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comparison pep_pointer.xml @ 0:149ed6a9680f draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer commit ac27a958fcb897c3cb56db313ebd282805b01103
author galaxyp
date Fri, 29 Dec 2017 12:37:22 -0500
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1 <tool id="pep_pointer" name="PepPointer" version="0.1.1">
2 <description>classify genomic location of peptides</description>
3 <requirements>
4 <requirement type="package" version="2.7.9">python</requirement>
5 </requirements>
6 <command detect_errors="aggressive"><![CDATA[
7 python '$__tool_directory__/pep_pointer.py' '$gtf_input.gtf' '$bed' '$classified'
8 ]]></command>
9 <inputs>
10 <conditional name="gtf_input">
11 <param type="select" name="gtf_source" label="Choose the source of the GTF file">
12 <option value="cached" selected="true">Built-in</option>
13 <option value="history">From history</option>
14 </param>
15 <when value="cached">
16 <param name="gtf" type="select" format="gtf" label="GTF file with the genome of interest">
17 <options from_data_table="pep_pointer"/>
18 </param>
19 </when>
20 <when value="history">
21 <param type="data" name="gtf" format="gtf" label="GTF file with the genome of interest"/>
22 </when>
23 </conditional>
24 <param type="data" name="bed" format="bed" label="BED file with chromosomal coordinates of peptide"/>
25 </inputs>
26 <outputs>
27 <data format="tabular" name="classified" label="${tool.name} on ${on_string}">
28 <actions>
29 <action name="column_names" type="metadata" default="chrom,chromStart,chromStop,name,score,strand,annotation"/>
30 </actions>
31 </data>
32 </outputs>
33 <tests>
34 <test>
35 <param name="gtf_source" value="history"/>
36 <param name="gtf" value="mus17.gtf"/>
37 <param name="bed" value="novel_peptides_17.bed"/>
38 <output name="classified" file="classified_novel_peptides.txt"/>
39 </test>
40 </tests>
41 <help><![CDATA[
42 **PepPointer**
43
44 Given chromosomal locations of peptides in a BED file, PepPointer classifies them as CDS, UTR, exon, intron, or intergene.
45 ]]></help>
46 <citations>
47 <citation type="bibtex">
48 @misc{peppointer,
49 author={Kumar, Praveen},
50 year={2017},
51 title={PepPointer}
52 }
53 </citation>
54 </citations>
55 </tool>