Mercurial > repos > earlhaminst > lotus2
changeset 5:7f33525b85d0 draft
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit afc479781e6d2a0fa8d8044bdfbbb1fb30b6e208"
| author | earlhaminst |
|---|---|
| date | Thu, 03 Jun 2021 16:23:18 +0000 |
| parents | 59b8864c9fa0 |
| children | fc78d02657a9 |
| files | lotus2.xml |
| diffstat | 1 files changed, 1 insertions(+), 3 deletions(-) [+] |
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--- 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" />