<tool id="deeptools_bigwigCorrelate" name="bigwigCorrelate" version="@WRAPPER_VERSION@.0">
    <description>correlates pairs of BigWig files</description>
    <macros>
        <token name="@BINARY@">bigwigCorrelate</token>
        <import>deepTools_macros.xml</import>
    </macros> 
   <expand macro="requirements" />
    <command>
<![CDATA[
        #set files=[]
        #set labels=[]

        @multiple_input_bigwigs@

        bigwigCorrelate

        $mode.modeOpt

        @THREADS@

        --bwfiles '#echo "' '".join($files)#'
        --labels '#echo "' '".join($labels)#'
        #if $filterPercentile:
            --filterPercentile $filterPercentile
        #end if
        --corMethod $corMethod

        --plotFile $outFileName

        #if $output.showOutputSettings == "yes"
            --outRawCounts '$outFileRawCounts' 
            --outFileCorMatrix '$outFileCorMatrix'
            --plotFileFormat '$output.outFileFormat'
        #else:
            --plotFileFormat 'png'
        #end if

        #if $mode.modeOpt == "bins":
            --binSize '$mode.binSize'
        #else:
            --BED $mode.region_file
        #end if

        #### options available in both modes
        #if str($region.value) != '':
            --region '$region'
        #end if

        #if $advancedOpt.showAdvancedOpt == "yes":

            $advancedOpt.includeZeros

            #if $advancedOpt.zMin:
                --zMin $advancedOpt.zMin
            #end if
            #if $advancedOpt.zMax:
                --zMax $advancedOpt.zMax
            #end if
            --colorMap '$advancedOpt.colorMap'

            #if $plotTitle and str($plotTitle).strip() != "":
                --plotTitle '$plotTitle'
            #end if
            $plotNumbers

        #end if
]]>
    </command>

    <inputs>
        <expand macro="multiple_input_bigwigs" />

        <param name="filterPercentile" type="float" optional="True" value="" min="0.0" max="100.0"
            label="Percentile used to filter out extreme outliers"
            help ="If not specified, it is automatically set to 99.9 in analyses
                    using Pearson correlation! This means that values
                    above that threshold, which consistently occur in all
                    datasets, will not be taken into account for the
                    correlation analysis. This behavior can be overridden
                    by a user specified value from within the 0.0 to 100.0
                    range. (--filterPercentile)"/>

        <param name="corMethod" type="select" label="Correlation method" help="(--corMethod)">
            <option value="spearman" selected="True">Spearman</option>
            <option value="pearson">Pearson</option>
        </param>

        <conditional name="mode">
            <param name="modeOpt" type="select" label="Choose computation mode" 
                help="In the bins mode, the correlation is computed based on equal length bins.
                In the BED file mode, as list of genomic regions in BED format has to be given.
                For each region in the BED file the number of overlapping reads is counted in
                each of the BAM files. Then the correlation is computed.">
                <option value="bins" selected="true">Bins</option>
                <option value="BED-file">Limit correlation to certain regions (BED file)</option>
            </param>
            <when value="bins">
                <param name="binSize" type="integer" value="10000" min="1" 
                    label="Bin size in bp"
                    help="Length in base pairs for a window used to sample the genome. (--binSize)"/>
            </when>
            <when value="BED-file">
                <param name="region_file" type="data" format="bed"
                    label="Region file in BED format"
                    help="Correlation is computed for the number of reads that overlap such regions."/>
            </when>
        </conditional>

        <expand macro="bigwigCorrelate_mode_actions" />
        <conditional name="output">
            <param name="showOutputSettings" type="select" label="Show advanced output settings" >
                <option value="no" selected="true">no</option>
                <option value="yes">yes</option>
            </param>
            <when value="no" />
            <when value="yes">
                <expand macro="input_image_file_format"/>
                <param name="saveRawCounts" type="boolean" label="Save the bin counts"/>
                <param name="saveCorMatrix" type="boolean" label="Save the correlation matrix"/>
            </when>
        </conditional>

    </inputs>
    <outputs>
        <expand macro="output_image_file_format" />
        <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
            <filter>
            ((
                output['showOutputSettings'] == 'yes' and 
                output['saveRawCounts'] is True
            ))
            </filter>
        </data>
        <data format="tabular" name="outFileCorMatrix" label="${tool.name} on ${on_string}: correlation matrix">
            <filter>
            ((
                output['showOutputSettings'] == 'yes' and 
                output['saveCorMatrix'] is True
            ))
            </filter>
        </data>
    </outputs>
    <tests>
        <test>
            <repeat name="input_files">
                <param name="bigwigfile" value="test.bw" ftype="bigwig" />
                <param name="label" value="first bigwig file" />
            </repeat>
            <repeat name="input_files">
                <param name="bigwigfile" value="test.bw" ftype="bigwig" />
                <param name="label" value="second bigwig file" />
            </repeat>
            <param name="modeOpt" value="bins" />
            <param name="binSize" value="10" />
            <param name="showOutputSettings" value="no" />
            <param name="corMethod" value="spearman" />
            <output name="outFileName" file="bigwigCorrelate_result1.png" ftype="png" compare="sim_size" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

bigwigCorrelate computes the overall similarity between two or more bigWig
files based on coverage means of genomic regions. The correlation analysis
is performed for the entire genome by running the program in 'bins' mode,
or for certain regions only in 'BED-file' mode. Pearson or Spearman analyses
are available to compute correlation coefficients. Results are saved to a
heat map file. Further output files are optional.


**Output files**:

- **diagnostic plot**: clustered heatmap displaying the values for each pair-wise correlation
- data matrix (optional): if you want to plot the correlation values using a different program, e.g. R, this matrix can be used


-----

@REFERENCES@
]]>
    </help>
    <expand macro="citations" />
</tool>