Mercurial > repos > jay > pdaug_uversky_plot

comparison PDAUG_Uversky_Plot/PDAUG_Uversky_Plot.xml @ 0:070fc1da6df7 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author jay
date Wed, 28 Oct 2020 01:56:46 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:070fc1da6df7
1 <tool id="pdaug_uversky_plot" name="PDAUG Uversky Plot" version="0.1.0" python_template_version="3.6">
2 <description>Uversky plot to analyze ordered and disordered proteins</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 python '$__tool_directory__/PDAUG_Uversky_Plot.py' --Fasta1 '$input1' --Fasta2 '$input2' --OutFile 'out.png'
13
14 ]]></command>
15
16 <inputs>
17 <param name="input1" type="data" format="fasta" label="First fasta file" argument= "--Fasta1" help="First fasta file with Peptides"/>
18 <param name="input2" type="data" format="fasta" label="Second fasta file" argument="--Fasta2" help="Second fasta file with Peptides"/>
19 </inputs>
20
21 <outputs>
22 <data name='output2' format='png' label="${tool.name} on $on_string - (PNG)" from_work_dir="out.png"/>
23 </outputs>
24
25 <tests>
26 <test>
27 <param name="input1" value="test1.fasta"/>
28 <param name="input2" 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 plot divides analyze peptide sequences on globular and IDP subsets based on their mean net charge versus mean hydropathy. The line represents the permeable boundary between both subsets.
39
40 -----
41
42 **Inputs**
43 * **--Fasta1** The first fasta file.
44 * **--Fasta2** The second fasta file.
45
46 -----
47
48 **Outputs**
49 * Return html file.]]></help>
50 <citations>
51 <citation type="bibtex">
52 @misc{PDAUGGITHUB,
53 author = {Joshi, Jayadev and Blankenberg, Daniel},
54 year = {2020},
55 title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling},
56 publisher = {GitHub},
57 journal = {GitHub repository},
58 url =
59 {https://github.com/jaidevjoshi83/pdaug.git},
60 }
61 </citation>
62
63 <citation type="bibtex">
64 @article{konopka_marciniak_dyrka_2017,
65 title={Quantiprot - a Python package for quantitative analysis of protein sequences},
66 volume={18},
67 DOI={10.1186/s12859-017-1751-4},
68 number={1},
69 journal={BMC Bioinformatics},
70 author={Konopka, Bogumił M. and Marciniak, Marta and Dyrka, Witold},
71 year={2017}
72 }
73 </citation>
74 </citations>
75 </tool>
76
77
78