Mercurial > repos > jay > pdaug_peptide_ngrams
comparison PDAUG_Peptide_Ngrams/PDAUG_Peptide_Ngrams.xml @ 0:7557b48b2872 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author | jay |
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date | Wed, 28 Oct 2020 02:10:12 +0000 |
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1 <tool id="pdaug_peptide_ngrams" name="PDAUG Peptide Ngrams" version="0.1.0" python_template_version="2.7"> | |
2 <description>Counts n-grams in the entire sequence set and fitting their distribution with the power-law distribution (Zipf’s law)</description> | |
3 | |
4 <requirements> | |
5 <requirement type="package" version="2.7.18">python</requirement> | |
6 <requirement type="package" version="1.4.6">powerlaw</requirement> | |
7 <requirement type="package" version="0.2.4">quantiprot</requirement> | |
8 </requirements> | |
9 | |
10 <command detect_errors="exit_code"><![CDATA[ | |
11 | |
12 python2 '$__tool_directory__/PDAUG_Peptide_Ngrams.py' -f1 '$fasta1' -f2 '$fasta2' --OutFile 'out.png' | |
13 | |
14 ]]></command> | |
15 | |
16 <inputs> | |
17 <param name="fasta1" type="data" format="fasta" label="First fasta file" argument= "--fasta1" help="First fasta file"/> | |
18 <param name="fasta2" type="data" format="fasta" label="Second fasta file" argument= "--fasta2" help="First fasta file"/> | |
19 </inputs> | |
20 | |
21 <outputs> | |
22 <data name='output2' format='png' label="${tool.name} on $on_string - (PNG)" from_work_dir="out.png"/> | |
23 </outputs> | |
24 | |
25 <tests> | |
26 <test> | |
27 <param name="fasta1" value="test1.fasta"/> | |
28 <param name="fasta2" value="test2.fasta"/> | |
29 <output name="output2" file="out.png"/> | |
30 </test> | |
31 </tests> | |
32 | |
33 <help><![CDATA[ | |
34 .. class:: infomark | |
35 | |
36 **What it does** | |
37 | |
38 This tool counts n-grams in the entire peptide sequence set and fitting their distribution with the power-law distribution (Zipf’s law) and plot the results. | |
39 | |
40 ----- | |
41 | |
42 **Inputs** | |
43 * **--InFile** Takes fasta file as input with peptide sequences. | |
44 | |
45 ----- | |
46 | |
47 **Outputs** | |
48 * Returns html report 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 <citation type="bibtex"> | |
62 @article{konopka_marciniak_dyrka_2017, | |
63 title={Quantiprot - a Python package for quantitative analysis of protein sequences}, | |
64 volume={18}, | |
65 DOI={10.1186/s12859-017-1751-4}, | |
66 number={1}, | |
67 journal={BMC Bioinformatics}, | |
68 author={Konopka, Bogumił M. and Marciniak, Marta and Dyrka, Witold}, | |
69 year={2017} | |
70 } | |
71 </citation> | |
72 </citations> | |
73 </tool> | |
74 | |
75 | |
76 |