annotate ST Kinamine/STKinamine.xml @ 0:27b9583c0290 draft default tip

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<tool id="kinamineST_java" name="Kinamine_Serine_Threonine" version="0.5.0">
    <description>Extracts phospho-S/T motifs</description>
    <requirements>
       <requirement type="package">openjdk</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
        mkdir -p outputs &&
        ## KimaMine relies on the file name extension for the fasta file
        ln -s '$reference' reference.fasta &&
        java -Djava.awt.headless=true -jar '$__tool_directory__/ST_KinaMine.jar' '$FDRreport' reference.fasta outputs $fdr output
    ]]></command>
    <inputs>
        <param format="tabular" name="FDRreport" type="data" label="Distinct Peptide Report from S/T KALIP"/>
        <param format="fasta" name="reference" type="data" label="Protein FASTA reference"/>
        <param name="fdr" type="float" value="1" min="1"  max="100"  label="FDR"/>
        <param name="outGroup" type="text" value="kinase" label="Kinase Name"/>
    </inputs>      
    <outputs>
        <data format="csv" name="Substrates" from_work_dir="outputs/output_Substrates.csv" label="${outGroup}_Substrates.csv"/>
        <data format="csv" name="SBF" from_work_dir="outputs/output_SubBackFreq.csv" label="${outGroup}_SubstrateBackgroundFrequency.csv"/>
    </outputs>
    <tests>
        <test>
            <param name="FDRreport" ftype="txt" value="FDRreport.csv"/>
            <param name="reference" ftype="fasta" value="reference.fasta"/>
            <param name="SBF" ftype="csv" value="SBF.csv"/>
            <output name="Substrates" ftype="csv" file="output_Substrates.csv"/>
            <output name="SBF" ftype="csv" file="output_SubBackFreq.csv"/>
        </test>
    </tests>

    
    <help><![CDATA[
	
	THIS TOOL IS INTENDED TO USE ONLY WITH SERINE-THREONINE KALIP OUTPUTS!  IF YOURS IS A TYROSINE KINASE, TURN BACK AND DO NOT USE THIS TOOL!
	
Kinamine takes a Distinct Peptide Report and extracts from it all peptides containing a phospho(Y), along with the 7 amino acids N- and C- terminal to the pY in that peptide (assuming they were discovered at a threshold above the given FDR value).  This file is the *Substrates* file
Additionally, all discovered peptides are assumed to have come from a protein.  For every phospho(Y) peptide, KinaMine takes the associated protein accession number, searches the FASTA file for that accession number and returns the amino acid percent composition of the protein(s) which that peptide came from.  This file is the *Substrate Background Frequency* file
This tool is intended to be used in conjunction with Negative Motif Finder and Kinatest, the three together creating a GalaxyP version of the KINATEST-ID workbook.

===========
Inputs
===========
**Distinct Peptide Report**
This is a the Distinct Peptide Summary of a Protein Pilot search (though the summary must be exported as a .txt file in this case).  The Distinct Peptide Summary is one of the tabs in .xlsx file created by Protein Pilot, it can be exported to a .txt file by normal excel functions

**FASTA reference**
This should be a FASTA taken from the Reviewed Human Uniprot database, consisting of all human proteins merged and filtered with a list of common Mass Spectrometry contaminants (cRAP)

**Intended Purpose**
This tool is intended for Academic use.  
This tool is intended as part of a KALIP-KINATEST pipeline.  
Briefly, KALIP involved treating cell lysate first with trypsin, second with phosphotase, and finally with a given kinase, then running that cell lysate on a Mass Spec to discover what peptides were present.  
KinaMine then extracts only the phospho-Y peptides and the proteins they came from.  Negative Motif finder finds all pY-containing peptides that could have been discovered but weren't.  Kinatest then uses all this data to discover candidate substrates which will be specific for the given kinase and no others.  From the discovered substrates, a biosensor can be made.


    ]]></help>
    <citations>
        <citation type="doi">10.1021/ja507164a</citation>
    </citations>
</tool>