comparison PDAUG_Peptide_Ngrams/PDAUG_Peptide_Ngrams.xml @ 0:7557b48b2872 draft

"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author jay
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
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76