annotate KT-ID fisher test/kinatestid_r_fisher.xml @ 7:77f3a77f0ca2 draft default tip

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<tool id="kinatestid_fisher_r" name="Kinatest-ID using Fisher's Exact Test" version="0.5.0">
    <description>determine kinase's preferred sequence motif</description>
    <requirements>
       <requirement type="package">R</requirement>
    </requirements>
    <command><![CDATA[
        ln -s '$substrates' substrates.csv && 
        ln -s '$negatives' negatives.csv && 
        ln -s '$SBF' SBF.csv &&
        ln -s '$__tool_directory__/screener7-7.csv' screener &&
        ln -s '$__tool_directory__/OnlyTheRequiredSubBackFreqData.RData' thedata.RData &&
        Rscript '$__tool_directory__/7-7-fisher-galaxy_working.R'
    ]]></command>
    <inputs>
        <param format="csv" name="substrates" type="data" label="Positive/Phosphorylated Substrate List"/>
        <param format="csv" name="negatives" type="data" label="Negative/unPhosphorylated Substrate List"/>
        <param format="csv" name="SBF" type="data" label="Substrate Background Frequency List"/>
		<param name="outGroup" type="text" value="kinase" label="Kinase Name"/>
    </inputs>      
    <outputs>
        <data format="csv" name="odds_table" from_work_dir="output1.csv" label="${outGroup}_Fisher Odds Table"/>
        <data format="csv" name="char_table" from_work_dir="output2.csv" label="${outGroup}_Characterization Table"/>
    </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 tool is intended for use in conjunction with a Kinamine tool and a Negative Motif Finder tool.  Using the outputs from those two functions (The Positive and Negative substrates as well as the Substrate Background Frequency) this tool calculates the kinases preferred substrate motif.


    ]]></help>
    <citations>
        <citation type="doi">10.1074/mcp.RA118.001111</citation>
    </citations>
</tool>