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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 32b9c48c81639a81be24bb3e2f48dc0a81c0deca"
author | jay |
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date | Sun, 09 Jan 2022 03:52:11 +0000 |
parents | 20a0454c5347 |
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<tool id="pdaug_peptide_data_access" name="PDAUG Peptide Data Access" version="0.1.0"> <description>Fetch peptide data from inbuild datasets and public databases</description> <requirements> <requirement type="package" version="0.24.2">pandas</requirement> <requirement type="package" version="4.1.2">modlamp</requirement> <requirement type="package" version="8.0.21">mysql-connector-python</requirement> </requirements> <stdio> <exit_code range="1" level="fatal" /> </stdio> <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/PDAUG_Peptide_Data_Access.py' -d '$SelectDatasets.DataBaseType' -o '$output1' #if $SelectDatasets.DataBaseType == "AMPvsTMP" -d 'AMPvsTMP' #end if #if $SelectDatasets.DataBaseType == "AMPvsUniProt" -d 'AMPvsUniProt' #end if #if $SelectDatasets.DataBaseType == "ACPvsTMP" -d 'ACPvsTMP' #end if #if $SelectDatasets.DataBaseType == "ACPvsRandom" -d 'ACPvsRandom' #end if #if $SelectDatasets.DataBaseType == "query_apd" -L '$SelectDatasets.list1' #end if #if $SelectDatasets.DataBaseType == "query_camp" -L '$SelectDatasets.list1' #end if ]]></command> <inputs> <conditional name="SelectDatasets"> <param name="DataBaseType" type="select" label="Datasets" argument="--DataBaseType" help="Name of the data set."> <option value="AMPvsTMP" selected="true" > AMPvsTMP </option> <option value="AMPvsUniProt" > AMPvsUniProt </option> <option value="ACPvsTMP"> ACPvsTMP </option> <option value="ACPvsRandom"> ACPvsRandom </option> <option value="query_apd"> Query APD Database</option> <option value="query_camp" > Query CAMP Database </option> </param> <when value="AMPvsTMP"> </when> <when value="AMPvsUniProt"> </when> <when value="ACPvsTMP"> </when> <when value="ACPvsRandom"> </when> <when value="query_apd"> <param name="list1" type='text' argument="-List" label="List of integers as IDs" help="List of integers as IDs" /> </when> <when value="query_camp"> <param name="list2" type='text' argument="-List" label="List of integers as IDs" help="List of integers as IDs" /> </when> </conditional> </inputs> <outputs> <data name='output1' format='tabular' label="${tool.name} $on_string - ${SelectDatasets.DataBaseType} (tabular)" /> </outputs> <tests> <test> <param name="DataBaseType" value="AMPvsTMP"/> <output name="output1" file="Out.tsv"/> </test> <!-- This test has consistently failed over several months, due to inability to access host/URL http://aps.unmc.edu/AP/database/query_output.php?ID=00004 <test> <param name="DataBaseType" value="query_apd"/> <param name="list1" value="4,5,6" /> <output name="output1" file="apd.tsv" lines_diff="8"/> </test> --> <test> <param name="DataBaseType" value="query_camp"/> <param name="list2" value="3,4,5,9" /> <output name="output1" file="camp.tsv" lines_diff="10"/> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** This tool returns inbuild peptide data sets. * **AMPvsTMP** Antimicrobial peptides (AMP) consist of an intersection of all activity annotations of the APD2 and CAMP databases, where gram-positive, gram-negative, and antifungal exact matches were observed versus transmenbrane peptides (TMP) extracted from alpha-helical transmembrane regions of proteins for classification. * **AMPvsUniProt** AMP consisting of the whole APD3 versus UniProt peptides randomly extracted from the UniProt database, to be used for classification. * **ACPvsTMP** Anticancer Peptide (ACP) sequences from the CancerPPD database versus TM extracted from alpha-helical transmembrane regions of proteins for classification. * **ACPvsRandom** ACP sequences from the CancerPPD database versus Random peptides generated randomly with the amino acid composition of AMPs. * **query_apd** Retrive sequences from the antimicrobial peptide database APD. * **query_camp** Retrive sequences from the antimicrobial peptide database CAMP. ----- **Inputs** * **--DataBaseType** Takes dataset name as input. ----- **Outputs** * Returns a tabular file with peptide sequences and class labels.]]></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>