Mercurial > repos > jay > pdaug_peptide_core_descriptors
comparison PDAUG_Peptide_Core_Descriptors/PDAUG_Peptide_Core_Descriptors.xml @ 0:0fc091fb7e8f draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author | jay |
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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> | |
76 | |
77 | |
78 |