# HG changeset patch
# User earlhaminst
# Date 1622737398 0
# Node ID 7f33525b85d06a1eb46b8965bd944fa76fed1597
# Parent  59b8864c9fa07fe2a9feba9b1c7698bfe7ed00d8
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit afc479781e6d2a0fa8d8044bdfbbb1fb30b6e208"

diff -r 59b8864c9fa0 -r 7f33525b85d0 lotus2.xml
--- a/lotus2.xml	Thu Jun 03 15:44:44 2021 +0000
+++ b/lotus2.xml	Thu Jun 03 16:23:18 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="lotus2" name="LotuS2" version="@VERSION@+galaxy2" profile="20.01">
+<tool id="lotus2" name="LotuS2" version="@VERSION@+galaxy3" profile="20.01">
     <description>fast OTU processing pipeline</description>
     <macros>
         <token name="@VERSION@">2.06</token>
@@ -138,7 +138,6 @@
 #end if
 -tax_group $tax_args.tax_group
 -keepUnclassified $tax_args.keepUnclassified
--useBestBlastHitOnly $tax_args.useBestBlastHitOnly
 -LCA_cover $tax_args.LCA_cover
 -LCA_frac $tax_args.LCA_frac
 -lulu $tax_args.lulu
@@ -279,7 +278,6 @@
                 <option value="fungi">fungal 18S/23S/ITS annotation</option>
             </param>
             <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" />
-            <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)" />
             <param argument="-LCA_cover" type="float" min="0" max="1" value="0.9" label="Minimum horizontal coverage of an OTU sequence against ref DB"/>
             <param argument="-LCA_frac" type="float" min="0" max="1" value="0.9" label="Minimum fraction of reads with identical taxonomy"/>
             <param argument="-lulu" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Use LULU to merge OTUs based on their occurrence" />