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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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8 _JAVA_OPTIONS=\${_JAVA_OPTIONS:-'-Xmx2048m -Xms256m'} &&
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9 export _JAVA_OPTIONS &&
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10 java -jar $__tool_directory__/JSPP.jar $__tool_directory__/tool-data/eukarya.smx $input1 $output1
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11 ]]></command>
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12 <inputs>
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1
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13 <param type="data" name="input1" format="fasta" label="Sequence Fasta"/>
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14 </inputs>
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15 <outputs>
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16 <data name="output1" format="gff" from_work_dir="seq.out" />
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17 </outputs>
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18 <tests>
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19 <test>
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20 <param name="input1" value="seq.fa"/>
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21 <output name="output1" file="seq.out"/>
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22 </test>
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23 </tests>
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24 <help><![CDATA[
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2
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25 USAGE: JSPP positive-matrix.smx sequences.fasta result.txt
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0
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26
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27 ]]></help>
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28 <citations>
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29 <citation type="bibtex">
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30 @misc{predsi,
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31 author = {Kalls, L},
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32 year = {2004},
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33 title = {A combined transmembrane topology and signal peptide prediction method},
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34 url = {https://www.ncbi.nlm.nih.gov/pubmed/15111065},
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35 }</citation>
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36 </citations>
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37 </tool>
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