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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 20:20:40 +0000 |
parents | dd4523d4ae2f |
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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> <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/PDAUG_Sequence_Property_Based_Descriptors.py' --InFile '$input1' --DesType '$SelectDiscriptor.DesType' #if $SelectDiscriptor.DesType == 'GetPAAC' --Lamda '$SelectDiscriptor.Lamda' --Weight '$SelectDiscriptor.Weight' #end if #if $SelectDiscriptor.DesType == 'GetAPAAC' --Lamda '$SelectDiscriptor.Lamda' --Weight '$SelectDiscriptor.Weight' #end if #if $SelectDiscriptor.DesType == 'GetSOCN' --MaxLag '$SelectDiscriptor.MaxLag' #end if #if $SelectDiscriptor.DesType =='GetQSO' --MaxLag '$SelectDiscriptor.MaxLag' --Weight '$SelectDiscriptor.Weight' #end if #if $SelectDiscriptor.DesType =='All' --MaxLag '$SelectDiscriptor.MaxLag' --Weight '$SelectDiscriptor.Weight' --Lamda '$SelectDiscriptor.Lamda' #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="GetAAComp">GetAAComp</option> <option value="GetDPComp">GetDPComp</option> <option value="GetTPComp" selected="true">GetTPComp</option> <option value="GetMoreauBrotoAuto">GetMoreauBrotoAuto</option> <option value="GetMoranAuto">GetMoranAuto</option> <option value="GetGearyAuto">GetGearyAuto</option> <option value="GetCTD">GetCTD</option> <option value="GetPAAC">GetPAAC</option> <option value="GetAPAAC">GetAPAAC</option> <option value="GetSOCN">GetSOCN</option> <option value="GetQSO">GetQSO</option> <option value="GetTriad">GetTriad</option> <option value="BinaryDescriptor">Binary Descriptor</option> <option value="All">All</option> </param> <when value="GetPAAC" > <param name="Lamda" type="integer" label="Lamda" value="10" help="A non negative integer"/> <param name="Weight" type="float" label="Weight" value="0.5" help="Any value within the range from 0.05 to 0.7"/> </when> <when value="GetAPAAC" > <param name="Lamda" type="integer" label="Lamda" value="10" help="A non negative integer"/> <param name="Weight" type="float" label="Weight" value="0.5" help="Any value within the range from 0.05 to 0.7"/> </when> <when value="GetQSO"> <param name="MaxLag" type="integer" label="MaxLag" value="10" help="A non negative integer"/> <param name="Weight" type="float" label="Weight" value="0.5" help="Any value within the range from 0.05 to 0.7"/> </when> <when value="GetSOCN"> <param name="MaxLag" type="integer" label="MaxLag" value="10" help="A non negative integer"/> </when> <when value="All" > <param name="Lamda" type="integer" value="10" label="Lamda" help="A non negative integer"/> <param name="Weight" type="float" value="0.5" label="Weight" help="Weight"/> <param name="MaxLag" type="integer" value="10" label="Lamda" help="A non negative integer"/> </when> <when value="GetAAComp" > </when> <when value="GetDPComp" > </when> <when value="GetTPComp" > </when> <when value="GetMoreauBrotoAuto" > </when> <when value="GetGearyAuto" > </when> <when value="GetCTD" > </when> <when value="GetPAAC" > </when> <when value="GetAPAAC" > </when> <when value="GetSOCN"> </when> <when value="GetQSO"> </when> <when value="GetTriad"> </when> <when value="GetMoranAuto" > </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="10"/> <param name="Weight" value="0.5"/> <param name="MaxLag" value="10"/> <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. * **GetAAComp** Amino acid compositon descriptors. * **GetDPComp** Dipeptide composition descriptors. * **GetTPComp** Tri-peptide composition descriptors. * **GetMoreauBrotoAuto** Normalized Moreau-Broto autocorrelation descriptors. * **GetMoranAuto** Moran autocorrelation descriptors. * **GetGearyAuto** Geary autocorrelation descriptors. * **GetCTD** Composition Transition Distribution descriptors. * **GetPAAC** Type I Pseudo amino acid composition descriptors. * **GetAPAAC** Amphiphilic (Type II) Pseudo amino acid composition descriptors. * **GetSOCN** Sequence order coupling numbers. * **GetQSO** Quasi sequence order descriptors default is 10, maxlag is the maximum lag. (The length of the protein should be larger than maxlag). * **GetTriad** Calculate the conjoint triad features from the protein sequence. * **Binary Descriptors** Calculate the conjoint triad features from the protein sequence. * **All** Calculates all the available descriptors except binary. **Inputes** * **Input fasta file** Fasta file with peptide sequences. * **Lamda** lamda reflects the rank of correlation, must be a non-Negative integer. Lamda should NOT be larger than the length of the input protein sequence. * **Weight** weight is designed for the users to put weight on the additional PseAA components. Any value within the range from 0.05 to 0.7 for the weight factor can be used. * **Maxlag** maxlag is the maximum lag. a non negative integer. The length of the protein should be larger than maxlag. ----- **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>