comparison mergeBed.xml @ 2:457b09031d57 draft

Uploaded

1:82aac94b06c3

<tool id="bedtools_mergebed" name="Merge BED files" version="@WRAPPER_VERSION@.0">
    <description>(mergeBed)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />

        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>
        <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>
        <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**

  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.

::

  $ 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 
==========================================================================

  $ 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>

2:457b09031d57

<tool id="bedtools_mergebed" name="Merge BED files" version="@WRAPPER_VERSION@.1">
    <description>(mergeBed)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />

        mergeBed
            -i "${input}"
            $strand
            -d $distance
            $header
            @C_AND_O_ARGUMENT@
            > "${output}"
]]>
    </command>
    <inputs>
        <param  name="input" format="bam,bed,gff,vcf" type="data" label="Sort the following BAM/BED/VCF/GFF file"/>

        </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="c_and_o_argument" />
    </inputs>
    <outputs>
        <data format="bed" name="output" metadata_source="input" label="Merged ${input.name}"/>
    </outputs>
    <tests>

        </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>
        <test>
            <param name="input" value="mergedBed4.bed" ftype="bed" />
            <param name="distance" value="1000" />
            <repeat name="c_and_o_argument_repeat">
                <param name="col" value="1"/>
                <param name="operation" value="count"/>
            </repeat>
            <output name="output" file="mergedBed_result5.bed" ftype="bed" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

  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.

::

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


==========================================================================
*-d* Controlling how close two features must be in order to merge 
==========================================================================

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


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