<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">0.9.1</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">21.01</token>
    <xml name="biotools">
        <xrefs>
            <xref type="bio.tools">cojac</xref>
        </xrefs>
    </xml>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">cojac</requirement>
            <yield/>
        </requirements>
    </xml>
    <xml name="version">
        <version_command>echo @TOOL_VERSION@</version_command>
    </xml>
    <xml name="vocdir_input">
        <conditional name="voc_source">
            <param name="choice" type="select"
                   label="Source of lineage definitions"
                   help="Cojac detects lineage evidence based on lineage mutation patterns deined in tool-specific yaml format. You can choose between the (possibly outdated) definitions shipped with the tool or definitions provided as a collection of yaml datasets in your history. See the tool help below for more details.">
                <option value="builtin">Lineage definitions shipped with the tool</option>
                <option value="custom">YAML dataset collection in history</option>
            </param>
            <when value="builtin"/>
            <when value="custom">
                <param name="collection" type="data_collection" collection_type="list" format="yaml" label="Collection of lineage definitions" />
            </when>
        </conditional>
    </xml>
    <token name="@VOCDIR_COMMAND@"><![CDATA[
#if $voc_config.choice == 'custom'
    mkdir -p voc &&
    #for $input_file in $voc_config.collection
        ln -s '$input_file' 'voc/$input_file.element_identifier' &&
    #end for
#else
    DB_PATH="\$(dirname "\$(dirname "\$(which cojac)")")/share/cojac/voc" &&
    ln -s "\$DB_PATH" voc &&
#end if
]]></token>
    <token name="@HELP_HEADER@"><![CDATA[
What it does
============

The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples.
]]></token>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1101/2021.01.08.21249379</citation>
        </citations>
    </xml>
</macros>