view kinatestid_r/kinatestid_r.xml @ 8:927eaf73feca draft

Changed read.csv(inputs) to read.csv("inputs")

<tool id="kinatestid_r" name="Kinatest-ID 7_to_7" version="0.1.0">
    <description>calculate optimal substrates</description>
    <requirements>
       <requirement type="package">R</requirement>
    </requirements>
    <command><![CDATA[
        ln -s '$__tool_directory__/screener7-7.csv' screener &&
        ln -s '$substrates' input1 && 
        ln -s '$negatives' input2 && 
        ln -s '$SBF' input3 &&
        Rscript '$__tool_directory__/Kinatest-R_part1.R' &&
        Rscript '$__tool_directory__/Kinatest-R_part2.R' &&
        mv output1 output1.csv &&
        mv output2 output2.csv &&
        mv output3 output3.csv
    ]]></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"/>
    </inputs>      
    <outputs>
        <data format="csv" name="SDtable" from_work_dir="output1.csv" label="Standard Deviation Table"/>
        <data format="csv" name="EPM" from_work_dir="output2.csv" label="Endogenous Probability Matrix"/>
        <data format="csv" name="Characterization" from_work_dir="output3.csv" label="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 KinaMine.jar and Negative Motif Finder.  Using the outputs from those two functions (The Positive and Negative substrates as well as the Substrate Background Frequency) this tool calculates optimal substrates
    ]]></help>
    <citations>
        <citation type="doi">10.1021/ja507164a</citation>
    </citations>
</tool>