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comparison pep_pointer.xml @ 0:032f1ee171ed draft

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author pravs
date Fri, 22 Dec 2017 04:33:12 -0500
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1 <tool id="pep_pointer" name="PepPointer: classify genomic location of peptides" version="0.1.0">
2 <requirements>
3 <requirement type="package" version="2.7.9">python</requirement>
4 </requirements>
5 <command detect_errors="aggressive"><![CDATA[
6 python '$__tool_directory__/pep_pointer.py' '$gtf' '$bed' '$classified'
7 ]]></command>
8 <inputs>
9 <param type="data" name="gtf" format="gtf" label="GTF file with the genome of interest"/>
10 <param type="data" name="bed" format="bed" label="BED file with chromosomal coordinates of peptide"/>
11 </inputs>
12 <outputs>
13 <data format="tabular" name="classified"/>
14 </outputs>
15 <tests>
16 <test>
17 <param name="gtf" value="mus17.gtf"/>
18 <param name="bed" value="novel_peptides_17.bed"/>
19 <output name="classified" file="classified_novel_peptides.txt"/>
20 </test>
21 </tests>
22 <help><![CDATA[
23 **PepPointer**
24
25 Given chromosomal locations of peptides in a BED file, PepPointer classifies them as CDS, UTR, exon, intron, or intergene.
26 ]]></help>
27 <citations>
28 <citation type="bibtex">
29 @misc{peppointer,
30 author={Kumar, Praveen},
31 year={2017},
32 title={PepPointer}
33 }
34 </citation>
35 </citations>
36 </tool>