<tool id="rgDGE" name="Digital differential expression" version="0.01">
  <description>for RNA counts</description>
  <command interpreter="python">rgDGE.py --output_html "$html_file.files_path" --input_matrix "$input1" --treatcols "$Treat_cols" 
       --treatname "$treatment_name" --ctrlcols "$Control_cols" --ctrlname "$control_name" --output_tab "$outtab" --output_html 
        "$html_file" --output_dir "$html_file.files_path" --method "edgeR"
  </command>
  <inputs>
    <param name="input1"  type="data" format="tabular" label="Select an input matrix - rows are contigs, columns are counts for each sample"
       help="Use the DGE matrix preparation tool to create these matrices from BAM files and a BED file of contigs"/>
    <param name="treatment_name" type="text" value="Treatment" size="50" label="Treatment Name"/>
    <param name="Treat_cols" label="Select columns containing treatment." type="data_column" data_ref="input1" numerical="True" 
         multiple="true" use_header_names="true" size="120" display="checkboxes">
        <validator type="no_options" message="Please select at least one column."/>
    </param>

    <param name="control_name" type="text" value="Control" size="50" label="Control Name"/>
    <param name="Control_cols" label="Select columns containing control." type="data_column" data_ref="input1" numerical="True" 
         multiple="true" use_header_names="true" size="120" display="checkboxes">
        <validator type="no_options" message="Please select at least one column."/>
    </param>

        <param name="method" type="select" label="Method" >
            <option value="edgeR" selected="true">edgeR</option>
            <option value="DESeq">DESeq - coming soonish!</option>
        </param>

  </inputs>
  <outputs>
    <data format="tabular" name="outtab" label="${on_string}_DGE.xls"/>
    <data format="html" name="html_file" label="${on_string}_DGE.html"/>
  </outputs>
<tests>
<test>
<param name='input1' value='DGEtest.xls' ftype='tabular' />
 <param name='treatment_name' value='case' />
 <param name='control_name' value='control' />
 <param name='Treat_cols' value='c3,c6,c9' />
 <param name='Control_cols' value='c2,c5,c8' />
 <output name='outtab' file='DGEtest1out.xls' ftype='tabular' compare='diff' />
 <output name='html_file' file='DGEtest1out.html' ftype='html' compare='diff' lines_diff='20' />
</test>
</tests>
<help>
.. class:: infomark
    
**What it does**

Performs digital differential gene expression analysis between two groups (eg a treatment and control) each with biological replicates, from count data arranged in a matrix as a tabular file.

**Input**

A matrix consisting of non-negative integers. The matrix must have a unique header row identifiying the samples, as well as a unique set of row names 
as  the first column. To create appropriate input files, the "Multiple BAMs to matrix" tool takes multiple bam files containing mapped RNAseq reads mapped to a reference genome, and a BED file containing (eg Refseq) contigs. A count matrix containing contigs as rows and samples as
columns will be created and can then be used in this tool to estimate differential gene expression using methods appropriate for count data.

**Output**

A tabular file containing relative expression levels, statistical estimates of differential expression probability, the R script, log and sessionInfo, and some helpful diagnostic plots.

.. class:: infomark

**Attribution**
DGE.R was originally written by: S.Lunke and A.Kaspi.
Wrapping for Galaxy and general kibbitzing from Ross Lazarus.
This tool wrapts the edgeR_ Bioconductor package so all calculations and plots are controlled by that code. See edgeR_ for all documentation and appropriate attribution. 
Recommended reference is Mark D. Robinson, Davis J. McCarthy, Gordon K. Smyth, PMCID: PMC2796818

 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
 .. _edgeR: http://www.bioconductor.org/packages/2.3/bioc/html/edgeR.html

</help>

</tool>