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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author | jay |
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date | Wed, 28 Oct 2020 02:23:51 +0000 |
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children | 7dc979925e31 |
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<tool id="pdaug_sequence_property_based_descriptors" name="PDAUG Sequence Property Based Descriptors" version="0.1.0"> <description>Calculates sequence based descriptors of the peptide sequences</description> <requirements> <requirement type="package" version="2.7.18">python</requirement> <requirement type="package" version="0.24.2">pandas</requirement> <requirement type="package" version="1.0">pydpi</requirement> </requirements> <stdio> <exit_code range="1" level="fatal" /> </stdio> <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/PDAUG_Sequence_Property_Based_Descriptors.py' --InFile '$input1' --DesType '$SelectDiscriptor.DesType' #if '$SelectDiscriptor.DesType' == 'PAAC' --Lamda '$SelectDiscriptor.Lamda' --Weight '$SelectDiscriptor.Weight' #end if #if $SelectDiscriptor.DesType == 'APAAC' --Lamda '$SelectDiscriptor.Lamda' --Weight '$SelectDiscriptor.Weight' #end if #if $SelectDiscriptor.DesType == 'All' --Lamda '$SelectDiscriptor.Lamda' --Weight '$SelectDiscriptor.Weight' #end if -O '$output1' ]]></command> <inputs> <param name="input1" type="data" format="fasta" label="Input fasta file" help="Input fasta file with peptides"/> <conditional name="SelectDiscriptor"> <param name="DesType" type="select" label="Descriptor Type" argument=""> <option value="PAAC">PAAC</option> <option value="APAAC">APAAC</option> <option value="CTD" selected="true">CTD</option> <option value="DPComp">DPComp</option> <option value="GearyAuto">GearyAuto</option> <option value="MoranAuto">MoranAuto</option> <option value="MoreauBrotoAuto">MoreauBrotoAuto</option> <option value="QSO">QSO</option> <option value="SOCN">SOCN</option> <option value="TPComp">TPComp</option> <option value="BinaryDescriptor">Binary Descriptor</option> <option value="All">All</option> </param> <when value="PAAC" > <param name="Lamda" type="integer" label="Lamda" value="50" argument="--Lamda" help="Lamda"/> <param name="Weight" type="float" label="Weight" value="0.5" argument="--Weight" help="Weight"/> </when> <when value="APAAC" > <param name="Lamda" type="integer" value="50" argument="--Lamda" help="Lamda"/> <param name="Weight" type="float" value="0.5" argument="--Weight" help="Weight"/> </when> <when value="All" > <param name="Lamda" type="integer" value="50" label="Lamda" argument="--Lamda" help="Lamda"/> <param name="Weight" type="float" value="0.5" argument="--Weight" help="Weight"/> </when> <when value="DPComp" > </when> <when value="GearyAuto" > </when> <when value="MoranAuto" > </when> <when value="MoreauBrotoAuto" > </when> <when value="QSO" > </when> <when value="SOCN" > </when> <when value="CTD" > </when> <when value="TPComp" > </when> <when value="BinaryDescriptor" > </when> </conditional> </inputs> <outputs> <data name='output1' format='tabular' label="${tool.name} on $on_string - ${SelectDiscriptor.DesType} (tabular)" /> </outputs> <tests> <test> <param name="input1" value="positive.fasta"/> <param name="DesType" value="All"/> <param name="Lamda" value="5"/> <param name="Weight" value="0.5"/> <output name="output1" value="Out.tsv"/> </test> <test> <param name="input1" value="positive.fasta"/> <param name="DesType" value="BinaryDescriptor"/> <output name="output1" value="Out1.tsv"/> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** This tool calculates sequence property based descriptor for a peptide descriptor. * **AAC** This option calculates amino acid composition descriptors (20). * **DPComp** This option calculates dipeptide composition descriptors (400). * **TPComp** This option calculates tri-peptide composition descriptors (8000). * **MoreauBrotoAuto** This option calculates Normalized Moreau-Broto autocorrelation descriptors (depend on the given properties, the default is 240). * **MoranAuto** This option calculates Moran autocorrelation descriptors (depend on the given properties, the default is 240). * **GearyAuto** This option calculates Geary autocorrelation descriptors (depend on the given properties, the default is 240). * **CTD** This option calculates Composition, Transition, Distribution descriptors(200). * **SOCN** This option calculates sequence order coupling numbers (depend on the choice of maxlag, the default is 60). * **QSO** This option calculates quasi-sequence order descriptors (depend on the choice of maxlag, the default is 100). * **PAAC** This option calculates pseudo amino acid composition descriptors (depend on the choice of lamda, the default is 50). * **APAAC** This option calculates amphiphilic pseudo amino acid composition descriptors, (depend on the choice of lamda, the default is 50). * **BinaryDescriptor** This option calculates the binary descriptor of peptide sequences (All the peptides should be the same length). * **All** This option calculates all the descriptors except the binary descriptor. ----- **Inputs** * **--InFile** A fasta file with peptide sequences. * **--Lamda** PAAC & APAAC descriptors (depend on the choice of lamda, the default is 50). * **--Weight** PAAC & APAAC descriptors (depend on the choice of lamda, the default is 0.5). * **--DesType** Select the descriptor type. ----- **Outputs** * Returns tabular file with descriptors. ]]></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{cao_liang_yan_tan_xu_liu_2013, title={PyDPI: Freely Available Python Package for Chemoinformatics, Bioinformatics, and Chemogenomics Studies}, volume={53}, DOI={10.1021/ci400127q}, number={11}, journal={Journal of Chemical Information and Modeling}, author={Cao, Dong-Sheng and Liang, Yi-Zeng and Yan, Jun and Tan, Gui-Shan and Xu, Qing-Song and Liu, Shao}, year={2013}, pages={3086–3096}} </citation> </citations> </tool>