<tool id="cpm_tpm_rpk" name="Generate CPM, TPM, RPK" version="0.1.0">
    <description>from raw counts expression values</description>
    <requirements>
        <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" level="fatal" description="Tool exception" />
    </stdio>
    <command detect_errors="exit_code"><![CDATA[ 
Rscript $__tool_directory__/cpm_tpm_rpk.R 
-d $input 
-t $option.type_transfo 
-s $input_sep 
-c $input_header 
#if $option.type_transfo == "tpm":
-f $option.gene_file 
--gene_sep $option.gene_sep 
--gene_header $option.gene_header
#end if 
#if $option.type_transfo == "rpk":
-f $option.gene_file 
--gene_sep $option.gene_sep 
--gene_header $option.gene_header
#end if
-l $log
#if $log == "FALSE":
-o ${output}
#end if
#if $log == "TRUE":
-o ${output_log}
#end if
]]></command>
    <inputs>
        <param name="input" type="data" format="txt" label="Raw counts of expression data"/>
        <param name="input_sep" type="select" label="Input column separator">
            <option value="tab" selected="true">Tabs</option>
            <option value=",">Comma</option>
            <option value="\ ">Whitespace</option>
            <option value=".">Dots</option>
                        <option value="_">Underscores</option>
                        <option value="-">Dashes</option>
        </param>
        <param name="input_header" type="select" label="Consider first line of input file as header?">
            <option value="TRUE" selected="true">Yes</option>
            <option value="FALSE">No</option>
        </param>
                <conditional name="option">
                    <param name="type_transfo" type="select" label="Type of transformation">
                              <option value="cpm" selected="true">CPM</option>
                               <option value="tpm">TPM</option>
                               <option value="rpk">RPK</option>
                       </param>
            <when value="tpm">
                <param name="gene_file" type="data" format="txt" label="Gene length file"/> 
                <param name="gene_sep" type="select" label="Gene length column separator">
                    <option value="tab" selected="true">Tabs</option>
                           <option value=",">Commas</option>
                    <option value="\ ">Whitespaces</option>
                    <option value=".">Dots</option>
                    <option value="_">Underscores</option>
                    <option value="-">Dashes</option>
                </param>
                <param name="gene_header" type="select" label="Consider first line of gene length file as header ?">
                    <option value="TRUE" selected="true">Yes</option>
                    <option value="FALSE">No</option>
                </param>
            </when>
                        <when value="rpk">
                                <param name="gene_file" type="data" format="txt" label="Gene length file"/>
                                <param name="gene_sep" type="select" label="Gene length column separator">
                                        <option value="tab" selected="true">Tabs</option>
                                        <option value=",">Commas</option>
                                        <option value="\ ">Whitespaces</option>
                                        <option value=".">Dots</option>
                                        <option value="_">Underscores</option>
                                        <option value="-">Dashes</option>
                                </param>
                                <param name="gene_header" type="select" label="Consider first line of gene length file as header ?">
                                        <option value="TRUE" selected="true">Yes</option>
                                        <option value="FALSE">No</option>
                                </param>
                        </when>
            <when value="cpm">
            </when>
        </conditional>
        <param name="log" type="select" label="Data should be log transformed ?">
            <option value="FALSE" selected="true">No</option>
            <option value="TRUE">Yes</option>
        </param>
    </inputs>
    <outputs>
        <data name="output" format="tabular" label="${option.type_transfo} from ${on_string}">
            <filter>log == "FALSE"</filter>
        </data>
        <data name="output_log" format="tabular" label="log2(${option.type_transfo} +1) from ${on_string}">
            <filter>log == "TRUE"</filter>
                </data>
    </outputs>
    <tests>
        <test>
            <param name="input" value="counts.tab" ftype="tabular"/>
            <param name="type_transfo" value="cpm"/>
            <output name="output" file="cpm.tab" ftype="tabular"/>
        </test>
        <test>
            <param name="input" value="counts.tab" ftype="tabular"/>
            <param name="type_transfo" value="cpm"/>
            <param name="log" value="TRUE"/>
            <output name="output" file="logcpm.tab" ftype="tabular"/>
        </test>
        <test>
            <param name="input" value="counts.tab" ftype="tabular"/>
            <param name="type_transfo" value="tpm"/>
            <param name="gene_file" value="gene_length.tab" ftype="tabular"/>
            <param name="gene_header" value="TRUE"/>
            <output name="output" file="tpm.tab" ftype="tabular"/>
        </test>
        <test>
            <param name="input" value="counts.tab" ftype="tabular"/>
            <param name="type_transfo" value="tpm"/>
            <param name="gene_file" value="gene_length.tab" ftype="tabular"/>
            <param name="gene_header" value="TRUE"/>
            <param name="log" value="TRUE"/>
            <output name="output" file="logtpm.tab" ftype="tabular"/>
        </test>
        <test>
            <param name="input" value="counts.tab" ftype="tabular"/>
            <param name="type_transfo" value="rpk"/>
            <param name="gene_file" value="gene_length.tab" ftype="tabular"/>
            <param name="gene_header" value="TRUE"/>
            <output name="output" file="rpk.tab" ftype="tabular"/>
        </test>
        <test>
            <param name="input" value="counts.tab" ftype="tabular"/>
            <param name="type_transfo" value="rpk"/>
            <param name="gene_file" value="gene_length.tab" ftype="tabular"/>
            <param name="gene_header" value="TRUE"/>
            <param name="log" value="TRUE"/>
            <output name="output" file="logrpk.tab" ftype="tabular"/>
        </test>
    </tests>
    <help>

**What it does**

And returns a table of normalized expression values.

Normalization can be:

- CPM (Counts Per Million) are obtained by dividing counts by the library counts sum and multiplying the results by a million.
- RPK (Reads Per Kilobases) are obtained by dividing read counts by gene lengths (expressed in kilo-nucleotides).
- TPM (Transcripts Per Million) are obtained by dividing RPK values by the sum of all RPK values in a sample and multiplying the results by 1 million.

RPK and TPM require a two-column correspondance table gene_name - gene length where the length is specified in nucleotide. Both these metrics are relevant only for sequencing of full length RNAs.

Note: do not comment you header line if you have header line in you tabular input (ie do not start the header line with a '#' character)

Computed values may be log-transformed (log2([CPM or RPK or TPM]+1))

    </help>
</tool>