view 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"

<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>