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comparison lotus2.xml @ 5:7f33525b85d0 draft

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"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
comparison
equal deleted inserted replaced
4:59b8864c9fa0 5:7f33525b85d0
1 <tool id="lotus2" name="LotuS2" version="@VERSION@+galaxy2" profile="20.01"> 1 <tool id="lotus2" name="LotuS2" version="@VERSION@+galaxy3" profile="20.01">
2 <description>fast OTU processing pipeline</description> 2 <description>fast OTU processing pipeline</description>
3 <macros> 3 <macros>
4 <token name="@VERSION@">2.06</token> 4 <token name="@VERSION@">2.06</token>
5 <xml name="refDB_macro"> 5 <xml name="refDB_macro">
6 <conditional name="refDB_cond"> 6 <conditional name="refDB_cond">
136 #if $tax_args.amplicon_cond.amplicon_type in ('ITS', 'ITS1', 'ITS2'): 136 #if $tax_args.amplicon_cond.amplicon_type in ('ITS', 'ITS1', 'ITS2'):
137 -ITSx $tax_args.amplicon_cond.ITSx_macro 137 -ITSx $tax_args.amplicon_cond.ITSx_macro
138 #end if 138 #end if
139 -tax_group $tax_args.tax_group 139 -tax_group $tax_args.tax_group
140 -keepUnclassified $tax_args.keepUnclassified 140 -keepUnclassified $tax_args.keepUnclassified
141 -useBestBlastHitOnly $tax_args.useBestBlastHitOnly
142 -LCA_cover $tax_args.LCA_cover 141 -LCA_cover $tax_args.LCA_cover
143 -LCA_frac $tax_args.LCA_frac 142 -LCA_frac $tax_args.LCA_frac
144 -lulu $tax_args.lulu 143 -lulu $tax_args.lulu
145 -buildPhylo $tax_args.buildPhylo 144 -buildPhylo $tax_args.buildPhylo
146 145
277 <param argument="-tax_group" type="select" label="Tax group"> 276 <param argument="-tax_group" type="select" label="Tax group">
278 <option value="bacteria" selected="true">bacterial 16S rDNA annnotation</option> 277 <option value="bacteria" selected="true">bacterial 16S rDNA annnotation</option>
279 <option value="fungi">fungal 18S/23S/ITS annotation</option> 278 <option value="fungi">fungal 18S/23S/ITS annotation</option>
280 </param> 279 </param>
281 <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" /> 280 <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" />
282 <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)" />
283 <param argument="-LCA_cover" type="float" min="0" max="1" value="0.9" label="Minimum horizontal coverage of an OTU sequence against ref DB"/> 281 <param argument="-LCA_cover" type="float" min="0" max="1" value="0.9" label="Minimum horizontal coverage of an OTU sequence against ref DB"/>
284 <param argument="-LCA_frac" type="float" min="0" max="1" value="0.9" label="Minimum fraction of reads with identical taxonomy"/> 282 <param argument="-LCA_frac" type="float" min="0" max="1" value="0.9" label="Minimum fraction of reads with identical taxonomy"/>
285 <param argument="-lulu" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Use LULU to merge OTUs based on their occurrence" /> 283 <param argument="-lulu" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Use LULU to merge OTUs based on their occurrence" />
286 <param argument="-buildPhylo" type="select" label="Build OTU phylogeny"> 284 <param argument="-buildPhylo" type="select" label="Build OTU phylogeny">
287 <option value="0">Disable</option> 285 <option value="0">Disable</option>