<?xml version="1.0" encoding="UTF-8"?>
<tool id="voom_transform" name="Voom transform" version="3.29.0-0">
    <description>transform count data to fit linear modelling</description>
    <requirements>
        <requirement type="package" version="3.29.0">bioconductor-limma</requirement>
        <requirement type="package" version="1.20.0">r-getopt</requirement>
    </requirements>
    
    <version_command>echo $(R --version | grep -i version | head -n 1)", Limma: "$(R --vanilla --slave -e "library(limma) ; cat(sessionInfo()\$otherPkgs\$limma\$Version)")</version_command>
    
    <command detect_errors="exit_code"><![CDATA[
        Rscript
            #if str($include_rdata) == 'true'
                --save
            #end if
            '${__tool_directory__}/voom_transform.R'
            -e '${input_select.expression_matrix}'
            -t '${output_matrix}'
        
        #if str($include_rdata) == 'true'
            && cp '.RData' '$output_rdata'
        #end if
    
    ]]></command>
    
    <inputs>
        <conditional name="input_select">
            <param name="input_format" type="select" label="Output format">
                <option value="1">Single expression matrix (header + multi column)</option>
                <!-- <option value="2">Count files (no header + 1 sample per file)</option>-->
            </param>
            
            <when value="1">
                <param name="expression_matrix" type="data" format="txt,tabular" />
            </when>
            <!-- 
            <when value="2">
                repeat / input type = multiple
            </when>
             -->
        </conditional>
        
        <param name="include_rdata" type="boolean" truevalue="true" falsevalue="" label="Save RData object" />
        
        <!-- normalization param
        -->
        
    </inputs>
    
    <outputs>
        <data name="output_matrix" format="tabular"
              label="${tool.name} on $on_string" />

        <data name="output_rdata" format="RData" label="${tool.name} on $on_string (RData)">
            <filter>str(include_rdata) in ['true', true]</filter>
        </data>
    </outputs>
    
    <tests>
        <test>
            <param name="input_format" value="1" />
            <param name="expression_matrix" value="em.txt" />
             
            <output name="output_matrix" value="em_transformed.txt" />
        </test>
    </tests>
    
    <help><![CDATA[
        
    ]]></help>
    
    <citations>
        <citation type="doi">10.1093/nar/gkv007</citation>
    </citations>
</tool>