<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.

**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>