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comparison lotus2.xml @ 19:a3d31a68f291 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 3d69a14f20c8088412cf3729814be721b0db778c
author earlhaminst
date Mon, 21 Nov 2022 11:49:15 +0000
parents 6c22795e1be0
children 1d660ee0b1c8
comparison
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18:6c22795e1be0 19:a3d31a68f291
1 <tool id="lotus2" name="LotuS2" version="@VERSION@+galaxy1" profile="20.09"> 1 <tool id="lotus2" name="LotuS2" version="@VERSION@+galaxy2" 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@">2.21</token> 4 <token name="@VERSION@">2.21</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">
303 <option value="fungi">fungal 18S/23S/ITS annotation</option> 303 <option value="fungi">fungal 18S/23S/ITS annotation</option>
304 </param> 304 </param>
305 <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" /> 305 <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" />
306 <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)"/> 306 <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)"/>
307 <param argument="-LCA_frac" type="float" min="0" max="1" value="" optional="true" label="Minimum fraction of reads with identical taxonomy (optional)"/> 307 <param argument="-LCA_frac" type="float" min="0" max="1" value="" optional="true" label="Minimum fraction of reads with identical taxonomy (optional)"/>
308 <param argument="-lulu" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use LULU to merge OTUs based on their occurrence" /> 308 <param argument="-lulu" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Use LULU to merge OTUs based on their occurrence" />
309 <param argument="-buildPhylo" type="select" label="Build OTU phylogeny"> 309 <param argument="-buildPhylo" type="select" label="Build OTU phylogeny">
310 <option value="0">Disable</option> 310 <option value="0">Disable</option>
311 <option value="1" selected="true">Use fasttree2</option> 311 <option value="1" selected="true">Use fasttree2</option>
312 <option value="2">Use iqtree2</option> 312 <option value="2">Use iqtree2</option>
313 </param> 313 </param>