify this parameter. If not specified, LotuS2 will select an appropriate default for the chosen clustering algorithm." />
0
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284 <param argument="-deactivateChimeraCheck" type="select" label="Chimera check">
6
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285 <option value="" selected="true">(Default)</option>
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286 <option value="0">OTU chimera checks</option>
0
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287 <option value="1">No chimera check at all</option>
2
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288 <option value="2">Disable deNovo chimera check</option>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
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289 <option value="3">Disable ref based chimera check</option>
0
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290 </param>
6
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291 <param argument="-chim_skew" type="integer" min="0" value="" optional="true" label="Skew in chimeric fragment abundance" />
0
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292 </section>
17
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293 <section name="tax_args" title="Other Taxonomy Options">
4
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294 <conditional name="amplicon_cond">
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295 <param argument="-amplicon_type" type="select" label="Amplicon type">
6
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296 <option value="" selected="true">(Default)</option>
4
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297 <option value="LSU">LSU Large subunit (23S/28S)</option>
6
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298 <option value="SSU">SSU small subunit (16S/18S)</option>
4
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299 <option value="ITS">ITS internal transcribed spacer</option>
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300 <option value="ITS1">ITS1</option>
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301 <option value="ITS2">ITS2</option>
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302 </param>
8
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303 <when value="" />
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304 <when value="LSU" />
0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c"
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305 <when value="SSU" />
4
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
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306 <when value="ITS">
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307 <expand macro="ITSx_macro" />
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308 </when>
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309 <when value="ITS1">
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310 <expand macro="ITSx_macro" />
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311 </when>
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312 <when value="ITS2">
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313 <expand macro="ITSx_macro" />
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314 </when>
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315 </conditional>
0
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316 <param argument="-tax_group" type="select" label="Tax group">
6
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317 <option value="" selected="true">(Default)</option>
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318 <option value="bacteria">bacterial 16S rDNA annnotation</option>
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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319 <option value="fungi">fungal 18S/23S/ITS annotation</option>
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320 </param>
22
ceb2cb800298 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4
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321 <param argument="-keepUnclassified" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Keep unclassified OTUs" help="Includes unclassified OTUs (no Phylum assignment) in OTU and taxa abundance matrix calculations" />
10
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322 <param argument="-LCA_cover" type="float" min="0" max="1" value="" optional="true" label="Minimum horizontal coverage of an OTU sequence against ref DB (optional)"/>
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323 <param argument="-LCA_frac" type="float" min="0" max="1" value="" optional="true" label="Minimum fraction of reads with identical taxonomy (optional)"/>
20
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324 <param argument="-lulu" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use LULU to merge OTUs based on their occurrence" />
2
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parents: 1
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325 <param argument="-buildPhylo" type="select" label="Build OTU phylogeny">
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
326 <option value="0">Disable</option>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
327 <option value="1" selected="true">Use fasttree2</option>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
328 <option value="2">Use iqtree2</option>
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
329 </param>
15
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda"
earlhaminst
parents: 14
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330 <param argument="-taxExcludeGrep" type="text" value="" label="Taxonomic groups to exclude, as a regular expression" help="OTUs matching this regular expression will be assigned as unknown, and by default removed">
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda"
earlhaminst
parents: 14
diff changeset
331 <sanitizer>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda"
earlhaminst
parents: 14
diff changeset
332 <valid initial="default">
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda"
earlhaminst
parents: 14
diff changeset
333 <add value="|" />
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda"
earlhaminst
parents: 14
diff changeset
334 <add value="$" />
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda"
earlhaminst
parents: 14
diff changeset
335 </valid>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda"
earlhaminst
parents: 14
diff changeset
336 </sanitizer>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda"
earlhaminst
parents: 14
diff changeset
337 </param>
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
338 </section>
17
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
339 <section name="other_opts" title="Other options">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
340 <param argument="-sdmopt" type="data" format="txt" optional="true" label="SDM option file (optional)" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
341 <param argument="-platform" type="select" label="Sequencing platform">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
342 <option value="" selected="true">(Default)</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
343 <option value="miSeq">miSeq</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
344 <option value="hiSeq">hiSeq</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
345 <option value="454">454</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
346 <option value="PacBio">PacBio</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
347 </param>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
348 <param argument="-barcode" type="data" format="fastqsanger" optional="true" label="Barcode (MID) sequences (optional)" help="FASTQ file with barcodes (in the processed mi/hiSeq format), if provided by the sequencer" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
349 <conditional name="offtarget_cond">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
350 <param argument="-offtargetDB" type="select" label="Remove likely contaminant OTUs/ASVs based on alignment to host genome" help="Useful for low-bacterial biomass samples to remove possible host genome contaminations">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
351 <option value="no" selected="true">Disabled</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
352 <option value="cached">Use a built-in genome</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
353 <option value="history">Use a genome from history</option>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
354 </param>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
355 <when value="no" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
356 <when value="cached">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
357 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
358 <options from_data_table="all_fasta">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
359 <filter type="sort_by" column="2" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
360 <validator type="no_options" message="No reference genomes are available" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
361 </options>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
362 </param>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
363 </when>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
364 <when value="history">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
365 <param name="ref_file" type="data" format="fasta,fasta.gz" label="FASTA reference genome" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
366 </when>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
367 </conditional>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
368 <param argument="-useMini4map" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use minimap2 instead of VSEARCH to map back reads to OTUs" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
369 </section>
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
370 </inputs>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
371
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
372 <outputs>
7
692832801d70 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 81334bedc488edc36581c015b5a4c06926ec236c"
earlhaminst
parents: 6
diff changeset
373 <data name="outputs" format="zip" label="${tool.name} on ${on_string}: Complete LotuS2 output" from_work_dir="output.zip" />
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
374 <data name="otu" format="tabular" label="${tool.name} on ${on_string}: OTU abundance matrix" from_work_dir="output/OTU.txt" />
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
375 <data name="otu_fna" format="fasta" label="${tool.name} on ${on_string}: FASTA-formatted extended OTU seed sequences" from_work_dir="output/OTU.fna" />
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
376 <data name="OTUphylo_nwk" format="newick" label="${tool.name} on ${on_string}: Newick-formatted phylogenetic tree between sequences" from_work_dir="output/OTUphylo.nwk" />
2
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
377 <data name="mapping" format="tabular" label="${tool.name} on ${on_string}: mapping file" from_work_dir="output/primary/in.map" />
4
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
parents: 3
diff changeset
378 <data name="runlog" format="txt" label="${tool.name} on ${on_string}: main log file" from_work_dir="output/LotuSLogS/LotuS_run.log" />
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
379 </outputs>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
380
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
381 <tests>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
382 <test>
15
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda"
earlhaminst
parents: 14
diff changeset
383 <conditional name="inputs">
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda"
earlhaminst
parents: 14
diff changeset
384 <param name="paired_or_single" value="single"/>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda"
earlhaminst
parents: 14
diff changeset
385 <param name="input" value="Anh_sample1.fastq.gz,Anh_sample2.fastq.gz" ftype="fastqsanger.gz"/>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda"
earlhaminst
parents: 14
diff changeset
386 </conditional>
17
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
387 <conditional name="clu_cond">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
388 <param name="clustering" value="3" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
389 </conditional>
15
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda"
earlhaminst
parents: 14
diff changeset
390 <section name="clu_args">
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda"
earlhaminst
parents: 14
diff changeset
391 <param name="derepMin" value="1" />
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda"
earlhaminst
parents: 14
diff changeset
392 </section>
17
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
393 <section name="tax_args">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
394 <param name="lulu" value="false" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
395 </section>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
396 <section name="other_opts">
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
397 <param name="platform" value="454" />
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
398 </section>
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
399 <output name="otu" file="OTU.txt" compare="sim_size" />
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
400 <output name="otu_fna" file="OTU.fna" compare="sim_size" />
2
cf56a6553385 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents: 1
diff changeset
401 <output name="mapping" file="mapping.txt" />
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
402 </test>
4
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
parents: 3
diff changeset
403 <test>
15
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda"
earlhaminst
parents: 14
diff changeset
404 <conditional name="inputs">
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda"
earlhaminst
parents: 14
diff changeset
405 <param name="paired_or_single" value="paired_collection"/>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda"
earlhaminst
parents: 14
diff changeset
406 <param name="pair_input">
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda"
earlhaminst
parents: 14
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407 <collection type="list:paired">
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda"
earlhaminst
parents: 14
diff changeset
408 <element name="Anh_sample">
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda"
earlhaminst
parents: 14
diff changeset
409 <collection type="paired">
20
1d660ee0b1c8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e532d288f092df22f32805cea50583fe16a1070f
earlhaminst
parents: 19
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410 <element name="forward" value="Arabidopsis_R1.fastqsanger.gz" ftype="fastqsanger.gz" />
1d660ee0b1c8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e532d288f092df22f32805cea50583fe16a1070f
earlhaminst
parents: 19
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411 <element name="reverse" value="Arabidopsis_R2.fastqsanger.gz" ftype="fastqsanger.gz" />
15
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda"
earlhaminst
parents: 14
diff changeset
412 </collection>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda"
earlhaminst
parents: 14
diff changeset
413 </element>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda"
earlhaminst
parents: 14
diff changeset
414 </collection>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda"
earlhaminst
parents: 14
diff changeset
415 </param>
6e9fd3e0dcbb "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda"
earlhaminst
parents: 14
diff changeset
416 </conditional>
20
1d660ee0b1c8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e532d288f092df22f32805cea50583fe16a1070f
earlhaminst
parents: 19
diff changeset
417 <param name="map" value="mapping_paired.txt" ftype="tabular" />
17
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
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418 <section name="tax_args">
20
1d660ee0b1c8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e532d288f092df22f32805cea50583fe16a1070f
earlhaminst
parents: 19
diff changeset
419 <param name="lulu" value="true" />
17
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
420 </section>
8
0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c"
earlhaminst
parents: 7
diff changeset
421 <output name="otu" file="OTU_paired.txt" compare="sim_size" />
0fddee8b1f7e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit bdade08328554140c46dd473081787773644c11c"
earlhaminst
parents: 7
diff changeset
422 <output name="otu_fna" file="OTU_paired.fna" compare="sim_size" />
4
59b8864c9fa0 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
earlhaminst
parents: 3
diff changeset
423 </test>
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
424 </tests>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
425
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
426 <help><![CDATA[
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
427 If you have separate FASTA and quality files, these can be combined in a FASTQ file using the "Combine FASTA and QUAL into FASTQ" tool.
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
428
17
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
429 .. class:: infomark
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
430
20
1d660ee0b1c8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e532d288f092df22f32805cea50583fe16a1070f
earlhaminst
parents: 19
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431 The full LotuS2 **documentation** can be found at `<https://lotus2.earlham.ac.uk/>`_.
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
432 ]]></help>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
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433 <citations>
17
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
434 <citation type="doi">10.1186/s40168-022-01365-1</citation>
28f284a679ce planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd
earlhaminst
parents: 16
diff changeset
435 <citation type="doi">10.1186/s40168-021-01012-1</citation>
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
436 </citations>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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437 </tool>