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comparison PDAUG_Peptide_Core_Descriptors/PDAUG_Peptide_Core_Descriptors.xml @ 0:0fc091fb7e8f draft

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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author jay
date Wed, 28 Oct 2020 02:12:57 +0000
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1 <tool id="pdaug_peptide_core_descriptors" name="PDAUG Peptide Core Descriptors" version="0.1.0">
2 <description>Calculates core descriptors of peptide sequences</description>
3
4 <requirements>
5 <requirement type="package" version="0.24.2">pandas</requirement>
6 <requirement type="package" version="4.2.1">modlamp</requirement>
7 </requirements>
8 <stdio>
9 <exit_code range="1" level="fatal" />
10 </stdio>
11 <command detect_errors="exit_code"><![CDATA[
12
13 python '$__tool_directory__/PDAUG_Peptide_Core_Descriptors.py' -I '$input1' -N '$ngrams' -O '$output1'
14
15 ]]></command>
16
17 <inputs>
18 <param name="input1" type="data" label="Input file" format="fasta" argument= "--InFile1" help="Input fasta file with peptides"/>
19 <param name="ngrams" type="integer" label="ngram size" value="3" help="ngram size"/>
20 </inputs>
21
22 <outputs>
23 <data name='output1' format='tabular' label="${tool.name} on $on_string - n-grams (tabular)" />
24 </outputs>
25 <tests>
26 <test>
27 <param name="input1" value="test.fasta"/>
28 <param name="ngrams" value="3" />
29 <output name="output1" file="Out.tsv"/>
30 </test>
31 </tests>
32 <help><![CDATA[
33 .. class:: infomark
34
35 **What it does**
36
37 Calculates the frequency of ngrames in peptide sequences.
38
39 -----
40
41 **Inputs**
42 * **--InFile** Fasta file with peptide sequences as Input File.
43 * **--Ngrams** Integer value of Ngrams frequency to be calculated.
44
45 -----
46
47 **Outputs**
48 * **--OutFile** Returns tabular data file. ]]></help>
49 <citations>
50 <citation type="bibtex">
51 @misc{PDAUGGITHUB,
52 author = {Joshi, Jayadev and Blankenberg, Daniel},
53 year = {2020},
54 title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling},
55 publisher = {GitHub},
56 journal = {GitHub repository},
57 url =
58 {https://github.com/jaidevjoshi83/pdaug.git},
59 }
60 </citation>
61
62 <citation type="bibtex">
63 @article{müller_gabernet_hiss_schneider_2017,
64 title={modlAMP: Python for antimicrobial peptides},
65 volume={33},
66 DOI={10.1093/bioinformatics/btx285},
67 number={17},
68 journal={Bioinformatics},
69 author={Müller, Alex T and Gabernet, Gisela and Hiss, Jan A and Schneider, Gisbert},
70 year={2017},
71 pages={2753–2755}
72 }
73 </citation>
74 </citations>
75 </tool>
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