comparison zippable Kinamine/Kinamine.xml @ 1:a125f38e8c07 draft

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author jfb
date Tue, 20 Feb 2018 14:41:44 -0500
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1 <tool id="kinamine_java" name="Kinamine_7_to_7" version="0.5.0">
2 <description>Extracts phosphorylated motifs</description>
3 <requirements>
4 <requirement type="package" version="8.0.1440.1">Java</requirement>
5 </requirements>
6 <command><![CDATA[
7 mkdir -p output &&
8 java -Djava.awt.headless=true -cp '$__tool_directory__/Kinamine.jar' kinamine.KinaMine $FDRreport $reference output $fdr
9 ]]></command>
10 <inputs>
11 <param format="txt" name="FDRreport" type="data" label="Distinct Peptide Report"/>
12 <param format="fasta" name="reference" type="data" label="FASTA reference genome"/>
13 <param name="fdr" type="integer" value"1" min="1" max="100" label="FDR"/>
14 <param name="outGroup" type="text" value"kinase" label="Kinase Name"/>
15 </inputs>
16 <outputs>
17 <data format="csv" name="Substrates" from_work_dir="output_Substrates.csv" label="${outGroup}_Substrates.csv"/>
18 <data format="csv" name="SBF" from_work_dir="output2_Substrate Background Frequency.csv" label="$[outGroup]_Substrate Background Frequency"/>
19 </outputs>
20 <tests>
21 <test>
22 <param name="FDRreport" ftype="txt" value="FDRreport.csv"/>
23 <param name="reference" ftype="fasta" value="reference.fasta"/>
24 <param name="SBF" ftype="csv" value="SBF.csv"/>
25 <output name="SDtable" file="SDtable.csv"/>
26 <output name="EPM" file="EPM.csv"/>
27 <output name="Characterization" file="Characterization.csv"/>
28 </test>
29 </tests>
30
31
32 <help><![CDATA[
33 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.
34
35 ===========
36 Inputs
37 ===========
38 **Distinct Peptide Report**
39 This is... ask Minervo
40
41 **FASTA reference**
42 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
43
44 ]]></help>
45 <citations>
46 <citation type="doi">10.1021/ja507164a</citation>
47 </citations>
48 </tool>
49