<tool id="tracy_basecall" name="tracy Basecall" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
    <description>from Sanger chromatogram tracefile</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
        tracy basecall --pratio $pratio --format $format --output '$output' '$tracefile'
    ]]></command>
    <inputs>
        <param name="tracefile" type="data" format="ab1,scf" label="Chromatogram tracefile" />
        <param argument="--pratio" type="float" label="Peak ratio to call a base" value="0.33" min="0" />
        <param argument="--format" type="select" label="Output format">
            <option value="fasta" selected="true">FASTA</option>
            <option value="fastq">FASTQ</option>
            <option value="tsv">TSV (tabular)</option>
            <option value="json">JSON</option>
        </param>
    </inputs>
    <outputs>
        <data name="output" format="fasta" label="tracy basecall on ${on_string}">
            <change_format>
                <when input="format" value="fasta" format="fasta"/>
                <when input="format" value="fastq" format="fastq"/>
                <when input="format" value="tsv" format="tabular"/>
                <when input="format" value="json" format="json" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1"> <!-- test 1 -->
            <param name="tracefile" value="input1_r.ab1" ftype="ab1" />
            <output name="output" file="output1.fasta" ftype="fasta" />
        </test>
        <test expect_num_outputs="1"> <!-- test 2 -->
            <param name="tracefile" value="input1_r.ab1" ftype="ab1" />
            <param name="format" value="json" />
            <output name="output" file="output1.json" ftype="json" />
        </test>
        <test expect_num_outputs="1"> <!-- test 3 -->
            <param name="tracefile" value="input1_r.ab1" ftype="ab1" />
            <param name="pratio" value="0.2" />
            <output name="output" file="output2.fasta" ftype="fasta" />
        </test>
        <test expect_num_outputs="1"> <!-- test 4 -->
            <param name="tracefile" value="input2.scf" ftype="scf" />
            <param name="format" value="fasta" />
            <output name="output" file="output3.fasta" ftype="fasta" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Basecall a chromatogram trace file (using tracy_) and output the primary sequence (highest peak) in FASTQ or FASTA format. If FASTQ
format is used, the quality scores are Sanger quality scores.

@pratio@

Read more here_

.. _tracy: https://github.com/gear-genomics/tracy
.. _here: https://www.gear-genomics.com/docs/tracy/cli/#basecalling-a-chromatogram-trace-file

    ]]></help>
    <expand macro="citations" />
</tool>