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1 <tool id="pep_pointer" name="PepPointer: classify genomic location of peptides" version="0.1.0">
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2 <requirements>
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3 <requirement type="package" version="2.7.9">python</requirement>
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4 </requirements>
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5 <command detect_errors="aggressive"><![CDATA[
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6 python '$__tool_directory__/pep_pointer.py' '$gtf' '$bed' '$classified'
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7 ]]></command>
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8 <inputs>
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9 <param type="data" name="gtf" format="gtf" label="GTF file with the genome of interest"/>
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10 <param type="data" name="bed" format="bed" label="BED file with chromosomal coordinates of peptide"/>
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11 </inputs>
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12 <outputs>
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13 <data format="tabular" name="classified"/>
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14 </outputs>
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15 <tests>
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16 <test>
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17 <param name="gtf" value="mus17.gtf"/>
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18 <param name="bed" value="novel_peptides_17.bed"/>
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19 <output name="classified" file="classified_novel_peptides.txt"/>
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20 </test>
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21 </tests>
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22 <help><![CDATA[
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23 **PepPointer**
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24
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25 Given chromosomal locations of peptides in a BED file, PepPointer classifies them as CDS, UTR, exon, intron, or intergene.
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26 ]]></help>
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27 <citations>
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28 <citation type="bibtex">
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29 @misc{peppointer,
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30 author={Kumar, Praveen},
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31 year={2017},
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32 title={PepPointer}
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33 }
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34 </citation>
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35 </citations>
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36 </tool>
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