Mercurial > repos > iuc > bedtools
view bamToBed.xml @ 12:7b3aaff0d78c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
author | iuc |
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date | Fri, 28 Oct 2016 12:54:40 -0400 |
parents | 607c0576c6ab |
children | a33db97b220c |
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<tool id="bedtools_bamtobed" name="BAM to BED" version="@WRAPPER_VERSION@.0"> <description>converter</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"> <requirement type="package" version="1.2">samtools</requirement> </expand> <expand macro="stdio" /> <command> <![CDATA[ #if $input.extension == 'bam' and $option == "-bedpe": samtools sort -n "${input}" ./input && #else ln -s "${input}" ./input.bam && #end if bedtools bamtobed $option $ed_score $split #if $tag and str($tag).strip(): -tag "${tag}" #end if -i ./input.bam > "${output}" ]]> </command> <inputs> <param format="bam" name="input" type="data" label="Convert the following BAM file to BED"/> <param name="option" type="select" label="What type of BED output would you like"> <option value="">Create a 6-column BED file</option> <option value="-bed12">Create a full, 12-column "blocked" BED file</option> <option value="-bedpe">Create a paired-end, BEDPE format</option> </param> <expand macro="split" /> <param name="ed_score" type="boolean" truevalue="-ed" falsevalue="" checked="false" label="Use alignment's edit-distance for BED score" help="(-ed)" /> <param name="tag" type="text" optional="true" label="Use other NUMERIC BAM alignment tag as the BED score" help="(-tag)"/> </inputs> <outputs> <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/> </outputs> <tests> <test> <param name="input" value="srma_in3.bam" ftype="bam" /> <param name="option" value="" /> <param name="tag" value="" /> <output name="output" file="bamToBed_result1.bed" ftype="bed" /> </test> <test> <param name="input" value="srma_in3.bam" ftype="bam" /> <param name="option" value="" /> <param name="tag" value="NM" /> <output name="output" file="bamToBed_result2.bed" ftype="bed" /> </test> </tests> <help> <![CDATA[ **What it does** bedtools bamtobed is a conversion utility that converts sequence alignments in BAM format into BED, BED12, and/or BEDPE records. .. class:: infomark The "Report spliced BAM alignment..." option breaks BAM alignments with the "N" (splice) operator into distinct BED entries. For example, using this option on a CIGAR such as 50M1000N50M would, by default, produce a single BED record that spans 1100bp. However, using this option, it would create two separate BED records that are each 50bp in size and are separated by 1000bp (the size of the N operation). This is important for RNA-seq and structural variation experiments. .. class:: warningmark If using a custom BAM alignment TAG as the BED score, note that this must be a numeric tag (e.g., type "i" as in NM:i:0). @REFERENCES@ ]]> </help> <expand macro="citations" /> </tool>