<tool id="kronik" name="Kronik" version="2.02">
    <description>processes Hardklör features to find peptides by chromatographic profiling</description>
    <requirements>
        <requirement type="package" version="2.02">kronik</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" level="fatal" description="Error occurred while running Kronik"/>
    </stdio>
    <command>kronik -c $c -d $d -g $g -m $m -n $n -p $p "$inputfile" "$output"</command>
    <inputs>
        <param name="inputfile" type="data" format="hk" label="Hardklör isotope distributions" />
        <param name="c" type="integer" value="5" label="Contaminant threshold in minutes" help="Peptides persisting for longer than this value are excluded" />
        <param name="d" type="integer" value="3" label="Match tolerance" help="Minimum consecutive scans peptide must be found in" />
        <param name="g" type="integer" value="1" label="Gap tolerance" help="Maximum amount of scans a peptide can skip to be considered in results" />
        <param name="m" type="integer" value="8000" label="Max mass (Da)" help="Maximum mass of peptide isotope distribution" />
        <param name="n" type="integer" value="600" label="Min mass (Da)" help="Minimum mass of peptide isotope distribution" />
        <param name="p" type="integer" value="10" label="Mass accuracy (ppm)" help="Peptides in adjacent scans must differ by less than this value to be called the same." />
    </inputs>
    <outputs>
        <data format="kr" name="output" />
    </outputs>
    <tests>
        <test>
            <param name="inputfile" value="hardklor_result.hk"/>
            <output name="output" file="kronik_result.kr" />
        </test>
    </tests>
    <help>
Krönik filters, validates, and summarizes peptide features identified with Hardklör from data obtained during liquid chromatography mass spectrometry (LC-MS). Hardklör and Krönik were designed to rapidly identify peptide and protein features in high resolution spectra of complex mixtures. These algorithms were developed to meet the demands of modern mass spectrometers that are capable of generating large amounts of robust mass spectrometry data. Spectra containing tens to hundreds of overlapping ion signals are reduced to a relevant list of observed monoisotopic mass values, charge states, and signal intensity values when using Hardklör. These features are then filtered, validated, and summarized by using Krönik for the analysis of liquid chromatography mass spectrometry (LC-MS) data. 
    </help>
    <citations>
        <citation type="doi">10.1002/0471250953.bi1318s37</citation>
    </citations>
</tool>