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comparison lotus2.xml @ 22:ceb2cb800298 draft

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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
comparison
equal deleted inserted replaced
21:fa84bba02a62 22:ceb2cb800298
1 <tool id="lotus2" name="LotuS2" version="@VERSION@+galaxy2" 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@">2.23</token> 4 <token name="@VERSION@">2.28.1</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>
10 </param> 10 </param>
11 <when value="cached"> 11 <when value="cached">
12 <param argument="-ref_db" type="select" label="Using reference database" help="Select database from the list"> 12 <param argument="-ref_db" type="select" label="Using reference database" help="Select database from the list">
13 <option value="" selected="true">(Default)</option> 13 <option value="" selected="true">(Default)</option>
14 <option value="KSGP">Bacteria, Archaea, Eukaryotes SSU (KSGP)</option>
14 <option value="SLV">Silva LSU (23/28S) or SSU (16/18S) (SLV)</option> 15 <option value="SLV">Silva LSU (23/28S) or SSU (16/18S) (SLV)</option>
15 <option value="GG">Greengenes (GG)</option> 16 <option value="GG2">GreenGenes2 SSU (GG2)</option>
16 <option value="UNITE">ITS focused on fungi (UNITE)</option> 17 <option value="UNITE">ITS fungi specific (UNITE)</option>
17 <option value="PR2">SSU focused on Protists (PR2)</option> 18 <option value="PR2">LSU spezialized on Ocean environmentas (PR2)</option>
18 <option value="beetax">Bee gut specific database and tax names (beetax)</option> 19 <option value="beetax">Bee gut specific SSU (beetax)</option>
19 <option value="HITdb">Human gut microbiota (HITdb)</option> 20 <option value="HITdb">Human gut specific SSU (HITdb)</option>
20 </param> 21 </param>
21 <param argument="-greengenesSpecies" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Create greengenes output labels instead of OTU" /> 22 <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." />
22 </when> 23 </when>
23 <when value="history"> 24 <when value="history">
24 <param name="ref_fasta" type="data" format="@REF_FASTA_FORMATS@" label="Taxonomy reference sequences" help="In FASTA format" /> 25 <param name="ref_fasta" type="data" format="@REF_FASTA_FORMATS@" label="Taxonomy reference sequences" help="In FASTA format" />
25 <param argument="-tax4refDB" type="data" format="tabular" label="Taxonomy reference lineages" help="Tab-separated file with 2 columns mapping each FASTA header of the reference sequences to a GTDB-style taxonomy string" /> 26 <param argument="-tax4refDB" type="data" format="tabular" label="Taxonomy reference lineages" help="Tab-separated file with 2 columns mapping each FASTA header of the reference sequences to a GTDB-style taxonomy string" />
26 </when> 27 </when>
37 <requirements> 38 <requirements>
38 <requirement type="package" version="@VERSION@">lotus2</requirement> 39 <requirement type="package" version="@VERSION@">lotus2</requirement>
39 </requirements> 40 </requirements>
40 <version_command>lotus2 --version</version_command> 41 <version_command>lotus2 --version</version_command>
41 <command detect_errors="exit_code"><![CDATA[ 42 <command detect_errors="exit_code"><![CDATA[
42 #import os.path
43 #import re 43 #import re
44
45 LOTUS2_DIR=\$(dirname "\$(realpath "\$(which lotus2)")") &&
46 if [ ! -e "\$LOTUS2_DIR/DB" ]; then
47 {
48 echo "LotuS2 databases missing in \$LOTUS2_DIR, these needs to be installed with:" &&
49 echo "perl autoInstall.pl -condaDBinstall" &&
50 echo "We currently recommend to use a conda environment instead of a biocontainer to prevent this problem.";
51 } >&2 &&
52 exit 1;
53 fi &&
54
44 #def symlink_basename($f, strip_ext=False): 55 #def symlink_basename($f, strip_ext=False):
45 #set $fn = re.sub('[^\w\-_.]', '_', $f.name) 56 #set $fn = re.sub('[^\w\-_.]', '_', $f.name)
46 #if strip_ext: 57 #if strip_ext:
47 #if $fn.endswith('.gz'): 58 #if $fn.endswith('.gz'):
48 #set $fn = $fn[:-3] 59 #set $fn = $fn[:-3]
303 <param argument="-tax_group" type="select" label="Tax group"> 314 <param argument="-tax_group" type="select" label="Tax group">
304 <option value="" selected="true">(Default)</option> 315 <option value="" selected="true">(Default)</option>
305 <option value="bacteria">bacterial 16S rDNA annnotation</option> 316 <option value="bacteria">bacterial 16S rDNA annnotation</option>
306 <option value="fungi">fungal 18S/23S/ITS annotation</option> 317 <option value="fungi">fungal 18S/23S/ITS annotation</option>
307 </param> 318 </param>
308 <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" /> 319 <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" />
309 <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)"/> 320 <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)"/>
310 <param argument="-LCA_frac" type="float" min="0" max="1" value="" optional="true" label="Minimum fraction of reads with identical taxonomy (optional)"/> 321 <param argument="-LCA_frac" type="float" min="0" max="1" value="" optional="true" label="Minimum fraction of reads with identical taxonomy (optional)"/>
311 <param argument="-lulu" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use LULU to merge OTUs based on their occurrence" /> 322 <param argument="-lulu" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use LULU to merge OTUs based on their occurrence" />
312 <param argument="-buildPhylo" type="select" label="Build OTU phylogeny"> 323 <param argument="-buildPhylo" type="select" label="Build OTU phylogeny">
313 <option value="0">Disable</option> 324 <option value="0">Disable</option>