comparison lotus2.xml @ 22:ceb2cb800298 draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4a26b06e9f772e8af6f4c235ea4ee61ad383bfb4

21:fa84bba02a62

<tool id="lotus2" name="LotuS2" version="@VERSION@+galaxy2" profile="20.09">
    <description>fast OTU processing pipeline</description>
    <macros>
        <token name="@VERSION@">2.23</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">
                    <option value="cached">Use a built-in taxonomy database</option>
                    <option value="history">Use a taxonomy from history</option>
                </param>
                <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="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>
                    </param>
                    <param argument="-greengenesSpecies" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Create greengenes output labels instead of OTU" />
                </when>
                <when value="history">
                    <param name="ref_fasta" type="data" format="@REF_FASTA_FORMATS@" label="Taxonomy reference sequences" help="In FASTA format" />
                    <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" />
                </when>

    <requirements>
        <requirement type="package" version="@VERSION@">lotus2</requirement>
    </requirements>
    <version_command>lotus2 --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
#import os.path
#import re
#def symlink_basename($f, strip_ext=False):
    #set $fn = re.sub('[^\w\-_.]', '_', $f.name)
    #if strip_ext:
        #if $fn.endswith('.gz'):
            #set $fn = $fn[:-3]

            <param argument="-tax_group" type="select" label="Tax group">
                <option value="" selected="true">(Default)</option>
                <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="-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" />
            <param argument="-buildPhylo" type="select" label="Build OTU phylogeny">
                <option value="0">Disable</option>

22:ceb2cb800298

<tool id="lotus2" name="LotuS2" version="@VERSION@+galaxy0" profile="20.09">
    <description>fast OTU processing pipeline</description>
    <macros>
        <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">
                    <option value="cached">Use a built-in taxonomy database</option>
                    <option value="history">Use a taxonomy from history</option>
                </param>
                <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="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" 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" />
                    <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" />
                </when>

    <requirements>
        <requirement type="package" version="@VERSION@">lotus2</requirement>
    </requirements>
    <version_command>lotus2 --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
#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:
        #if $fn.endswith('.gz'):
            #set $fn = $fn[:-3]

            <param argument="-tax_group" type="select" label="Tax group">
                <option value="" selected="true">(Default)</option>
                <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 (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" />
            <param argument="-buildPhylo" type="select" label="Build OTU phylogeny">
                <option value="0">Disable</option>