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Update LotuS2 wrapper to 2.28.1 #165

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Nov 11, 2023
Merged

Update LotuS2 wrapper to 2.28.1 #165

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1 change: 1 addition & 0 deletions .tt_biocontainer_skip
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Original file line number Diff line number Diff line change
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tools/ete
tools/lotus2
31 changes: 21 additions & 10 deletions tools/lotus2/lotus2.xml
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<tool id="lotus2" name="LotuS2" version="@VERSION@+galaxy2" profile="20.09">
<tool id="lotus2" name="LotuS2" version="@VERSION@+galaxy0" profile="20.09">
<description>fast OTU processing pipeline</description>
<macros>
<token name="@VERSION@">2.23</token>
<token name="@VERSION@">2.28.1</token>
<xml name="refDB_macro" token_ref_fasta_formats="fasta,fasta.gz">
<conditional name="refDB_cond">
<param argument="-refDB" type="select" label="Taxonomy reference database">
Expand All @@ -11,14 +11,15 @@
<when value="cached">
<param argument="-ref_db" type="select" label="Using reference database" help="Select database from the list">
<option value="" selected="true">(Default)</option>
<option value="KSGP">Bacteria, Archaea, Eukaryotes SSU (KSGP)</option>
<option value="SLV">Silva LSU (23/28S) or SSU (16/18S) (SLV)</option>
<option value="GG">Greengenes (GG)</option>
<option value="UNITE">ITS focused on fungi (UNITE)</option>
<option value="PR2">SSU focused on Protists (PR2)</option>
<option value="beetax">Bee gut specific database and tax names (beetax)</option>
<option value="HITdb">Human gut microbiota (HITdb)</option>
<option value="GG2">GreenGenes2 SSU (GG2)</option>
<option value="UNITE">ITS fungi specific (UNITE)</option>
<option value="PR2">LSU spezialized on Ocean environmentas (PR2)</option>
<option value="beetax">Bee gut specific SSU (beetax)</option>
<option value="HITdb">Human gut specific SSU (HITdb)</option>
</param>
<param argument="-greengenesSpecies" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Create greengenes output labels instead of OTU" />
<param argument="-greengenesSpecies" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Create greengenes output labels instead of OTU" help="To be used with greengenes specific programs such as BugBase." />
</when>
<when value="history">
<param name="ref_fasta" type="data" format="@REF_FASTA_FORMATS@" label="Taxonomy reference sequences" help="In FASTA format" />
Expand All @@ -39,8 +40,18 @@
</requirements>
<version_command>lotus2 --version</version_command>
<command detect_errors="exit_code"><![CDATA[
#import os.path
#import re

LOTUS2_DIR=\$(dirname "\$(realpath "\$(which lotus2)")") &&
if [ ! -e "\$LOTUS2_DIR/DB" ]; then
{
echo "LotuS2 databases missing in \$LOTUS2_DIR, these needs to be installed with:" &&
echo "perl autoInstall.pl -condaDBinstall" &&
echo "We currently recommend to use a conda environment instead of a biocontainer to prevent this problem.";
} >&2 &&
exit 1;
fi &&

#def symlink_basename($f, strip_ext=False):
#set $fn = re.sub('[^\w\-_.]', '_', $f.name)
#if strip_ext:
Expand Down Expand Up @@ -305,7 +316,7 @@ SMPL${i} ${symlink_basename($f.forward.dataset)},${symlink_basename($f.reverse.d
<option value="bacteria">bacterial 16S rDNA annnotation</option>
<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="-keepUnclassified" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Keep unclassified OTUs" help="Includes unclassified OTUs (no Phylum assignment) in OTU and taxa abundance matrix calculations" />
<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)"/>
<param argument="-LCA_frac" type="float" min="0" max="1" value="" optional="true" label="Minimum fraction of reads with identical taxonomy (optional)"/>
<param argument="-lulu" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use LULU to merge OTUs based on their occurrence" />
Expand Down
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