annotate bamToBed.xml @ 1:82aac94b06c3 draft

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<tool id="bedtools_bamtobed" name="Convert from BAM to BED" version="@WRAPPER_VERSION@.0">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        bedtools bamtobed
        $option
        $ed_score
        $split
        #if $tag and str($tag).strip():
          -tag "${tag}"
        #end if
        -i "${input}"
        > "${output}"
]]>
    </command>
    <inputs>
        <param format="bam" name="input" type="data" label="Convert the following BAM file to BED"/>
        <param name="option" type="select" label="What type of BED output would you like">
            <option value="">Create a 6-column BED file.</option>
            <option value="-bed12">Create a full, 12-column "blocked" BED file.</option>
            <option value="-bedpe">Create a paired-end, BEDPE format.</option>
        </param>
        <expand macro="split" />
        <param name="ed_score" type="boolean" truevalue="-ed" falsevalue="" checked="false"
            label="Use alignment's edit-distance for BED score" />
        <param name="tag" type="text" optional="true" label="Use other NUMERIC BAM alignment tag as the BED score"
            help="(-tag)"/>
    </inputs>
    <outputs>
        <data format="bed" name="output" metadata_source="input" label="${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).

.. class:: warningmark

If creating a BEDPE output (see output formatting options), the BAM file should be sorted by query name.

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