<tool id="topn" name="topn" version="0.0.1">
    <requirements>
        <requirement type="package" >r</requirement>
	    <requirement type="package" >r-optparse</requirement>
        <requirement type="package" >r-xcmswrapper</requirement>
    </requirements>
    <description>Get the top (n) peaks in selected retention time windows of an LC-MS experiment
    </description>

    <stdio>
        <exit_code range="1:" />
    </stdio>

    <command interpreter="Rscript"><![CDATA[
        topn.R
            --sample_metadata=$sample_metadata
            --out_dir=.
            --cores=\${GALAXY_SLOTS:-4}
            --galaxy_files='
                #for $i in $input
                    $i,
                #end for
                '
            --files='
                #for $i in $input
                    $i.name,
                #end for
                '
            #if $time_windows_cond.time_windows_choice== 'choose'
                --time_window_choice='
                #for $i, $j in enumerate($time_windows_cond.time_windows)
                    $j.min,$j.max;
                #end for
                '
            #else
                --time_window_choice='0,90;90,660;660,1230;1230,1800;'
            #end if
            --file_include=$file_include
            --scan_dens=$scan_dens
            --n=$n
            --snthr=$snthr
            --minfrac=$minfrac
            --polarity=$polarity
            --class=$class
            --ppm=$ppm

    ]]></command>
    <inputs>

        <param name="input" type="data_collection" collection_type="list"  format="mzxml,mzml,mzdata,netcdf"
                           label="File(s) from your history containing your chromatograms"
                           help="Select the dataset collection containing the files that were used
                                 for processing" />

        <param name="sample_metadata" type="data" format="tsv, tabular"
                           label="Sample meta-data"
                           help="Metadata for each file (can re-use the sample meta-data file used for XCMS merge" />

        <param name="class" type="text" label="class" value="blank"
                    help="XCMS class to use (default is to use the blank)"/>

        <param name="file_include" type="text" label="File include" value="2"
                    help="Indexes of selected class to calculate topn on (comma separated string) e.g. 1,2"/>

        <conditional name="time_windows_cond">
            <param name="time_windows_choice" type="select" label="time-windows"
                   help="Default time-windows for 30 min (1800 secs) divided as follows (secs)- 0 : 90 : 660 : 1230 : 1800" >
                <option value="default_18000" selected="true">Default windows for 30 min run </option>
                <option value="choose">User defined windows</option>
            </param>
            <when value="choose">
                <repeat name="time_windows" title="Time windows">
                    <param name="min" type="integer" label="min (sec)" value="0"/>
                    <param name="max" type="integer" label="max (sec)" value="90"/>
                </repeat>
            </when>
        </conditional>

        <param name="scan_dens" type="integer" label="Scan density" value="5"
                    help="for scan range x to y, take every 'n' scan (i.e. x, x+n, x+2n ... y)"/>

        <param name="n" type="integer" label="Number of peaks to select" value="100"
                    help="The number of most intense peaks to select "/>

        <param name="ppm" type="float" label="PPM tolerance" value="5"
                    help="Parts per million tolerance for m/z between scans "/>

        <param name="snthr" type="float" label="SNR threshold" value="100"
                    help="Signal to noise threshold"/>

        <param name="minfrac" type="float" label="minfrac" value="0.1" min="0" max="1"
                    help="Minimum fraction peak has to be present in windows (typically set low to catch more peaks)"/>
        <param name="polarity" type="select" label="Polarity">
                <option value="positive" selected="true" >Positive</option>
                <option value="negative" >Negative</option>
        </param>


    </inputs>
    <outputs>
	    <data name="topn_peaklist" format="tsv" label="topn_peaklist"
              from_work_dir="topn_peaklist.tsv" visible="true"/>
    </outputs>
    <tests>
    </tests>
    <help><![CDATA[

    ]]></help>
</tool>