<tool id="bedtools_mergebed" name="Merge BED files" version="@WRAPPER_VERSION@.0">
    <description>(mergeBed)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        mergeBed
            -i "${input}"
            $strand
            -d $distance
            $header
            > "${output}"
]]>
    </command>
    <inputs>
        <param  name="input" format="bam,bed,gff,vcf" type="data" label="Sort the following BAM/BED/VCF/GFF file"/>
        <param name="strand" type="select" label="Calculation based on strandedness?">
            <option value="" selected="True">Overlaps on either strand</option>
            <option value="-s">Force strandedness. That is, only merge features that are the same strand.</option>
            <option value="-S +">Force merge for forward strand only.</option>
            <option value="-S -">Force merge for reverse strand only.</option>
        </param>
        <param name="distance" type="integer" value="0"
            label="Maximum distance between features allowed for features to be merged"
            help="That is, overlapping and/or book-ended features are merged. (-d)"/>
        <expand macro="print_header" />
        <expand macro="choose_columns" />
        <expand macro="choose_operations">
            <expand macro="math_options" />
            <expand macro="additional_math_options" />
        </expand>
    </inputs>
    <outputs>
        <data format="bed" name="output" metadata_source="input" label="Merged ${input.name}"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="mergedBed1.bed" ftype="bed" />
            <output name="output" file="mergedBed_result1.bed" ftype="bed" />
        </test>
        <test>
            <param name="input" value="mergedBed2.bed" ftype="bed" />
            <param name="strandedness" value="-s" />
            <output name="output" file="mergedBed_result2.bed" ftype="bed" />
        </test>
        <test>
            <param name="input" value="mergedBed3.bed" ftype="bed" />
            <param name="report_number" value="-n" />
            <output name="output" file="mergedBed_result3.bed" ftype="bed" />
        </test>
        <test>
            <param name="input" value="mergedBed4.bed" ftype="bed" />
            <param name="distance" value="1000" />
            <output name="output" file="mergedBed_result4.bed" ftype="bed" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

bedtools merge combines overlapping or "book-ended" features in an interval file into a single feature which spans all of the combined features.


.. image:: $PATH_TO_IMAGES/merge-glyph.png


.. class:: warningmark

bedtools merge requires that you presort your data by chromosome and then by start position.


==========================================================================
Default behavior
==========================================================================
By default, ``bedtools merge`` combines overlapping (by at least 1 bp) and/or
bookended intervals into a single, "flattened" or "merged" interval.

::

  $ cat A.bed
  chr1  100  200
  chr1  180  250
  chr1  250  500
  chr1  501  1000

  $ bedtools merge -i A.bed
  chr1  100  500
  chr1  501  1000


==========================================================================
*-s* Enforcing "strandedness" 
==========================================================================
The ``-s`` option will only merge intervals that are overlapping/bookended
*and* are on the same strand.

::

  $ cat A.bed
  chr1  100  200   a1  1 +
  chr1  180  250   a2  2 +
  chr1  250  500   a3  3 -
  chr1  501  1000  a4  4 +

  $ bedtools merge -i A.bed -s
  chr1  100  250    +
  chr1  501  1000   +
  chr1  250  500    -


==========================================================================
*-n* Reporting the number of features that were merged 
==========================================================================
The -n option will report the number of features that were combined from the 
original file in order to make the newly merged feature. If a feature in the 
original file was not merged with any other features, a "1" is reported.

::

  $ cat A.bed
  chr1  100  200
  chr1  180  250
  chr1  250  500
  chr1  501  1000
  
  $ bedtools merge -i A.bed -n
  chr1  100  500  3
  chr1  501  1000 1


==========================================================================
*-d* Controlling how close two features must be in order to merge 
==========================================================================
By default, only overlapping or book-ended features are combined into a new 
feature. However, one can force ``merge`` to combine more distant features 
with the ``-d`` option. For example, were one to set ``-d`` to 1000, any 
features that overlap or are within 1000 base pairs of one another will be 
combined.

::

  $ cat A.bed
  chr1  100  200
  chr1  501  1000
  
  $ bedtools merge -i A.bed
  chr1  100  200
  chr1  501  1000

  $ bedtools merge -i A.bed -d 1000
  chr1  100  200  1000


=============================================================
*-nms* Reporting the names of the features that were merged
=============================================================
Occasionally, one might like to know that names of the features that were 
merged into a new feature. The ``-nms`` option will add an extra column to the 
``merge`` output which lists (separated by semicolons) the names of the
merged features.

::

  $ cat A.bed
  chr1  100  200  A1
  chr1  150  300  A2
  chr1  250  500  A3
 
  $ bedtools merge -i A.bed -nms
  chr1  100  500  A1,A2,A3
  

===============================================================
*-scores* Reporting the scores of the features that were merged
===============================================================
Similarly, we might like to know that scores of the features that were 
merged into a new feature. Enter the ``-scores`` option.  One can specify 
how the scores from each overlapping interval should be reported.

::

  $ cat A.bed
  chr1  100  200  A1 1
  chr1  150  300  A2 2
  chr1  250  500  A3 3
 
  $ bedtools merge -i A.bed -scores mean
  chr1  100  500  2
  
  $ bedtools merge -i A.bed -scores max
  chr1  100  500  3

  $ bedtools merge -i A.bed -scores collapse
  chr1  100  500  1,2,3

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