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author eduardo
date Mon, 03 Oct 2016 07:26:10 -0400
parents dda118a96cb0
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<tool id="PredSi" name="Predict Signal Peptides" version="0.1.0">
    <requirements>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
    _JAVA_OPTIONS=\${_JAVA_OPTIONS:-'-Xmx2048m -Xms256m'} && export _JAVA_OPTIONS && java -jar $__tool_directory__/JSPP.jar $__tool_directory__/tool-data/eukarya.smx $input1 $output1
    ]]></command>
    <inputs>
        <param type="data" name="input1" format="fasta" label="Sequence Fasta"/>
    </inputs>
    <outputs>
        <data name="output1" format="gff" from_work_dir="seq.out" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="seq.fa"/>
            <output name="output1" file="seq.out"/>
        </test>
    </tests>
    <help><![CDATA[
        USAGE: JSPP positive-matrix.smx sequences.fasta result.txt

    ]]></help>
    <citations>
        <citation type="bibtex">
@misc{predsi,
  author = {Hiller, K},
  year = {2004},
  title = {PrediSi: prediction of signal peptides and their cleavage positions},
  url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC441516/},
}</citation>
    </citations>
</tool>