<tool id="pdaug_tsvtofasta" name="PDAUG TSVtoFASTA" version="0.1.0">

  <description>Converts tabular peptide sequence data into fasta format</description>

  <requirements>
    <requirement type="package" version="0.24.2">pandas</requirement>
    <requirement type="package" version="4.1.2">modlamp</requirement> 
  </requirements>
  <stdio>
    <exit_code range="1" level="fatal" />
  </stdio>
    <command detect_errors="exit_code"><![CDATA[

            python '$__tool_directory__/PDAUG_TSVtoFASTA.py'  -I '$InFile' -M '$Method' 

            #if $Method == 'WithClassLabel'
              -P '$OutFile1' 
              -N '$OutFile2' 
            #end if

          #if $Method == 'NoClassLabel'
              -O '$OutFile3'
          #end if 
   
    ]]></command>

  <inputs>
    <param name="InFile" type="data" label="Input file" format="tabular" argument= "--InFile1" help="Input tabular file"/>
    <param name="Method" type="select" label="Data conversion"  argument="--Method" help="Split file if class labels are present" >   
      <option value="WithClassLabel"> WithClassLabel </option>
      <option value="NoClassLabel" selected="true" > NoClassLabel </option>
    </param> 
  </inputs>

  <outputs>
    <data name='OutFile1' format='fasta' label="${tool.name} on $on_string - ${Method} (tabular)" >  
       <filter>Method == "WithClassLabel"</filter>
    </data>

    <data name='OutFile2' format='fasta' label="${tool.name} on $on_string - ${Method} (tabular)">   
       <filter>Method == "WithClassLabel"</filter>
    </data>

    <data name='OutFile3' format='fasta' label="${tool.name} on $on_string - ${Method} (tabular)" >
      <filter>Method == "NoClassLabel"</filter>
    </data>
  </outputs>
  <tests>
    <test>
      <param name="InFile" value="test1.tsv"/>
      <param name="Method" value="WithClassLabel"/>
      <output name="OutFile1" file="test1/Positive.fasta"/>
      <output name="OutFile2" file="test1/Negative.fasta"/>
    </test>
    <test>
      <param name="InFile" value="test2.tsv"/>
      <param name="Method" value="NoClassLabel"/>
      <output name="OutFile3" file="test2/Out.fasta"/>
    </test>
  </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**

This tool converts tabular files into fasta file and split fasta file on the basis of the class label.

-----

**Inputs**
    * **--InFile** Takes input as Tabular file with or without label.

-----

**Outputs**
    * Returns fasta file.]]></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>
</citations>
</tool>