<tool id="tracy_decompose" name="tracy Decompose" version="@TOOL_VERSION@+galaxy0" profile="20.09">
    <description>heterozygous mutations (and call variants)</description>
    <macros>
        <import>macros.xml</import>
    </macros>    
    <expand macro="requirements" /> 
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
        #if $index_genome == True
            bgzip -c '$genome' > genome.fasta.gz ;
            tracy index -o genome.fasta.fm9 genome.fasta.gz &&
            #set refgenome = "genome.fasta.gz"
        #else
            #set refgenome = $genome
        #end if
        tracy decompose 
          --genome '$refgenome'
          $callVariants
          --pratio $pratio 
          --kmer $kmer.kmer 
          --support $kmer.support 
          --maxindel $maxindel 
          --trim $trim.trim 
          --trimLeft $trim.trimLeft 
          --trimRight $trim.trimRight 
          --linelimit $linelimit 
          --gapopen $alignment.gapopen
          --gapext $alignment.gapext
          --match $alignment.match
          --mismatch $alignment.mismatch
          '$tracefile'
    ]]></command>
    <inputs>
        <param argument="--genome" type="data" format="fasta,ab1,scf" label="FASTA, ABI or SCF format genome" />
        <param name="tracefile" type="data" format="ab1,scf" label="Sanger chromatogram tracefile to align" />
        <param name="index_genome" type="boolean" label="Pre-index the reference" help="Pre-indexing builds a FM index of the reference. This is required for sequences larger than 50 kilobases" />
        <param argument="--callVariants" type="boolean" truevalue="--callVariants" falsevalue="" label="Call variants in chromatogram" />
        <!-- annotate option is not yet supported -->
        <expand macro="common_options" />
        <expand macro="kmer_options" />
        <expand macro="alignment_options" />
        <expand macro="trim_options" />
        <expand macro="optional_outputs" />
    </inputs>
    <outputs>
        <expand macro="json_output" toolname="decompose" />
        <data name="out_fasta1" format="fasta" from_work_dir="out.align1" label="tracy decompose allele1 on ${on_string}" />
        <data name="out_fasta2" format="fasta" from_work_dir="out.align2" label="tracy decompose allele2 on ${on_string}" />
        <data name="out_fasta3" format="fasta" from_work_dir="out.align3" label="tracy decompose both alleles on ${on_string}" />
        <expand macro="tabular_output" toolname="decompose" />
        <data name="out_bcf" format="bcf" from_work_dir="out.bcf" label="tracy decompose variants on ${on_string}">
            <filter>callVariants</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="3">
            <param name="genome" value="reference1.fasta" ftype="fasta" />
            <param name="tracefile" value="input1.ab1" ftype="ab1" />
            <output name="out_fasta1" value="out1.align1.fasta" ftype="fasta" />    
            <output name="out_fasta2" value="out1.align2.fasta" ftype="fasta" />    
            <output name="out_fasta3" value="out1.align3.fasta" ftype="fasta" />    
        </test>
        <test expect_num_outputs="4">
            <param name="genome" value="reference1.fasta" ftype="fasta" />
            <param name="tracefile" value="input1.ab1" ftype="ab1" />
            <param name="callVariants" value="true" />
            <output name="out_fasta1" value="out1.align1.fasta" ftype="fasta" />    
            <output name="out_fasta2" value="out1.align2.fasta" ftype="fasta" />    
            <output name="out_fasta3" value="out1.align3.fasta" ftype="fasta" />    
            <output name="out_bcf" compare="sim_size" value="out1.bcf" ftype="bcf" />
        </test>
        <test expect_num_outputs="5">
            <param name="genome" value="reference1.fasta" ftype="fasta" />
            <param name="tracefile" value="input1.ab1" ftype="ab1" />
            <param name="callVariants" value="true" />
            <param name="optional_outputs" value="json" />
            <output name="out_json" ftype="json">
                <assert_contents>
                    <has_text text='"peakA": [5, 5, 5, 5, 5, 4' />
                </assert_contents>
            </output>
            <output name="out_fasta1" value="out1.align1.fasta" ftype="fasta" />    
            <output name="out_fasta2" value="out1.align2.fasta" ftype="fasta" />    
            <output name="out_fasta3" value="out1.align3.fasta" ftype="fasta" />    
            <output name="out_bcf" compare="sim_size" value="out1.bcf" ftype="bcf" />
        </test>
        <test expect_num_outputs="5">
            <param name="genome" value="reference1.fasta" ftype="fasta" />
            <param name="tracefile" value="input1.ab1" ftype="ab1" />
            <param name="callVariants" value="true" />
            <param name="optional_outputs" value="tabular" />
            <output name="out_stats" ftype="tabular">
                <assert_contents>
                    <has_text_matching expression="13\s1\s2\s2\s11\s2\sT\sG\sN\s5\sY" />
                </assert_contents>
            </output>
            <output name="out_fasta1" value="out1.align1.fasta" ftype="fasta" />    
            <output name="out_fasta2" value="out1.align2.fasta" ftype="fasta" />    
            <output name="out_fasta3" value="out1.align3.fasta" ftype="fasta" />    
            <output name="out_bcf" compare="sim_size" value="out1.bcf" ftype="bcf" />
        </test>
    </tests>
    <help><![CDATA[
**What this does**

Double-peaks in a trace file can cause alignment issues. This tool uses tracy_ to decompose 
heterozygous variants in a trace file into two separate alleles. Each allele is then aligned
separately to the reference sequence.

Optionally, variants between the trace file and the reference are also output in BCF format.

@pratio@

@trim_options@

@alignment@

Read more here_.

.. _tracy: https://github.com/gear-genomics/tracy
.. _here: https://www.gear-genomics.com/docs/tracy/cli/#deconvolution-of-heterozygous-mutations
    ]]></help>
    <expand macro="citations" />
</tool>