<tool id="protein_rna_correlation" name="protein_rna_correlation" version="0.0.2">
  <description>Correlation between protein and transcript expression  </description>
  <requirements>
    <requirement type="package" version="3.2.1">R</requirement>
    <requirement type="package" version="0.0.1">r-protrnacorr</requirement>
    <requirement type="package" version="1.5.0">x11</requirement>
    
  </requirements>
  <command detect_errors="exit_code" interpreter="Rscript"><![CDATA[protein_rna_correlation.r $pe_exp $ge_exp $pe_idcol $ge_idcol $pe_expcol $ge_expcol $pe_idtype $ge_idtype $organism_map $writeMapUnmap $doScale $html_file $html_file.files_path]]></command>
  <inputs>
    <param name="pe_exp" type="data" format="tabular">
      <label>Input Protein Expression File</label>
    </param>
    <param name="pe_idcol" type="integer" value="1">
      <label>Column: Protein/Gene ID</label>
    </param>
    <param name="pe_expcol" type="integer" value="1">
      <label>Column: Protein Expression Values</label>
    </param>
    
    <param name="ge_exp" type="data" format="tabular">
      <label>Input RNA Expression File</label>
    </param>
    
    <param name="ge_idcol" type="integer" value="1">
      <label>Column: RNA/Gene ID</label>
    </param>
    <param name="ge_expcol" type="integer" value="1">
      <label>Column: RNA Expression Values</label>
    </param>
    
    <param name="pe_idtype" type="select" label="Protein ID type">
        <option value="Ensembl_with_version" selected="True">Ensembl</option>
        <option value="uniprot">Uniprot</option>
        <option value="hgnc">HGNC</option>
    </param>
    
    <param name="ge_idtype" type="select" label="Transcript ID type">
        <option value="Ensembl_with_version" selected="True">Ensembl</option>
        <option value="uniprot">Uniprot</option>
        <option value="hgnc">HGNC</option>
    </param>
    
    <param name="organism_map" type="data" format="tabular">
        <label>Biomart ID Mapping file (.map)</label>
    </param>
    
    <param name="writeMapUnmap" type="boolean" checked="true" truevalue="1" falsevalue="0">
      <label>Create the list of Mapped and Unmapped Identifiers in HTML</label>
    </param>
    
    <param name="doScale" type="boolean" checked="true" truevalue="1" falsevalue="0">
      <label>Scale the abundance values</label>
    </param>
    
  </inputs>
  
  <outputs>
    <data format="html" name="html_file" label="protein_rna_corr_${tool.name}.html"/>
  </outputs>
  
  <tests>
        <test>
            <param name="pe_exp" value="PE_mouse_singlesample.txt"/>
            <param name="pe_idcol" value="7"/>
            <param name="ge_exp" value="GE_mouse_singlesample.txt"/>
            <param name="ge_idcol" value="1"/>
            <param name="pe_expcol" value="13"/>
            <param name="ge_expcol" value="10"/>
            <param name="pe_idtype" value="Ensembl_with_version"/>
            <param name="ge_idtype" value="Ensembl_with_version"/>
            <param name="organism_map" value="mmusculus_gene_ensembl__GRCm38.p6.map"/>
            <param name="writeMapUnmap" value="true"/>
            <param name="doScale" value="true"/>
            <output name="html_file" file="protein_rna_corr_protein_transcript_correlation.html"/>
        </test>
  </tests>
    
  <help><![CDATA[
Proteome Transcriptome Correlation
Developer: Priyabrata Panigrahi
  ]]></help>
  <citations>
      <citation type="bibtex">
@misc{protein_rna_correlation,
    author={Panigrahi, Priyabrata},
    year={2018},
    title={ProteinRNACorrelation}
}
      </citation>
    </citations>
</tool>