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0
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1 <tool id="PredSi" name="Predict Signal Peptides" version="0.1.0">
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2 <requirements>
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3 </requirements>
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4 <stdio>
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5 <exit_code range="1:" />
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6 </stdio>
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7 <command><![CDATA[
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4
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8 _JAVA_OPTIONS=\${_JAVA_OPTIONS:-'-Xmx2048m -Xms256m'} && export _JAVA_OPTIONS && java -jar $__tool_directory__/JSPP.jar $__tool_directory__/tool-data/eukarya.smx $input1 $output1
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9 ]]></command>
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10 <inputs>
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1
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11 <param type="data" name="input1" format="fasta" label="Sequence Fasta"/>
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12 </inputs>
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13 <outputs>
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14 <data name="output1" format="gff" from_work_dir="seq.out" />
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15 </outputs>
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16 <tests>
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17 <test>
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18 <param name="input1" value="seq.fa"/>
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19 <output name="output1" file="seq.out"/>
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20 </test>
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21 </tests>
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22 <help><![CDATA[
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23 USAGE: JSPP positive-matrix.smx sequences.fasta result.txt
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24
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25 ]]></help>
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26 <citations>
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27 <citation type="bibtex">
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28 @misc{predsi,
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5
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29 author = {Hiller, K},
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30 year = {2004},
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31 title = {PrediSi: prediction of signal peptides and their cleavage positions},
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32 url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC441516/},
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33 }</citation>
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34 </citations>
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35 </tool>
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