annotate PDAUG_Uversky_Plot/PDAUG_Uversky_Plot.xml @ 1:1915fd2723e3 draft

"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
author jay
date Tue, 29 Dec 2020 04:08:13 +0000
parents 070fc1da6df7
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1 <tool id="pdaug_uversky_plot" name="PDAUG Uversky Plot" version="0.1.0" python_template_version="3.6">
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
2 <description>Uversky plot to analyze ordered and disordered proteins</description>
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
3
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
4 <requirements>
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
5 <requirement type="package" version="2.7.18">python</requirement>
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
6 <requirement type="package" version="1.4.6">powerlaw</requirement>
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
7 <requirement type="package" version="0.2.4">quantiprot</requirement>
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
8 </requirements>
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
9
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
10 <command detect_errors="exit_code"><![CDATA[
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
11
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
12 python '$__tool_directory__/PDAUG_Uversky_Plot.py' --Fasta1 '$input1' --Fasta2 '$input2' --OutFile 'out.png'
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
13
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
14 ]]></command>
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
15
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
16 <inputs>
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
17 <param name="input1" type="data" format="fasta" label="First fasta file" argument= "--Fasta1" help="First fasta file with Peptides"/>
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
18 <param name="input2" type="data" format="fasta" label="Second fasta file" argument="--Fasta2" help="Second fasta file with Peptides"/>
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
19 </inputs>
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
20
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
21 <outputs>
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
22 <data name='output2' format='png' label="${tool.name} on $on_string - (PNG)" from_work_dir="out.png"/>
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
23 </outputs>
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
24
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
25 <tests>
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
26 <test>
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
27 <param name="input1" value="test1.fasta"/>
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
28 <param name="input2" value="test2.fasta"/>
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
29 <output name="output2" file="out.png"/>
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
30 </test>
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
31 </tests>
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
32
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
33 <help><![CDATA[
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
34 .. class:: infomark
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
35
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
36 **What it does**
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
37
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
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.
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
39
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
40 -----
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
41
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
42 **Inputs**
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
43 * **--Fasta1** The first fasta file.
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
44 * **--Fasta2** The second fasta file.
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
45
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
46 -----
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
47
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
48 **Outputs**
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
49 * Return html file.]]></help>
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
50 <citations>
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
51 <citation type="bibtex">
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
52 @misc{PDAUGGITHUB,
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
53 author = {Joshi, Jayadev and Blankenberg, Daniel},
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
54 year = {2020},
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
55 title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling},
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
56 publisher = {GitHub},
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
57 journal = {GitHub repository},
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
58 url =
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
59 {https://github.com/jaidevjoshi83/pdaug.git},
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
60 }
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
61 </citation>
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
62
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
63 <citation type="bibtex">
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
64 @article{konopka_marciniak_dyrka_2017,
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
65 title={Quantiprot - a Python package for quantitative analysis of protein sequences},
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
66 volume={18},
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
67 DOI={10.1186/s12859-017-1751-4},
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
68 number={1},
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
69 journal={BMC Bioinformatics},
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
70 author={Konopka, BogumiƂ M. and Marciniak, Marta and Dyrka, Witold},
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
71 year={2017}
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
72 }
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
73 </citation>
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
74 </citations>
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
75 </tool>
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
76
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
77
070fc1da6df7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
78