view bigwigCorrelate.xml @ 9:85c9cda86b1d draft default tip

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7

<tool id="deeptools_bigwig_correlate" name="bigwigCorrelate" version="@WRAPPER_VERSION@.0">
    <description>calculates average read coverages for a list of two or more 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@

        @BINARY@
            $mode.modeOpt

            @THREADS@

            --outFileName $outFile
            --bwfiles '#echo "' '".join($files)#'
            --labels '#echo "' '".join($labels)#'

            #if $outRawCounts:
                --outRawCounts '$outFileRawCounts'
            #end if

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

            #if str($region.value) != '':
                --region '$region'
            #end if
]]>
    </command>

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

        <conditional name="mode">
            <param name="modeOpt" type="select" label="Choose computation mode"
                help="In the bins mode, the correlation is computed using equally sized bins.
                In the BED file mode, a 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 BigWig 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 bases for a window used to sample the genome. (--binSize)"/>

                <expand macro="distanceBetweenBins" />
            </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="region_limit_operation" />
        <param argument="--outRawCounts" type="boolean" label="Save raw counts (coverages) to file" help=""/>

    </inputs>
    <outputs>
        <data format="deeptools_coverage_matrix" name="outFile" label="${tool.name} on ${on_string}: correlation matrix" />
        <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
            <filter>outRawCounts is True</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="bigwigfiles" value="test.bw,test.bw" ftype="bigwig" />
            <param name="modeOpt" value="bins" />
            <param name="binSize" value="10" />
            <param name="corMethod" value="spearman" />
            <output name="outFileName" file="bigwigCorrelate_result1.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
        </test>
        <!--test>
            <param name="bigwigfiles" value="test.bw,test.bw" ftype="bigwig" />
            <param name="modeOpt" value="BED-file" />
            <param name="region_file" value="bamCorrelate_regions.bed" />
            <param name="corMethod" value="pearson" />
            <param name="outRawCounts" value="True" />
            <output name="outFileRawCounts" file="bigwigCorrelate_result2.tabular" ftype="tabular" />
            <output name="outFileName" file="bigwigCorrelate_result2.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
        </test-->
    </tests>
    <help>
<![CDATA[
**What it does**

Given two or more bigWig files, bigwigCorrelate computes the average scores for each of the files in every genomic region.
This analysis is performed for the entire genome by running the program in 'bins' mode, or for certain user selected regions
in 'BED-file' mode. Typically the output of bigwigCorrelate is used by other tools, such as 'plotCorrelation' or 'plotPCA',
for visualization and diagnostic purposes.


**Output files**:

- **Coverage scores**: Coverage scores computed and saved in a format appropriate for 'plotCorrelation' or 'plotPCA'.

- Data matrix (optional,select to save raw counts to a file above): If you want to have a look at the coverage values
  or compute statistics yourself using a different program (like R).

-----

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