Mercurial > repos > jay > pdaug_peptide_structure_builder
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit d396d7ff89705cc0dd626ed32c45a9f4029b1b05"
author | jay |
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date | Wed, 12 Jan 2022 20:01:04 +0000 |
parents | 0118cc553f3b |
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<tool id="pdaug_peptide_structure_builder" name="PDAUG Peptide Structure Builder" version="0.1.0"> <description>Builds 3D structures of peptide sequences up to 3 amino acid </description> <requirements> <requirement type="package" version="0.24.2">pandas</requirement> <requirement type="package" version="1.0.1">fragbuilder</requirement> </requirements> <stdio> <exit_code range="1" level="fatal" /> </stdio> <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/PDAUG_Peptide_Structure_Builder.py' -p '$input1' ]]></command> <inputs> <param name="input1" type="data" format="fasta" argument= "--pep" label="Input file" help="Input fasta file with peptides"/> </inputs> <outputs> <collection name="output" type="list" label="${tool.name} on $on_string - (PDB)"> <discover_datasets pattern="__name_and_ext__" format='pdb' directory="DataFile" /> </collection> </outputs> <tests> <test> <param name="input1" value="test.fasta"/> <output_collection name="output" type="list" > <element name="GLF" file="DataFile/GLF.pdb" lines_diff="102" /> </output_collection> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** 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. ----- **Inputs** * **--InFile** A fasta file witth the peptide sequences. ----- **Outputs** * Return collection of peptides with 3D structure.]]></help> <citations> <citation type="bibtex"> @misc{PDAUGGITHUB, author = {Joshi, Jayadev and Blankenberg, Daniel}, year = {2020}, title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling}, publisher = {GitHub}, journal = {GitHub repository}, url = {https://github.com/jaidevjoshi83/pdaug.git}, } </citation> <citation type="bibtex"> @article{christensen_hamelryck_jensen_2013, title={FragBuilder: An efficient Python library to setup quantum chemistry calculations on peptides models}, DOI={10.7287/peerj.preprints.169v2}, author={Christensen, Anders Steen and Hamelryck, Thomas and Jensen, Jan H}, year={2013}} } </citation> </citations> </tool>