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comparison lotus2.xml @ 24:fede743a9002 draft

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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
comparison
equal deleted inserted replaced
23:469095a58c15 24:fede743a9002
1 <tool id="lotus2" name="LotuS2" version="@VERSION@+galaxy0" profile="20.09"> 1 <tool id="lotus2" name="LotuS2" version="@VERSION@+galaxy0" profile="20.09">
2 <description>fast OTU processing pipeline</description> 2 <description>fast OTU processing pipeline</description>
3 <macros> 3 <macros>
4 <token name="@VERSION@">2.28.1</token> 4 <token name="@VERSION@">2.30</token>
5 <xml name="refDB_macro" token_ref_fasta_formats="fasta,fasta.gz"> 5 <xml name="refDB_macro" token_ref_fasta_formats="fasta,fasta.gz">
6 <conditional name="refDB_cond"> 6 <conditional name="refDB_cond">
7 <param argument="-refDB" type="select" label="Taxonomy reference database"> 7 <param argument="-refDB" type="select" label="Taxonomy reference database">
8 <option value="cached">Use a built-in taxonomy database</option> 8 <option value="cached">Use a built-in taxonomy database</option>
9 <option value="history">Use a taxonomy from history</option> 9 <option value="history">Use a taxonomy from history</option>
258 </conditional> 258 </conditional>
259 <conditional name="aligner_cond"> 259 <conditional name="aligner_cond">
260 <param argument="-taxAligner" type="select" label="Taxonomy aligner for taxonomic profiling of OTUs"> 260 <param argument="-taxAligner" type="select" label="Taxonomy aligner for taxonomic profiling of OTUs">
261 <option value="0" selected="true">RDPclassifier (max likelihood)</option> 261 <option value="0" selected="true">RDPclassifier (max likelihood)</option>
262 <!-- <option value="1">Blast LCA against custom reference database</option> --> 262 <!-- <option value="1">Blast LCA against custom reference database</option> -->
263 <option value="2">LAMBDA, LCA against custom reference database</option> 263 <option value="2">Lambda, LCA against custom reference database</option>
264 <!-- <option value="4">VSEARCH LCA against custom reference database</option> --> 264 <!-- <option value="4">VSEARCH LCA against custom reference database</option> -->
265 </param> 265 </param>
266 <when value="0"> 266 <when value="0">
267 <param argument="-rdp_thr" type="float" min="0" max="1" value="0.8" optional="true" label="Confidence threshold for RDP (optional)"/> 267 <param argument="-rdp_thr" type="float" min="0" max="1" value="0.8" optional="true" label="Confidence threshold for RDP (optional)"/>
268 </when> 268 </when>