view bigwigCorrelate.xml @ 0:fa8c52637734 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty

<tool id="deeptools_bigwig_correlate" 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@

        @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 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)"/>

                <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**

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>