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comparison C and D finder/CandD.xml @ 0:3e5fdf933646 draft

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author jfb
date Fri, 25 May 2018 10:56:10 -0400
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1 <tool id="commonality_r" name="commonality_finder" version="1.0.0">
2 <description>finds commonality</description>
3 <requirements>
4 <requirement type="package">R</requirement>
5 </requirements>
6 <command><![CDATA[
7 ln -s '$input1' input1.csv &&
8 ln -s '$input2' input2.csv &&
9 ln -s '$input3' input3.csv &&
10 ln -s '$input4' input4.csv &&
11 ln -s '$input5' input5.csv &&
12 ln -s '$input6' input6.csv &&
13
14 Rscript '$__tool_directory__/CandD.R' NO NO YES
15 ]]></command>
16 <inputs>
17 <param format="csv" name="input1" type="data" label="First Substrate Set"/>
18 <param format="csv" name="input2" type="data" label="First Substrate Background Frequency"/>
19 <param format="csv" name="input3" type="data" label="Second Substrate Set"/>
20 <param format="csv" name="input4" type="data" label="Second Substrate Background Frequency"/>
21 <param format="csv" name="input5" type="data" label="Third Substrate Set"/>
22 <param format="csv" name="input6" type="data" label="Third Substrate Background Frequency"/>
23 <param name="outGroup" type="text" value="kinase" label="Kinase Name"/>
24 </inputs>
25 <outputs>
26 <data format="csv" name="substrates" from_work_dir="sharedmotifs.csv" label="${outGroup}_shared Substrates.csv"/>
27 <data format="csv" name="SBF" from_work_dir="sharedSBF.csv" label="${outGroup}_shared SBF.csv"/>
28 </outputs>
29 <tests>
30 <test>
31 <param name="input1.csv" ftype="csv" value="input1.csv"/>
32 <param name="positives" ftype="csv" value="substrates.csv"/>
33 <param name="SBF" ftype="csv" value="SBF.csv"/>
34 <output name="Negatives" file="negatives.csv"/>
35 </test>
36 </tests>
37 <help><![CDATA[
38 This tool uses the output from 3 Kinamine runs to determine what motifs are shared between the three runs
39 ]]></help>
40 <citations>
41 <citation type="doi">10.1021/ja507164a</citation>
42 </citations>
43 </tool>
44