<tool id="kinamine_java" name="Kinamine_7_to_7" version="0.5.0">
    <description>Extracts phosphorylated motifs</description>
    <requirements>
       <requirement type="package" version="8.0.1440.1">Java</requirement>
    </requirements>
    <command><![CDATA[
        mkdir -p output &&
        java -Djava.awt.headless=true -jar '$__tool_directory__/Kinamine 7 to 7.jar' $FDRreport $reference $fdr output 
    ]]></command>
    <inputs>
        <param format="txt" name="FDRreport" type="data" label="Distinct Peptide Report"/>
        <param format="fasta" name="reference" type="data" label="FASTA reference"/>
        <param name="fdr" type="integer" value"1" min="1"  max="100"  label="FDR"/>
        <param name="outGroup" type="text" value"kinase" label="Group Name"/>
    </inputs>      
    <outputs>
        <data format="csv" name="Substrates" from_work_dir="output/" label="${outGroup}_Substrates.csv"/>
        <data format="csv" name="SBF" from_work_dir="output2.csv" label="Substrate Background Frequency"/>
    </outputs>
    <tests>
        <test>
            <param name="substrates" ftype="csv" value="substrates.csv"/>
            <param name="negatives" ftype="csv" value="negatives.csv"/>
            <param name="SBF" ftype="csv" value="SBF.csv"/>
            <output name="SDtable" file="SDtable.csv"/>
            <output name="EPM" file="EPM.csv"/>
            <output name="Characterization" file="Characterization.csv"/>
        </test>
    </tests>

    
    <help><![CDATA[
This takes a Distinct Peptide Report and extracts from it all phospho-motifs that were discovered at a threshold above a given FDR value.  This tool is intended to be used in conjunction with Negative Motif Finder and Kinatest.R, the three together creating a GalaxyP version of the KINATEST-ID workbook.

===========
Inputs
===========
**Distinct Peptide Report**
This is... ask Minervo

**FASTA reference**
This should be a FASTA taken from the Reviewed Human Uniprot database, consisting of all human proteins plus a list of common Mass Spectrometry contaminants

    ]]></help>
    <citations>
        <citation type="doi">10.1021/ja507164a</citation>
    </citations>
</tool>