<tool id="presto_maskprimers" name="pRESTO MaskPrimers" version="@TOOL_VERSION@">
    <description>Removes primers and annotates sequences with primer and barcode identifiers.</description>
    
    <macros>
        <import>presto_macros.xml</import>
    </macros>
    
    <expand macro="requirements"/>
    
    <version_command>MaskPrimers.py --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
        ln -s '$fastq_in' in.fastq &&
        ln -s '$primers_in' primers.fasta && 
        MaskPrimers.py '$cc.command'
          --nproc "\${GALAXY_SLOTS:-1}"
          -s in.fastq
          -p primers.fasta
          --mode '$mode'
          --maxerror '$maxerror'
          $revpr
          $barcode
          
          #if $cc.command == "align"
            --maxlen '$cc.maxlen'
            --gap '$cc.gap_open' '$cc.gap_extend'
            $cc.skiprc
          #end if
          
          #if $cc.command == "score"
            --start '$cc.start'
          #end if

          --outdir=.
          --outname=tmp_mask 
          #if $capture_log
            --log '$log_out'
          #end if
    ]]></command>
    <inputs>
        <param argument="-s" name="fastq_in" type="data" format="fastq" label="Input FASTQ file"/>
        <param argument="-p" name="primers_in" type="data" format="fasta" label="Primer FASTA file"/>
        <param argument="--mode" type="select" value="mask" label="Mode" help="Specifies how identified primer sequences will be handled.">
            <option value="cut">Remove primer and preceding sequence (cut)</option>
            <option value="mask">Mask primer to Ns and remove preceding sequence (mask)</option>
            <option value="trim">Leave primer intact and remove preceding sequence (trim)</option>
            <option value="tag">Leave primer and preceding sequence intact (tag)</option>
        </param>
        <conditional name="cc">
            <param name="command" type="select" label="Command">
                <option value="align">Find primer matches using pairwise local alignment (align)</option>
                <option value="score">Find primer matches by scoring primers at a fixed position (score)</option>
            </param>
            <when value="align">
                <param argument="--maxlen" type="integer" value="50" label="Max Length" help="Maximum length of sequence window to search for primers."/>
                <param argument="--skiprc" type="boolean" value="false" truevalue="--skiprc" falsevalue="" label="Skip Reverse Complement" help="Skip checking of reverse complement sequences."/>
                <param name="gap_open" type="integer" value="1" label="Gap Open Penalty" help="Positive value of the gap open penalty."/>
                <param name="gap_extend" type="integer" value="1" label="Gap Extension Penalty" help="Positive value of the gap extension penalty."/>
            </when>
            <when value="score">
                <param argument="--start" type="integer" value="0" label="Start Position" help="The starting position of the primer."/>
            </when>
        </conditional>        
        <param argument="--revpr" type="boolean" value="false" truevalue="--revpr" falsevalue="" label="Reverse Match" help="Match the reverse complement of primer sequences against the ends of reads."/>
        <param argument="--barcode" type="boolean" value="false" truevalue="--barcode" falsevalue="" label="Extract Barcodes (UMIs)" help="Capture the sequence preceding the primer as a UMI."/>
        <param argument="--maxerror" type="float" value="0.2" label="Max Error Rate" help="Maximum allowable rate between read and primer sequence."/>
        <expand macro="presto-log-param"/>
    </inputs>

    <outputs>
        <data name="fastq_out" format="fastq" from_work_dir="tmp_mask_primers-pass.fastq"/>
        <expand macro="presto-log-output"/>
    </outputs>
    
    <tests>
        <test>
            <param  name="command" value="score"/>
            <param  name="fastq_in" value="presto_maskprimers_without_barcode_test_in.fastq"/>
            <param  name="start" value="0"/>
            <param  name="primers_in" value="read1_primers.fasta"/>
            <param  name="mode" value="cut"/>
            <param  name="maxerror" value="0.15"/>
            <output name="fastq_out" file="presto_maskprimers_without_barcode_test_score_out.fastq" sort="true"/>
        </test>
        <test>
            <param  name="command" value="score"/>
            <param  name="fastq_in" value="presto_maskprimers_with_barcode_test_in.fastq"/>
            <param  name="start" value="17"/>
            <param  name="barcode" value="true"/>
            <param  name="primers_in" value="read2_primers.fasta"/>
            <param  name="mode" value="cut"/>
            <param  name="maxerror" value="0.15"/>
            <output name="fastq_out" file="presto_maskprimers_with_barcode_test_score_out.fastq" sort="true"/>
        </test>
        <test>
            <param  name="command" value="align"/>
            <param  name="fastq_in" value="presto_maskprimers_without_barcode_test_in.fastq"/>
            <param  name="primers_in" value="read1_primers.fasta"/>
            <param  name="mode" value="cut"/>
            <param  name="maxerror" value="0.15"/>
            <param  name="maxlen" value="25"/>
            <output name="fastq_out" file="presto_maskprimers_without_barcode_test_align_out.fastq" sort="true"/>
        </test>
        <test>
            <param  name="command" value="align"/>
            <param  name="fastq_in" value="presto_maskprimers_with_barcode_test_in.fastq"/>
            <param  name="barcode" value="true"/>
            <param  name="primers_in" value="read2_primers.fasta"/>
            <param  name="mode" value="cut"/>
            <param  name="maxerror" value="0.15"/>
            <param  name="maxlen" value="25"/>
            <output name="fastq_out" file="presto_maskprimers_with_barcode_test_align_out.fastq" sort="true"/>
        </test>
    </tests>
    
    <help><![CDATA[
Removes primers and annotates sequences with primer and barcode identifiers

See the `pRESTO online help <@PRESTO_BASE_URL@/en/stable>`_ for more information.

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