<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">1.0.3</token>
    <token name="@PROFILE@">18.01</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">medaka</requirement>
            <yield />
        </requirements>
    </xml>
    <xml name="version_command">
        <version_command>medaka --version</version_command>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="bibtex">@online{medaka,
              author = {Oxford Nanopore Technologies Ltd.},
              title = {medaka},
              year = 2020,
              url = {https://github.com/nanoporetech/medaka},
              urldate = {2020-05-06}
            }</citation>
        </citations>
    </xml>

    <!--
        command
    -->

    <token name="@REF_FASTA@"><![CDATA[
        #if $reference_source.reference_source_selector == 'history':
            ln -f -s '$reference_source.ref_file' reference.fa &&
        #else:
            ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
        #end if
    ]]></token>

    <!--
        input
    -->

    <xml name="b" token_argument="-b">
        <param argument="@ARGUMENT@" type="integer" value="100" min="1" label="Set inference batch size"/>
    </xml>
    <xml name="model" token_argument="-m" token_label="Select model">
        <param argument="@ARGUMENT@" type="select" label="@LABEL@">
            <option value="r10_min_high_g303">r10_min_high_g303</option>
            <option value="r10_min_high_g340">r10_min_high_g340</option>
            <option value="r103_min_high_g345">r103_min_high_g345</option>
            <option value="r103_min_high_g360">r103_min_high_g360</option>
            <option value="r103_prom_high_g360">r103_prom_high_g360</option>
            <option value="r103_prom_snp_g3210">r103_prom_snp_g3210</option>
            <option value="r103_prom_variant_g3210">r103_prom_variant_g3210</option>
            <option value="r941_min_fast_g303">r941_min_fast_g303</option>
            <option value="r941_min_high_g303">r941_min_high_g303</option>
            <option value="r941_min_high_g330">r941_min_high_g330</option>
            <option value="r941_min_high_g340_rle">r941_min_high_g340_rle</option>
            <option value="r941_min_high_g344">r941_min_high_g344</option>
            <option value="r941_min_high_g351">r941_min_high_g351</option>
            <option value="r941_min_high_g360">r941_min_high_g360</option>
            <option value="r941_prom_fast_g303">r941_prom_fast_g303</option>
            <option value="r941_prom_high_g303">r941_prom_high_g303</option>
            <option value="r941_prom_high_g330">r941_prom_high_g330</option>
            <option value="r941_prom_high_g344">r941_prom_high_g344</option>
            <option value="r941_prom_high_g360" selected="true">r941_prom_high_g360</option>
            <option value="r941_prom_snp_g303">r941_prom_snp_g303</option>
            <option value="r941_prom_snp_g322">r941_prom_snp_g322</option>
            <option value="r941_prom_variant_g303">r941_prom_variant_g303</option>
            <option value="r941_prom_variant_g322">r941_prom_variant_g322</option>
        </param>
    </xml>
    <xml name="reference">
        <conditional name="reference_source">
            <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
                <option value="cached">Use a built-in genome</option>
                <option value="history">Use a genome from history</option>
            </param>
            <when value="cached">
                <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
                    <options from_data_table="all_fasta">
                        <filter type="sort_by" column="2"/>
                        <validator type="no_options" message="No reference genomes are available"/>
                    </options>
                    <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
                </param>
            </when>
            <when value="history">
                <param name="ref_file" type="data" format="fasta,fastq" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference"/>
            </when>
        </conditional>
    </xml>

    <!--
        Help
    -->

    <token name="@WID@"><![CDATA[
*medaka* is a tool suite to create a consensus sequence from nanopore sequencing data.

This task is performed using neural networks applied from a pileup of individual sequencing reads against a draft assembly. It outperforms graph-based methods operating on basecalled data, and can be competitive with state-of-the-art signal-based methods, whilst being much faster.
    ]]></token>
    <token name="@REFERENCES@"><![CDATA[
More information are available in the `manual <https://nanoporetech.github.io/medaka/index.html>`_ and `github <https://github.com/nanoporetech/medaka>`_.
    ]]></token>
</macros>