<tool id="diffbind" name="DiffBind" version="2.0.1">
    <description> differential binding analysis of ChIP-Seq peak data</description>
    <requirements>
        <requirement type="binary">Rscript</requirement>
        <requirement type="R-module">DESeq2</requirement>
        <requirement type="package" version="3.0.1">R_3_0_1</requirement>
        <requirement type="package" version="1.0.17">deseq2</requirement>
        <requirement type="package" version="1.8.3">diffbind</requirement>
    </requirements>
    <command>
        ## seems that diffbind also needs file extensions to work properly
        #set $counter = 1
        #for $sample in $samples:
            ln -s $sample.bamreads #echo str($counter) + "_bamreads.bam"# &amp;&amp;
            ln -s ${sample.bamreads.metadata.bam_index} #echo str($counter) + "_bamreads.bai"# &amp;&amp;
            ln -s $sample.bamcontrol #echo str($counter) + "_bamcontrol.bam"# &amp;&amp;
            ln -s ${sample.bamcontrol.metadata.bam_index} #echo str($counter) + "_bamcontrol.bai"# &amp;&amp;
            #set $counter = $counter + 1
        #end for

        Rscript /usr/local/galaxy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/bgruening/diffbind/7929c8b3f6f9/diffbind/diffbind.R
            -i $infile
            -o $outfile
            -p $plots
            -f $format
    </command>
    <stdio>
        <regex match="Execution halted" 
           source="both" 
           level="fatal" 
           description="Execution halted." />
        <regex match="Input-Error 01" 
           source="both" 
           level="fatal" 
           description="Error in your input parameters: Make sure you only apply factors to selected samples." />
        <regex match="Error in" 
           source="both" 
           level="fatal" 
           description="An undefined error occured, please check your intput carefully and contact your administrator." />
    </stdio>
    <inputs>
        <repeat name="samples" title="Samples" min="2">
            <param name="sample_id" type="text" value="Sample ID" label="Specify a sample id" help="e.g. BT474.1-" />
            <param name="tissue" type="text" value="Tissue" label="Specify the tissue" help="e.g. BT474" />
            <param name="factor" type="text" value="Factor Name" label="Specify a factor name" help="e.g. ER" />
            <param name="condition" type="text" value="Condition" label="Specify the condition" help="e.g. Resistent" />
            <param name="replicate" type="integer" value="1" label="Specify the replicate number" help="e.g. 1" />
            <param format="bam" name="bamreads" type="data" label="Read BAM file" help="Specify the Read BAM file, used for Peak calling."/>
            <param format="bam" name="bamcontrol" type="data" label="Control BAM file" help="Specify the Control BAM file, used for Peak calling."/>
            <param format="bed" name="peaks" type="data" label="Peak file" help="Result of your Peak calling experiment."/>
        </repeat>
        <param name="pdf" type="boolean" truevalue="" falsevalue="" checked="true" 
            label="Visualising the analysis results"
            help="output an additional PDF files" />
        <param name="format" type="select" label="Output Format">
            <option value="bed">BED</option>
            <option value="gff">GFF</option>
            <option value="wig">WIG</option>
        </param>
    </inputs>
    <configfiles>
<configfile name="infile">
SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks
#set $counter = 1
#for $sample in $samples:
$sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,#echo str($counter) + '_bamreads.bam'#,#echo str($counter) + '_bamcontrol.bam'#,$sample.peaks
#set $counter = $counter + 1
#end for
</configfile>
    </configfiles>
    <outputs>
        <data format="bed" name="outfile" label="Differential binding sites on ${on_string}">
            <change_format>
                <when input="format" value="wig" format="wig" />
                <when input="format" value="gff" format="gff" />
            </change_format>
        </data>
        <data format="pdf" name="plots" label="Differential binding sites on ${on_string}">
            <filter>pdf == True</filter>
        </data>
    </outputs>

    <help>

.. class:: infomark

**What it does** 


------

**References** 

DiffBind_ Authors:  Rory Stark, Gordon Brown

.. _DiffBind: http://www.bioconductor.org/packages/release/bioc/html/DiffBind.html

Wrapper authors: Bjoern Gruening, Pavankumar Videm

    </help>
</tool>