Mercurial > repos > jay > pdaug_peptide_structure_builder
comparison PDAUG_Peptide_Structure_Builder/PDAUG_Peptide_Structure_Builder.xml @ 0:0118cc553f3b draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author | jay |
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date | Wed, 28 Oct 2020 02:04:41 +0000 |
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1 <tool id="pdaug_peptide_structure_builder" name="PDAUG Peptide Structure Builder" version="0.1.0"> | |
2 <description>Builds 3D structures of peptide sequences up to 3 amino acid </description> | |
3 | |
4 <requirements> | |
5 <requirement type="package" version="0.24.2">pandas</requirement> | |
6 <requirement type="package" version="1.0.1">fragbuilder</requirement> | |
7 </requirements> | |
8 <stdio> | |
9 <exit_code range="1" level="fatal" /> | |
10 </stdio> | |
11 <command detect_errors="exit_code"><![CDATA[ | |
12 python '$__tool_directory__/PDAUG_Peptide_Structure_Builder.py' -p '$input1' | |
13 | |
14 ]]></command> | |
15 | |
16 <inputs> | |
17 <param name="input1" type="data" format="fasta" argument= "--pep" label="Input file" help="Input fasta file with peptides"/> | |
18 </inputs> | |
19 | |
20 <outputs> | |
21 <collection name="output" type="list" label="${tool.name} on $on_string - (PDB)"> | |
22 <discover_datasets pattern="__name_and_ext__" format='pdb' directory="DataFile" /> | |
23 </collection> | |
24 </outputs> | |
25 | |
26 <tests> | |
27 <test> | |
28 <param name="input1" value="test.fasta"/> | |
29 <output_collection name="output" type="list" > | |
30 <element name="GLF" file="DataFile/GLF.pdb" lines_diff="102" /> | |
31 </output_collection> | |
32 </test> | |
33 </tests> | |
34 <help><![CDATA[ | |
35 .. class:: infomark | |
36 | |
37 **What it does** | |
38 | |
39 This tool generates 3D structures of peptide sequences up to three amino acids that can be utilizedĀ for peptide docking with macromolecules with tools such as Autodock Vina. | |
40 | |
41 ----- | |
42 | |
43 **Inputs** | |
44 * **--InFile** A fasta file witth the peptide sequences. | |
45 | |
46 ----- | |
47 | |
48 **Outputs** | |
49 * Return collection of peptides with 3D structure.]]></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{christensen_hamelryck_jensen_2013, | |
65 title={FragBuilder: An efficient Python library to setup quantum chemistry calculations on peptides models}, DOI={10.7287/peerj.preprints.169v2}, | |
66 author={Christensen, Anders Steen and Hamelryck, Thomas and Jensen, Jan H}, | |
67 year={2013}} | |
68 } | |
69 </citation> | |
70 </citations> | |
71 </tool> |