<tool id="protein_rna_correlation" name="protein_rna_correlation" version="0.1.0">
  <description>Correlation between protein and rna expression (Single Sample)</description>
  <requirements>
    <requirement type="package" version="3.3.1">r-base</requirement>
    <requirement type="package" version="1.18.0">bioconductor-rgalaxy</requirement>
    <requirement type="package" version="1.21.0">bioconductor-biocinstaller</requirement>
    <requirement type="package" version="1.9">rmarkdown</requirement>
    <requirement type="package" version="1.9">MASS</requirement>
    <requirement type="package" version="1.8-23">mgcv</requirement>
    <requirement type="package" version="0.4.1">DMwR</requirement>
    <requirement type="package" version="1.11.4">data.table</requirement>
    <requirement type="package" version="3.0.1">gplots</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">
      <label>Column: Protein/Gene ID</label>
    </param>
    <param name="pe_expcol" type="integer">
      <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">
      <label>Column: RNA/Gene ID</label>
    </param>
    <param name="ge_expcol" type="integer">
      <label>Column: RNA Expression Values</label>
    </param>
    
    <param name="pe_idtype" type="select">
        <option value='ensembl' selected>Ensembl</option>
        <option value='uniprot'>Uniprot</option>
        <option value='hgnc'>HGNC</option>
    </param>
    
    <param name="ge_idtype" type="select">
        <option value='ensembl' selected>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="method" type="select" label="Correlation Method">
    <option value="pearson" selected="true">Pearson</option>
    <option value="spearman">Spearman</option>
    <option value="kendall">Kendall</option>
    </param>-->
    
    <param name="writeMapUnmap" type="boolean">
      <label>Create the list of Mapped and Unmapped Identifiers in HTML</label>
    </param>
    
    <param name="doScale" type="boolean">
      <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="method" value="pearson"/>
            <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="1"/>
            <param name="doScale" value="1"/>
            <output name="html_file" file="PE_abundance_GE_abundance_pearson.html"/>
        </test>
  </tests>
    
  <help>
Proteome Transcriptome Correlation
Developer: Priyabrata Panigrahi
  </help>
</tool>