<tool id="freyja_variants" name="Freyja: Call variants"
      version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
      profile="@PROFILE@">
    <description>
        and get sequencing depth information
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools"/>
    <expand macro="requirements"/>
    <expand macro="version"/>
    <command detect_errors="exit_code"><![CDATA[
ln -s '$bam_file' 'bam_file' &&
ln -s '$ref_file' 'ref_file' &&
freyja variants 
    'bam_file'
    --variants variants 
    --depths '$depths'
    --ref 'ref_file'
    ]]></command>
    <inputs>
        <param name="bam_file" type="data" format="bam" label="BAM file"
               help="After primer trimming and alignment to reference genome."/>
        <param name="ref_file" argument="--ref" type="data" format="fasta"
               label="Reference sequence file"
               help="Note that the reference should match the fasta file used for alignment."/>
    </inputs>
    <outputs>
        <data name="variants" format="tabular" label="${tool.name} on ${on_string}: Variant call"
              from_work_dir="variants.tsv">
        </data>
        <data name="depths" format="tabular" label="${tool.name} on ${on_string}: Sequencing depth"
              from_work_dir="depths.tsv">
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <param name="bam_file" value="test.bam"/>
            <param name="ref_file" value="NC_045512_Hu-1.fasta"/>
            <output name="variants" ftype="tabular">
                <assert_contents>
                    <has_text text="REF_CODON"/>
                    <has_text text="NC_045512.2"/>
                </assert_contents>
            </output>
            <output name="depths" ftype="tabular">
                <assert_contents>
                    <has_text text="NC_045512.2"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
@HELP_HEADER@

Information about **freyja variants** method
============================================

The method uses both samtools and iVar. 

.. class:: warningmark

   Note that the reference should match the fasta file used for alignment. 

Outputs
=======

We get both variant call and sequencing depth information with this command.

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