Mercurial > repos > jay > pdaug_peptide_core_descriptors
view PDAUG_Peptide_Core_Descriptors/PDAUG_Peptide_Core_Descriptors.xml @ 5:a6b122ac6f80 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
author | jay |
---|---|
date | Sun, 31 Jan 2021 02:21:54 +0000 |
parents | 0fc091fb7e8f |
children |
line wrap: on
line source
<tool id="pdaug_peptide_core_descriptors" name="PDAUG Peptide Core Descriptors" version="0.1.0"> <description>Calculates core descriptors of peptide sequences</description> <requirements> <requirement type="package" version="0.24.2">pandas</requirement> <requirement type="package" version="4.2.1">modlamp</requirement> </requirements> <stdio> <exit_code range="1" level="fatal" /> </stdio> <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/PDAUG_Peptide_Core_Descriptors.py' -I '$input1' -N '$ngrams' -O '$output1' ]]></command> <inputs> <param name="input1" type="data" label="Input file" format="fasta" argument= "--InFile1" help="Input fasta file with peptides"/> <param name="ngrams" type="integer" label="ngram size" value="3" help="ngram size"/> </inputs> <outputs> <data name='output1' format='tabular' label="${tool.name} on $on_string - n-grams (tabular)" /> </outputs> <tests> <test> <param name="input1" value="test.fasta"/> <param name="ngrams" value="3" /> <output name="output1" file="Out.tsv"/> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** Calculates the frequency of ngrames in peptide sequences. ----- **Inputs** * **--InFile** Fasta file with peptide sequences as Input File. * **--Ngrams** Integer value of Ngrams frequency to be calculated. ----- **Outputs** * **--OutFile** Returns tabular data file. ]]></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{müller_gabernet_hiss_schneider_2017, title={modlAMP: Python for antimicrobial peptides}, volume={33}, DOI={10.1093/bioinformatics/btx285}, number={17}, journal={Bioinformatics}, author={Müller, Alex T and Gabernet, Gisela and Hiss, Jan A and Schneider, Gisbert}, year={2017}, pages={2753–2755} } </citation> </citations> </tool>