Mercurial > repos > jay > pdaug_peptide_data_access
diff PDAUG_Peptide_Data_Access/PDAUG_Peptide_Data_Access.xml @ 0:6c12ca9f5d88 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author | jay |
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date | Wed, 28 Oct 2020 01:59:25 +0000 |
parents | |
children | f85327600c11 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Data_Access/PDAUG_Peptide_Data_Access.xml Wed Oct 28 01:59:25 2020 +0000 @@ -0,0 +1,132 @@ +<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 == "query_apd" + -L $SelectDatasets.list1 + #end if + + #if $SelectDatasets.DataBaseType == "query_camp" + -L $SelectDatasets.list2 + #end if + + ]]></command> + + + <inputs> + + <conditional name="SelectDatasets"> + + <param name="DataBaseType" type="select" label="Datasets" argument="--DataBaseType" help="Name of the data set."> + <option value="AMPvsTM" selected="true" > AMPvsTM </option> + <option value="AMPvsUniProt" > AMPvsUniProt </option> + <option value="ACPvsTM"> ACPvsTM </option> + <option value="ACPvsRandom"> ACPvsRandom </option> + <option value="query_apd"> Query APD Database</option> + <option value="query_camp" > Query CAMP Database </option> + </param> + + + + <when value="query_apd"> + <param name="list1" type='text' argument="-List" label="List of integers as IDs" help="List of integers as IDs" /> + </when> + + <when value="query_camp"> + <param name="list2" type='text' argument="-List" label="List of integers as IDs" help="List of integers as IDs" /> + </when> + + </conditional> + + + </inputs> + + <outputs> + <data name='output1' format='tabular' label="${tool.name} $on_string - ${SelectDatasets.DataBaseType} (tabular)" /> + </outputs> + + <tests> + <test> + <param name="DataBaseType" value="AMPvsTM"/> + <output name="output1" file="out.tsv"/> + </test> + + <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. + + * **AMPvsTM** This option returns Antimicrobial peptides and transmembrane sequences. + * **AMPvsUniProt** This option returns AMPs from the APD3 and other peptides from the UniProt database. + * **ACPvsTM** This option returns anticancer peptides (CancerPPD) and helical transmembrane sequences. + * **ACPvsRandom** This option returns anticancer peptides (CancerPPD) and random scrambled AMP sequences. + +----- + +**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> + + +