annotate bigwigAverage.xml @ 2:4a53856a5b85 draft default tip

planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 4a4029b5c2e725b7cebc27217b76d23910508412

<tool id="deeptools_bigwig_average" name="bigwigAverage" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
    <description>normalizes and average multiple bigWig files</description>
    <macros>
        <token name="@BINARY@">bigwigAverage</token>
        <import>deepTools_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command>
<![CDATA[
        @BINARY@
            @THREADS@
            --bigwigs
            #for $b in $bigwigs:
                $b
            #end for
            --outFileName '$outFileName'
            --outFileFormat '$outFileFormat'

            #if str($region).strip() != '':
                --region '$region'
            #end if

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

              $advancedOpt.skipNAs
              --scaleFactors '$advancedOpt.scaleFactors'
              --binSize $advancedOpt.binSize

                @blacklist@

            #end if
]]>
    </command>
    <inputs>
        <param name="bigwigs" format="bigwig" type="data" label="Treatment bigwig file" multiple="true" />

        <param name="outFileFormat" type="select" label="Coverage file format">
            <option value="bigwig" selected="true">bigwig</option>
            <option value="bedgraph">bedgraph</option>
        </param>

        <expand macro="region_limit_operation" />

        <conditional name="advancedOpt">
            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
                <option value="no" selected="true">no</option>
                <option value="yes">yes</option>
            </param>
            <when value="no" />
            <when value="yes">
                <param argument="--binSize" type="integer" value="50" min="1"
                    label="Length, in bases, of the non-overlapping bins used for averaging the score over the regions length"
                    help="Size of the bins in bases for the output of the bigwig/bedgraph file."/>

                <expand macro="skipNAs" />
                <param name="scaleFactors" type="text" value="1" label="Scale factors (one per bigwig separated by ':')" />
                <expand macro="blacklist" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="bigwig" name="outFileName">
            <change_format>
                <when input="outFileFormat" value="bigwig" format="bigwig" />
                <when input="outFileFormat" value="bedgraph" format="bedgraph" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="bigwigs" value="test.bw" ftype="bigwig" />
            <param name="showAdvancedOpt" value="yes" />
            <param name="outFileFormat" value="bigwig" />
            <param name="binSize" value="5" />
            <output name="outFileName" file="test_compated.bw" ftype="bigwig"
            compare="sim_size" delta="500" />
        </test>
        <test>
            <param name="bigwigs" value="test.bw" ftype="bigwig" />
            <param name="showAdvancedOpt" value="yes" />
            <param name="outFileFormat" value="bigwig" />
            <param name="binSize" value="5" />
            <param name="scaleFactors" value="0.5"/>
            <output name="outFileName" file="test_half.bw" ftype="bigwig"
                    compare="sim_size" delta="500" />
        </test>
        <test>
            <param name="bigwigs" value="test.bw,test_half.bw" ftype="bigwig" />
            <param name="showAdvancedOpt" value="yes" />
            <param name="outFileFormat" value="bigwig" />
            <param name="binSize" value="5" />
            <param name="scaleFactors" value="0.5"/>
            <output name="outFileName" file="bigwigAverage2.bw" ftype="bigwig"
            compare="sim_size" delta="500" />
        </test>
        <test>
            <param name="bigwigs" value="test.bw,test_half.bw" ftype="bigwig" />
            <param name="showAdvancedOpt" value="yes" />
            <param name="outFileFormat" value="bigwig" />
            <param name="binSize" value="5" />
            <param name="scaleFactors" value="1:2"/>
            <output name="outFileName" file="test_compated.bw" ftype="bigwig"
            compare="sim_size" delta="500" />
        </test>
    </tests>
    <help>
<![CDATA[

What it does
--------------

This tool compute average of multiple bigWig files based on the number of mapped reads. To
average the bigwig files, the genome is partitioned into bins of equal size,
then the scores (e.g., number of reads) found in each bigWig file are counted for such bins and, finally, an average value is reported.

Note that you can actually produce a human-readable bedGraph format instead of the compressed bigWig format if you're interested in having a look at the values yourself.

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