<tool id="prestor_abseq3" name="pRESTOr AbSeq3 Report" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Create HTML QC report from pRESTO outputs</description>
    <macros>
        <import>presto_macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <requirements>
          <requirement type="package" version="0.0.5">r-prestor</requirement>
    </requirements>
    
    <command detect_errors="exit_code"><![CDATA[
        ln -s '$qual1'    ./quality-1_table.tab &&
        ln -s '$qual2'    ./quality-2_table.tab &&
        ln -s '$primer1'  ./primers-1_table.tab &&
        ln -s '$primer2'  ./primers-2_table.tab &&
        ln -s '$cons1'    ./consensus-1_table.tab &&
        ln -s '$cons2'    ./consensus-2_table.tab &&
        ln -s '$assemble' ./assemble_table.tab &&
        ln -s '$maskqual' ./maskqual_table.tab &&
        ln -s '$cregion'  ./cregion_table.tab &&
        Rscript '${prestor_script}'
    ]]></command>
    
    <configfiles>
        <configfile name="prestor_script"><![CDATA[
library(prestor)
report_abseq3('.', sample='${sample}', output_dir='.', output_file='report.html', format='html')
        ]]>
        </configfile>
    </configfiles>

    <inputs>
        <param name="sample" type="text" label="Sample Name" help="Sample Name. Must not contain spaces.">
            <validator type="regex" message="Value may include alphanumeric characters, underscores and spaces.">[^\s]+</validator>
        </param>
        <param name="qual1" type="data" format="txt" label="ParseLog of FilterSeq(R1)" help="Output of running ParseLog on the log file from FilterSeq on Read 1."/>
        <param name="qual2" type="data" format="txt" label="ParseLog of FilterSeq(R2)" help="Output of running ParseLog on the log file from FilterSeq on Read 2."/>
        <param name="primer1" type="data" format="txt" label="ParseLog of MaskPrimers(R1)" help="Output of running ParseLog on the log file from MaskPrimers on Read 1."/>
        <param name="primer2" type="data" format="txt" label="ParseLog of MaskPrimers(R2)" help="Output of running ParseLog on the log file from MaskPrimers on Read 2."/>
        <param name="cons1" type="data" format="txt" label="ParseLog of BuildConsensus(R1)" help="Output of running ParseLog on the log file from BuildConsensus on Read 1."/>
        <param name="cons2" type="data" format="txt" label="ParseLog of BuildConsensus(R2)" help="Output of running ParseLog on the log file from BuildConsensus on Read 2."/>
        <param name="assemble" type="data" format="txt" label="ParseLog of AssemblePairs" help="Output of running ParseLog on the log file from AssemblePairs."/>
        <param name="maskqual" type="data" format="txt" label="ParseLog of FilterSeq(pairs)" help="Output of running ParseLog on the log file from FilterSeq on the consensus reads."/>
        <param name="cregion" type="data" format="txt" label="ParseLog of MaskPrimers(pairs)" help="Output of running ParseLog on the log file from MaskPrimers for the C Region."/>
    </inputs>

    <outputs>
        <data name="output" format="html" from_work_dir="report.html"/>
    </outputs>
    
    <tests>
        <test>
            <param  name="sample" value="TestSample"/>
            <param  name="qual1" value="prestor_logs/quality-1_table.tab"/>
            <param  name="qual2" value="prestor_logs/quality-2_table.tab"/>
            <param  name="primer1" value="prestor_logs/primers-1_table.tab"/>
            <param  name="primer2" value="prestor_logs/primers-2_table.tab"/>
            <param  name="cons1" value="prestor_logs/consensus-1_table.tab"/>
            <param  name="cons2" value="prestor_logs/consensus-2_table.tab"/>
            <param  name="assemble" value="prestor_logs/assemble_table.tab"/>
            <param  name="maskqual" value="prestor_logs/maskqual_table.tab"/>
            <param  name="cregion" value="prestor_logs/cregion_table.tab"/>
            <output name="output">
                <assert_contents>
                    <has_text text="pRESTO Report"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    
    <help><![CDATA[
Creates an HTML QC report from the log files generated when running pRESTO.

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