<tool id="hicexplorer_hicquickqc" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>get a first quality estimate of Hi-C data</description>
    <macros>
        <token name="@BINARY@">hicQuickQC</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[

        mkdir ./QCfolder &&
        mkdir $qc.files_path &&
        @BINARY@

            --samFiles
            #for $repeat in $samFiles:
                '${repeat.samFile}'
            #end for

            --restrictionCutFile '$restrictionCutFile'
            
            #if $restrictionSequence:
                --restrictionSequence '$restrictionSequence'
            #end if

            #if $danglingSequence:
                --danglingSequence '$danglingSequence'
            #end if
            --QCfolder ./QCfolder

            --lines $lines

        && mv ./QCfolder/* $qc.files_path/
        && mv $qc.files_path/hicQC.html $qc
        && mv $qc.files_path/*.log raw_qc
    ]]>    </command>
    <inputs>
        <!-- can we use multiple="true" with min="2" and max="2" ? -->
        <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process (forward/reverse)" help="Please use the special BAM datatype: qname_input_sorted.bam and use for 'bowtie2' the '--reorder' option to create a BAM file.">
            <param name="samFile" type="data" format="sam,qname_input_sorted.bam" />
        </repeat>
        <expand macro="restrictionCutFile" />
        <expand macro="restrictionSequence" />
        <expand macro="danglingSequence" />
        <param argument="--lines" optional="true" type="integer" label="Lines to analyze for the QC report" help= "Number of lines to consider for the qc test run." value="1000000" />
    </inputs>
    <outputs>
        <data name="qc" format="html" label="${tool.name} QC on ${on_string}" />
        <data name="raw_qc" from_work_dir="raw_qc" format="txt" label="${tool.name} raw QC on ${on_string}" />
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <repeat name="samFiles">
                <param name="samFile" value="small_test_R1_unsorted.sam" />
            </repeat>
            <repeat name="samFiles">
                <param name="samFile" value="small_test_R2_unsorted.sam" />
            </repeat>
            <param name="restrictionCutFile" value="DpnII_10k.bed" />
            <param name="restrictionSequence" value="GATC" />
            <param name="danglingSequence" value="GATC" />
            <param name="lines" value="1000" />
            <output name="raw_qc" file="hicQuickQC/QC.log" compare="diff" lines_diff="2" />
        </test>
    </tests>
    <help><![CDATA[

Quick QC
========

Get a quick impression on the quality of your Hi-C data. hicQuickQC considers the first n lines of two bam/sam files to get a first estimate of the quality of the data. It is highly recommended to set the restriction enzyme and dangling end parameter to get a good quality report.

The default is to read the first 1,000,000 reads of the mapped bam files to get a quality estimate of the Hi-C data.

For more information about HiCExplorer please consider our documentation on readthedocs.io_

.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
]]>    </help>
    <expand macro="citations" />
</tool>