Mercurial > repos > earlhaminst > lotus2
diff lotus2.xml @ 22:ceb2cb800298 draft
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4
author | earlhaminst |
---|---|
date | Sat, 11 Nov 2023 22:59:07 +0000 |
parents | fa84bba02a62 |
children | 469095a58c15 |
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--- a/lotus2.xml Sat Oct 28 09:58:00 2023 +0000 +++ b/lotus2.xml Sat Nov 11 22:59:07 2023 +0000 @@ -1,7 +1,7 @@ -<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"> @@ -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" /> @@ -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: @@ -305,7 +316,7 @@ <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" />