Mercurial > repos > earlhaminst > lotus2

annotate lotus2.xml @ 1:85da3173a488 draft

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"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
author earlhaminst
date Wed, 19 May 2021 02:38:24 +0000
parents 478e767a0e7a
children cf56a6553385
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478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
1 <tool id="lotus2" name="LotuS2" version="@VERSION@" profile="20.01">
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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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"
earlhaminst
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3 <macros>
1
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
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4 <token name="@VERSION@">2.05.1</token>
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
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5 <xml name="refDB_macro">
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
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6 <param argument="-refDB" type="select" label="Reference Database">
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
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7 <option value="SLV" selected="true">Silva LSU (23/28S) or SSU (16/18S) (SLV)</option>
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
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8 <option value="GG">Greengenes (GG)</option>
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
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9 <option value="UNITE">ITS focused on fungi (UNITE)</option>
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
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10 <option value="PR2">SSU focused on Protists (PR2)</option>
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
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11 <option value="beetax">Bee gut specific database and tax names (beetax)</option>
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
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12 <option value="HITdb">Human gut microbiota (HITdb)</option>
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
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13 </param>
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
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14 </xml>
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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15 </macros>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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16 <requirements>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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17 <requirement type="package" version="@VERSION@">lotus2</requirement>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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18 </requirements>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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19 <version_command>lotus2 --version</version_command>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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20 <command detect_errors="exit_code"><![CDATA[
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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21 mkdir input
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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22 &&
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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23 #if $inputs.paired_or_single == 'single':
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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24 #for i, f in enumerate($inputs.input):
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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25 #set ext = $f.ext.replace('sanger', '')
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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26 ln -s '$f' 'input/input${i}.${ext}' &&
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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27 #end for
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
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28 #elif $inputs.paired_or_single == 'paired':
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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29 #for i, f in enumerate($inputs.left_input):
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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30 #set ext = $f.ext.replace('sanger', '')
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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31 ln -s '$f' 'input/input${i}.1.${ext}' &&
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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32 #end for
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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33 #for i, f in enumerate($inputs.right_input):
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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34 #set ext = $f.ext.replace('sanger', '')
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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35 ln -s '$f' 'input/input${i}.2.${ext}' &&
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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36 #end for
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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37 #else:
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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38 #for i, f in enumerate($inputs.pair_input):
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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39 #set ext = $f.forward.ext.replace('sanger', '')
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
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40 ln -s '$f.forward' 'input/input${i}.1.${ext}' &&
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
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41 #set ext = $f.reverse.ext.replace('sanger', '')
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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42 ln -s '$f.reverse' 'input/input${i}.2.${ext}' &&
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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43 #end for
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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44 #end if
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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45
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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46 lotus2 -create_map mapping.txt -i input/ &&
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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47 cat mapping.txt &&
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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48
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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49 lotus2
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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50 -i input/
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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51 -o output
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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52 -tmpDir tmp_folder
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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53 -threads "\${GALAXY_SLOTS:-1}"
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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54 -map mapping.txt
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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55 -platform $platform
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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56 #if $barcode:
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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57 -barcode '$barcode'
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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58 #end if
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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59 #if $forwardPrimer:
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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60 -forwardPrimer '$forwardPrimer'
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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61 #end if
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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diff changeset
62 #if $reversePrimer:
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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63 -reversePrimer '$reversePrimer'
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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64 #end if
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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65
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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66 -clustering $clu_args.clustering
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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67 -id $clu_args.id
1
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
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68 #if $clu_args.derepMin:
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
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69 -derepMin '$clu_args.derepMin'
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
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70 #end if
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
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71 -deactivateChimeraCheck $clu_args.deactivateChimeraCheck
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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72 -chim_skew $clu_args.chim_skew
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
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73 -readOverlap $clu_args.readOverlap
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
74
1
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
75 -taxAligner $tax_args.aligner_cond.taxAligner
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
76 #if $tax_args.aligner_cond.taxAligner == '0':
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
77 -rdp_thr $tax_args.aligner_cond.rdp_thr
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
78 #elif $tax_args.aligner_cond.taxAligner == '3':
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
79 -utax_thr $tax_args.aligner_cond.utax_thr
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
80 #else:
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
81 -refDB $tax_args.aligner_cond.refDB
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
82 #end if
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
83 -amplicon_type $tax_args.amplicon_type
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
84 -tax_group $tax_args.tax_group
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
85 -keepUnclassified $tax_args.keepUnclassified
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
86 -useBestBlastHitOnly $tax_args.useBestBlastHitOnly
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
87 -LCA_cover $tax_args.LCA_cover
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
88 -LCA_frac $tax_args.LCA_frac
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
89 -greengenesSpecies $tax_args.greengenesSpecies
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
90
1
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
91 ; EXIT_VALUE=\$? ;
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
92
1
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
93 tar -cvzf output.tar.gz output/
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
94 &&
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
95 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
96 ]]></command>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
97
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
98 <inputs>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
99 <conditional name="inputs">
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
100 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
101 <option value="single" selected="true">Single-end</option>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
102 <option value="paired">Paired-end</option>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
103 <option value="paired_collection">Paired-end collection</option>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
104 </param>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
105 <when value="single">
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
106 <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
107 </when>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
108 <when value="paired">
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
109 <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
110 <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
111 </when>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
112 <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
113 <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
114 </when>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
115 </conditional>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
116 <param argument="-platform" type="select" label="Sequencing platform">
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
117 <option value="miSeq" selected="true">miSeq</option>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
118 <option value="hiSeq">hiSeq</option>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
119 <option value="454">454</option>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
120 <option value="PacBio">PacBio</option>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
121 </param>
1
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
122 <param argument="-barcode" type="data" format="fastqsanger" optional="true" label="Barcode (MID) sequences (optional)" help="FASTQ file with barcodes (in the processed mi/hiSeq format), if provided by the sequencer" />
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
123 <param argument="-forwardPrimer" type="text" value="" label="Forward primer used to amplify DNA region" help="E.g. 16S primer fwd" />
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
124 <param argument="-reversePrimer" type="text" value="" label="Reverse primer used to amplify DNA region" help="E.g. 16S primer rev" />
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
125 <section name="clu_args" title="Clustering Options">
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
126 <param argument="-clustering" type="select" label="Clustering algorithm">
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
127 <option value="1">UPARSE</option>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
128 <option value="2">swarm</option>
1
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
129 <option value="3">cd-hit</option>
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
130 <option value="6">unoise3</option>
1
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
131 <option value="7" selected="true">dada2</option>
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
132 </param>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
133 <param argument="-id" type="float" min="0" max="1" value="0.97" label="Clustering threshold for OTUs" />
1
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
134 <param argument="-derepMin" type="text" value="" label="Minimum size of dereplicated raw reads" help="E.g. 4:1,4:2,3:3 . See http://lotus2.earlham.ac.uk/images/Derep_options.pdf for how to specify this parameter" />
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
135 <param argument="-deactivateChimeraCheck" type="select" label="Chimera check">
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
136 <option value="0" selected="true">OTU chimera checks</option>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
137 <option value="1">No chimera check at all</option>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
138 <option value="2">Deactivate deNovo chimera check</option>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
139 <option value="3">Deactivate ref based chimera check</option>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
140 </param>
1
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
141 <param argument="-chim_skew" type="integer" min="0" value="2" label="Skew in chimeric fragment abundance" />
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
142 <param argument="-readOverlap" type="integer" min="0" value="300" label="Maximum number of basepairs that two reads are overlapping" />
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
143 </section>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
earlhaminst
parents:
diff changeset
144 <section name="tax_args" title="Taxonomy Options">
1
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
145 <conditional name="aligner_cond">
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
146 <param argument="-taxAligner" type="select" label="Taxonomy aligner">
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
147 <option value="0" selected="true">Deactivated (just use RDP)</option>
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
148 <option value="1">Blast</option>
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
149 <option value="2">Use LAMBDA to search against a 16S reference database for taxonomic profiling of OTUs</option>
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
150 <option value="3">Use UTAX with custom databases</option>
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
151 <option value="4">Use VSEARCH to align OTUs to custom databases</option>
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
152 </param>
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
153 <when value="0">
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
154 <param argument="-rdp_thr" type="float" min="0" max="1" value="0.8" label="Confidence threshold for RDP"/>
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
155 </when>
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
earlhaminst
parents: 0
diff changeset
156 <when value="1">
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
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157 <expand macro="refDB_macro" />
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
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158 </when>
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
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159 <when value="2">
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
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160 <expand macro="refDB_macro" />
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
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161 </when>
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
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162 <when value="3">
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
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163 <param argument="-utax_thr" type="float" min="0" max="1" value="0.8" label="Confidence threshold for UTAX"/>
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
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164 </when>
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
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165 <when value="4">
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
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166 <expand macro="refDB_macro" />
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
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167 </when>
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
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168 </conditional>
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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169 <param argument="-amplicon_type" type="select" label="Amplicon type">
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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170 <option value="LSU">LSU Large subunit (23S/28S)</option>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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171 <option value="SSU" selected="true">SSU small subunit (16S/18S)</option>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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172 <option value="ITS">ITS internal transcribed spacer</option>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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173 <option value="ITS1">ITS1</option>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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174 <option value="ITS2">ITS2</option>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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175 </param>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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176 <param argument="-tax_group" type="select" label="Tax group">
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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177 <option value="bacteria" selected="true">bacterial 16S rDNA annnotation</option>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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178 <option value="fungi">fungal 18S/23S/ITS annotation</option>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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179 </param>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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180 <param argument="-keepUnclassified" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Keep unclassified OTUs" help="Includes unclassified OTUs (i.e. no match in RDP/Blast database) in OTU and taxa abundance matrix calculations" />
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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181 <param argument="-useBestBlastHitOnly" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Use best blast hit only" help="If selected, do not use LCA (lowest common ancestor) to determine most likely taxonomic level (not recommended)" />
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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182 <param argument="-LCA_cover" type="float" min="0" max="1" value="0.9" label="Minimum horizontal coverage of an OTU sequence against ref DB"/>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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183 <param argument="-LCA_frac" type="float" min="0" max="1" value="0.9" label="Minimum fraction of reads with identical taxonomy"/>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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184 <param argument="-greengenesSpecies" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Create greengenes output labels instead of OTU" />
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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185 </section>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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186 </inputs>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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187
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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188 <outputs>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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189 <data name="otu" format="tabular" label="${tool.name} on ${on_string}: OTU abundance matrix" from_work_dir="output/OTU.txt" />
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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190 <data name="otu_biom" format="biom" label="${tool.name} on ${on_string}: biom-formatted OTU abundance matrix" from_work_dir="output/OTU.biom" />
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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191 <data name="otu_fna" format="fasta" label="${tool.name} on ${on_string}: FASTA-formatted extended OTU seed sequences" from_work_dir="output/OTU.fna" />
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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192 <data name="OTUphylo_nwk" format="newick" label="${tool.name} on ${on_string}: Newick-formatted phylogenetic tree between sequences" from_work_dir="output/OTUphylo.nwk" />
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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193 <data name="hiera_blast" format="tabular" label="${tool.name} on ${on_string}: OTU taxonomy assignments based on Blastn" from_work_dir="output/hiera_BLAST.txt" />
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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194 <data name="hiera_rdp" format="tabular" label="${tool.name} on ${on_string}: OTU taxonomy assignments based on RDP classifier" from_work_dir="output/hiera_RDP.txt" />
1
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
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195 <data name="primary" format="tar" label="${tool.name} on ${on_string}: All output files" from_work_dir="output.tar.gz" />
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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196 </outputs>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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197
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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198 <tests>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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199 <test>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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200 <param name="paired_or_single" value="single"/>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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201 <param name="input" value="Anh_sample1.fastq.gz,Anh_sample2.fastq.gz" ftype="fastqsanger.gz"/>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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202 <param name="platform" value="454" />
1
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
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203 <param name="clustering" value="3" />
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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204 <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"
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205 <output name="otu_fna" file="OTU.fna" compare="sim_size" />
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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206 <output name="hiera_rdp" file="hiera_RDP.txt" compare="sim_size" />
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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207 </test>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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208 </tests>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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209
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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210 <help><![CDATA[
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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211 If you have separate FASTA and quality files, these can be combined in a FASTQ file using the "Combine FASTA and QUAL into FASTQ" tool.
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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212
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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213 Documentation can be found at `<http://lotus2.earlham.ac.uk/>`_.
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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214 ]]></help>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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215 <citations>
1
85da3173a488 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
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216 <citation type="doi">10.1186/s40168-021-01012-1</citation>
0
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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217 </citations>
478e767a0e7a "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7"
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218 </tool>