Mercurial > repos > iuc > bedtools
view mergeBed.xml @ 18:18aeac3cd1db draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit dc0d10f28180ec2b2d1b0beac637601ea859e8f2
author | iuc |
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date | Sat, 21 Oct 2017 07:57:53 -0400 |
parents | 7308cc546a36 |
children | 95a3b2c25bd1 |
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<tool id="bedtools_mergebed" name="MergeBED" version="@WRAPPER_VERSION@.0"> <description>combine overlapping/nearby intervals into a single interval</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="stdio" /> <command> <![CDATA[ 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 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="c_and_o_argument"> <param name="col" type="data_column" data_ref="input" label="Specify the column(s) that should be summarized" help="(-c)" /> </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> <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** 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 - ========================================================================== *-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 @REFERENCES@ ]]> </help> <expand macro="citations" /> </tool>