<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">0.2</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="vocdir_option">
            <param name="choice" type="select"
                   label="Source of YAML files with definition of the variant of concerns"
                   help="Cojac ships with a directory with variant definitions yaml files (https://github.com/cbg-ethz/cojac/tree/master/voc), which the tool can access internally. You can also download the latest version of the yaml files from https://github.com/phe-genomics/variant_definitions and use it as a custom yamls defining the variant of concerns.">
                <option value="cache">Definitions shipped with the tool (can be outdated)</option>
                <option value="custom">From history</option>
            </param>
            <when value="cache"/>
            <when value="custom">
                <param name="voc_file" type="data" format="yaml" multiple="true"
                       label="YAML defining the variant of concern"/>
            </when>
        </conditional>
    </xml>
    <token name="@VOCDIR_COMMAND@"><![CDATA[
#if $vocdir_option.choice == 'custom'
    #set vocdir = 'voc/'
    #set file_paths1 = []
    mkdir -p voc &&
    #for $input_file in $voc_file
        #set $file_path = $vocdir + $input_file.element_identifier
        ln -s '$input_file' '$file_path' &&
        $file_paths1.append($file_path)
    #end for
#else
    DB_PATH="\$(dirname "\$(dirname "\$(which cooc-mutbamscan)")")/share/cojac" &&
    ln -s "\$DB_PATH" db &&
    #set $vocdir = 'db/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>