<tool id="ivar_consensus" name="ivar consensus" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
    <description>Call consensus from aligned BAM file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="exit_code"><![CDATA[
        #import re
        #set $clean_name = re.sub('[^\w\-]', '_', str($input_bam.element_identifier))
        ln -s '$input_bam' sorted.bam &&
        samtools mpileup -A -a -d 0 -Q 0 sorted.bam | ivar consensus
        -p consensus
        -q $min_qual
        -t $min_freq
        -c $min_indel_freq
        -m $min_depth
        $depth_action
        &&
        sed -i "s|consensus|$clean_name|" consensus.fa
    ]]></command>
    <inputs>
        <param name="input_bam" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/>
        <!-- Warning: integer params in the following define a max of 255 intentionally
        because the underlying C++ code of ivar defines them as uint8 and does not check for overflow! -->
        <param name="min_qual" argument="-q" type="integer" min="0" max="255" value="20" label="Minimum quality score threshold to count base"/>
        <param name="min_freq" argument="-t" type="float" min="0" max="1" value="0.0" label="Minimum frequency threshold">
            <help>
                <![CDATA[
           0 - Majority or most common base <br/>
         0.2 - Bases that make up atleast 20% of the depth at a position <br/>
         0.5 - Strict or bases that make up atleast 50% of the depth at a position <br/>
         0.9 - Strict or bases that make up atleast 90% of the depth at a position <br/>
           1 - Identical or bases that make up 100% of the depth at a position. Will have highest ambiguities 
        ]]>
            </help>
        </param>
        <param name="min_indel_freq" argument="-c" type="float" min="0" max="1" value="0.8" label="Minimum indel frequency threshold" help="Same meaning as the &quot;Minimum frequency threshold&quot; above, but applied to indels."/>
        <param name="min_depth" argument="-m" type="integer" min="1" max="255" value="10" label="Minimum depth to call consensus"/>
        <param name="depth_action" type="select" label="How to represent positions with coverage less than the minimum depth threshold">
            <option value="-k">Drop from output (-k)</option>
            <option value="-n N" selected="true">Represent as N (-n N)</option>
            <option value="-n -">Represent as - (-n -)</option>
        </param>
    </inputs>
    <outputs>
        <data name="consensus" format="fasta" label="${tool.name} on ${on_string} Consensus" from_work_dir="consensus.fa"/>
    </outputs>
    <tests>
        <test>
            <param name="input_bam" value="covid19/PC00101P_sub.trimmed.sorted.bam" />
            <output name="consensus" file="covid19/PC00101P_sub.fa" ftype="fasta" compare="contains" lines_diff="1"/>
        </test>
    </tests>
    <help><![CDATA[
    .. class:: infomark

    To generate a consensus sequence iVar uses the output of samtools mpileup
    command. The mpileup output must be piped into ivar consensus
    
    The command formed by this wrapper is :
    
    samtools mpileup -A -a -d 0 -Q 0 sorted.bam | ivar consensus [options]

    There are five parameters that can be set:

    - **Minimum quality**: the minimum quality of a base to be considered in calculations of variant frequencies at a given position

    - **Minimum frequency threshold**: the minimum frequency that the most likely base must surpass to be called as the consensus base at a position.

    - **Minimum indel frequency threshold**: has the same meaning as the previous threshold, but gets applied to indels specifically. Setting this threshold higher than the threshold applied to SNVs helps reduce indel artefacts in the generated consensus.

    - **Minimum depth to call consensus**: the minimum required depth to call a consensus base

    - **How to represent positions with coverage less than the minimum depth threshold**: for positions for which the above minimum depth to call a consensus base is not reached, you can choose one of three different actions:

      - Drop the position from the output entirely (-> the consensus sequence can become shorter than the reference used to produce the input BAM!)
      - Use an ``N``, or
      - Use a ``-`` to represent the position
    ]]>    </help>
    <expand macro="citations" />
</tool>