<tool id="chip_seq_ratio_1" name="ChIP-Seq Mapper" version="1.1.1.4">
    <stdio>
        <exit_code range="1:" level="fatal" description="Error"/>
    </stdio>
    <description></description>
    <requirements>
        <requirement type="package">r-base64enc</requirement>
        <requirement type="package">r-r2html</requirement>
        <requirement type="package">blast</requirement>
        <requirement type="package" version="3">python</requirement>
        <!-- <requirement type="package">chip_seq_ration</requirement> -->
    </requirements>
    <required_files>
        <include type="literal" path="ChipSeqRatioAnalysis.py"/>
        <include type="literal" path="ChipSeqRatioAnalysis.R"/>
    </required_files>
    <command> <![CDATA[
    which python && python --version &&
	python '$__tool_directory__'/ChipSeqRatioAnalysis.py
	--ChipSeq=${ChipFile}
	--InputSeq=${InputFile}
	--Contigs=${ContigFile}
	--output=${OutputFile}
	--html=${ReportFile}
	--max_cl=${MaxCl}
    --bitscore=$bitscore
    --nproc=16
    ]]>
    </command>

    <inputs>
        <param name="ChipFile" label="Chip reads" type="data" format="fasta"
               help="Reads in FASTA format"/>
        <param name="InputFile" label="Input reads" type="data" format="fasta"
               help="Reads in FASTA format"/>
        <param name="ContigFile" label="Reference - contig sequences" type="data"
               format="fasta"
               help="Contigs from RepeatExplorer clustering (the file &quot;contigs.fasta&quot;)"/>
        <param name="MaxCl" label="Number of top clusters to be shown in graph"
               type="integer" value="200"/>
        <param name="bitscore" label="Bit score threshold" type="integer" value="50"
               help="Similarity hits with lower bit score will not be used for ChIP/Input ratio calculation"/>
    </inputs>
    <outputs>
        <data name="OutputFile" format="tabular"
              label="csv table from ChIP-Seq-Mapper on datasets ${InputFile.hid} (Input) ${ChipFile.hid} (ChIP) and ${ContigFile.hid} (reference)"/>

        <data name="ReportFile" format="html"
              label="HTML report from ChIP-Seq-Mapper on datasets ${InputFile.hid} (Input) ${ChipFile.hid} (ChIP) and ${ContigFile.hid} (reference)"/>
    </outputs>

    <help>
        **What it does**

        The ChIP-seq Mapper evaluates the enrichment of repetitive sequences in sequencing
        data from chromatin
        immunoprecipitation experiments, using repeats identified by RepeatExplorer as the
        reference. The tool
        performs BLASTN similarity search of the read sequences to the reference,
        and the reads producing hits that passed the user-specified similarity threshold
        are assigned to the
        repeat clusters. The assignment is made to the cluster that produced the best
        similarity hit, and every
        read is assigned to only a single cluster. Following read mapping, the numbers of
        reads from the
        INPUT and ChIP samples are evaluated, and ChIP/INPUT ratios of the normalized read
        counts are reported
        for individual clusters.
        ChIP and INPUT reads should be of uniform lengths of at least 40 nt. The bit score
        threshold value should be
        adjusted based on the length of the analyzed reads (the value equal to the read
        length is recommended for a start).
        This method was first used in (`Neumann et al. 2012`__) for
        identification of repetitive sequences associated with centromeres:


        `PLoS Genet. Epub 2012 Jun 21. Stretching the rules: monocentric chromosomes with
        multiple centromere domains. Neumann P, Navrátilová A, Schroeder-Reiter E,
        Koblížková A, Steinbauerová V, Chocholová E, Novák P, Wanner G, Macas J.`__.

        .. __:
        http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002777
        .. __:
        http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002777

    </help>

</tool>