Mercurial > repos > jay > pdaug_sequence_property_based_descriptors
diff PDAUG_Sequence_Property_Based_Descriptors/PDAUG_Sequence_Property_Based_Descriptors.xml @ 0:6b6aec52638d draft
"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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Sequence_Property_Based_Descriptors/PDAUG_Sequence_Property_Based_Descriptors.xml Wed Oct 28 02:23:51 2020 +0000 @@ -0,0 +1,190 @@ +<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> + + +