annotate NMF/NMF.xml @ 1:a098e1274f63 draft

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<tool id="kinamine_java" name="Negative-Motif-Finder 7_to_7" version="1.0.0">
    <description>discover unphosphorylated substrates</description>
    <requirements>
       <requirement type="package">R</requirement>
    </requirements>
    <command><![CDATA[
		ln -s '$FASTA' input1.tabular && 
        ln -s '$positives' input2.csv &&
		ln -s '$SBF' input3.csv &&
        Rscript '$__tool_directory__/NMF.R'
    ]]></command>
    <inputs>
		<param format="csv" name="SBF" type="data" label="Substrate Background Frequency"/>
        <param format="tabular" name="FASTA" type="data" label="Human Proteome Reference"/>
        <param format="csv" name="positives" type="data" label="Positive/Phosphorylated Substrate List"/>
		<param name="outGroup" type="text" value"kinase" label="Kinase Name"/>
    </inputs>      
    <outputs>
        <data format="csv" name="Negatives" from_work_dir="output1.csv" label="${outGroup}_Negative Motifs.csv"/>
    </outputs>
    <tests>
        <test>
            <param name="FASTA" ftype="csv" value="reference.csv"/>
            <param name="positives" ftype="csv" value="substrates.csv"/>
            <param name="SBF" ftype="csv" value="SBF.csv"/>
			<output name="Negatives" file="negatives.csv"/>
        </test>
    </tests>
    <help><![CDATA[
Using the output from KinaMine, plus the Uniprot file that was used with KinaMine, this program finds all Y-centered motifs which *could* have been present as positive motifs but were not seen by the Mass Spec
This tool is intended to be used in conjunction with KinaMine 7-7 and Kinatest.R, the three together creating a GalaxyP version of the KINATEST-ID workbook.
===========
Inputs
===========
**Substrate Background Frequency**
**Positive/Phosphorylated Substrate List**
These two come directly from the KinaMine output

**Human Proteome Reference**
This should be a tabularized version of a FASTA taken from the Reviewed Human Uniprot database, consisting of all human proteins plus a list of common Mass Spectrometry contaminants.
This file should be created by using the same FASTA file used for KinaMine and running FASTA to Tabular on it using GalaxyP

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