view bigwig2summary.xml @ 22:bf77633cc603 draft default tip

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<tool id="bigwig2_summary" name="bigWig2Summary">
    <description> Extract summary information from a bigWig file across multiple genomic regions specified by the user. </description>
    <requirements>
        <requirement type="package" version="1.0">bigWigSummary</requirement>
        <requirement type="package" version="1.0">fetchChromSizes</requirement>
        <requirement type="package" version="1.0">bedClip</requirement>
    </requirements>
    <command interpreter="bash"> 
	bigwig2summary.sh -f $input_bw -b $input_bed -n $bins -o $assembly -t $type $header > $output
    </command>
    <inputs>
        <param name="input_bw" type="data" format="bigwig" label="Extract summary from" help="bigWig format."/>
        <param name="input_bed" type="data" format="tabular" label="using genomic regions in" help="TAB delimited BED-like file."/>
        <param name="bins" type="integer" value="1" label="Number of bins" help="Postitive integer"/>
        <param name="assembly" type="text" label="Orgamism assembly" help="E.g. hg19" />
        <param name="header" type="boolean" checked="False" truevalue="-e" falsevalue=" " label="Does the genomic region file contain a header?" />    
        <param name="type" type="select" label="Operation" help="">
	    <option value="mean">Average value in region (default)</option>
            <option value="min">Minimum value in region</option>
            <option value="max">Maximum value in region</option>
            <option value="std">Standard deviation in region</option>
            <option value="coverage">Percentage of region that is covered</option>
        </param>
    </inputs>
  
    <outputs>
        <data format="tabular" name="output"/> 
    </outputs>

    <tests>
        <test>
	    <param name="input_bw" value="1.bigwig" />
	    <param name="input_bed" value="1.bed" />
	    <param name="bins" value="3" />
	    <param name="assembly" value="hg19" />
	    <param name="header" value="true" />
	    <output name="output" file="1.tabular" />
        </test>
        <test>
            <param name="input_bw" value="1.bigwig" />
            <param name="input_bed" value="2.bed" />
            <param name="bins" value="5" />
            <param name="assembly" value="hg19" />
            <param name="header" value="true" />
            <output name="output" file="2.tabular" />
        </test>
    </tests>

    <help>

This tool extracts summary values (mean, min, max, std or coverage) from a **bigWig** file for a number of equal sized bins across genomic regions given in an a "BED-like" file.

The script this tool is based on is written by Jens Vilstrup Johansen and uses bigWigSummary_, bedClip_ and fetchChromSizes_.

.. _bigWigSummary: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigSummary 

.. _bedClip: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedClip

-- _fetchChromSizes: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes

-----

.. class:: infomark

The file contaning the genomic region must be TAB-delimited with at list 3 columns representing Chromosome, ChrStart and ChrEnd. If the file contains 6 columns (or more), column 6 is expected to contain strand information. Summary values from a negative strand will be reversed.
 
-----

**Example 1**

Input BED file::

  chr19   50178708        50180708
  chr6    90348174        90350174
  chr16   58495848        58497848
  chr5    180580242       180582242
  chr9    120177017       120179017  

Extract summary (*#* of bins = 3):: 

  0		0		0
  0.144886	0		0
  0.507327	1.14649		1.38456
  0.221471	0.144886	0.309857
  0.348944	0.426638	0.244495

**Example 2**

Input BED file (with strand information)::

  chr19	  50178708	50180708	NM_198318	0	+	PRMT1
  chr6	  90348174	90350174	NM_020466	0	-	LYRM2
  chr16	  58495848	58497848	NM_020465	0	+	NDRG4
  chr5 	  180580242	180582242	NM_206880	0	+	OR2V2
  chr9    120177017     120179017       NM_014010       0       -	ASTN2

Extract summary (*#* of bins = 3)::

  0		0		0
  0		0		0.144886
  0.507327	1.14649		1.38456
  0.221471	0.144886	0.309857
  0.244495	0.426638	0.348944

    </help>
</tool>