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1 <tool id="commonality_r" name="commonality_finder" version="1.1.0">
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2 <description>finds commonality</description>
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3 <requirements>
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4 <requirement type="package">R</requirement>
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5 </requirements>
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6 <command><![CDATA[
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7 ln -s '$input1' input1.csv &&
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8 ln -s '$input2' input2.csv &&
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9 ln -s '$input3' input3.csv &&
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10 ln -s '$input4' input4.csv &&
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11 ln -s '$input5' input5.csv &&
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12 ln -s '$input6' input6.csv &&
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13
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14 Rscript '$__tool_directory__/commonality-working jul 13 2020.R'
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15 ]]></command>
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16 <inputs>
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17 <param format="csv" name="input1" type="data" label="First Substrate Set"/>
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18 <param format="csv" name="input2" type="data" label="First Substrate Background Frequency"/>
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19 <param format="csv" name="input3" type="data" label="Second Substrate Set"/>
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20 <param format="csv" name="input4" type="data" label="Second Substrate Background Frequency"/>
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21 <param format="csv" name="input5" type="data" label="Third Substrate Set"/>
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22 <param format="csv" name="input6" type="data" label="Third Substrate Background Frequency"/>
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23 <param name="outGroup" type="text" value="kinase" label="Kinase Name"/>
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24 </inputs>
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25 <outputs>
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26 <data format="csv" name="substrates" from_work_dir="sharedmotifs.csv" label="${outGroup}_shared Substrates.csv"/>
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27 <data format="csv" name="SBF" from_work_dir="sharedSBF.csv" label="${outGroup}_shared SBF.csv"/>
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28 </outputs>
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29 <tests>
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30 <test>
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31 <param name="input1.csv" ftype="csv" value="input1.csv"/>
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32 <param name="positives" ftype="csv" value="substrates.csv"/>
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33 <param name="SBF" ftype="csv" value="SBF.csv"/>
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34 <output name="Negatives" file="negatives.csv"/>
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35 </test>
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36 </tests>
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37 <help><![CDATA[
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38 This tool uses the output from 3 Kinamine runs to determine what motifs are shared between the three runs
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39 ]]></help>
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40 <citations>
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41 <citation type="doi">10.1021/ja507164a</citation>
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42 </citations>
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43 </tool>
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