<tool id="bedtools_bedtobam" name="bedtools BED to BAM" version="@TOOL_VERSION@" profile="@PROFILE@">
    <description>converter</description>
    <expand macro="bio_tools" />
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command><![CDATA[
bedtools bedtobam
$bed12
-mapq $mapq
-g @GENOME_FILE@
-i '$input'
> '$output'
    ]]></command>
    <inputs>
        <param name="input" argument="-i" type="data" format="bed" label="Convert the following BED file to BAM"/>
        <param argument="-bed12" type="boolean" truevalue="-bed12" falsevalue="" checked="false"
            label="Indicate that the input BED file is in BED12 (a.k.a 'blocked' BED) format"
            help="If Selected, bedToBam will convert blocked BED features (e.g., gene annotaions) into 'spliced' BAM alignments by creating an appropriate CIGAR string"/>
        <expand macro="input_conditional_genome_file" />
        <param argument="-mapq" type="integer" value="255"
            label="Set a mapping quality (SAM MAPQ field) value for all BED entries" />
    </inputs>
    <outputs>
        <data name="output" format="bam" metadata_source="input" label="${input.name} (as BAM)"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="bedToBam1.bed" ftype="bed" />
            <param name="genome_file_opts_selector" value="hist" />
            <param name="genome" value="mm9_chr1.len" ftype="tabular" />
            <output name="output" file="bedToBam_result.bam" lines_diff="4" ftype="bam" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

bedToBam converts features in a feature file to BAM format. This is useful as an efficient means of storing large genome annotations in a compact, indexed format for visualization purposes.

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