<tool id="bedtools_bedtoigv" name="BED to IGV" version="@WRAPPER_VERSION@.0">
    <description>create batch script for taking IGV screenshots</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        bedToIgv
        -i '$input'
        #if $sort:
            -sort $sort
        #end if
        $clps
        $name
        -slop $slop
        -img $img
        > '$output'
]]>
    </command>
    <inputs>
        <param format="bed,gff,gff3,vcf" name="input" type="data" label="Create IGV batch script the following BED file"/>
        <param name="sort" type="select" label="Sort BAM file by" help="The type of BAM sorting you would like to apply to each image.">
            <option value="">No sorting at all (default)</option>
            <option value="base">base</option>
            <option value="position">position</option>
            <option value="strand">strand</option>
            <option value="quality">quality</option>
            <option value="sample">sample</option>
            <option value="readGroup">readGroup</option>
        </param>
        <param name="clps" type="boolean" truevalue="-clps" falsevalue="" label="Collapse the aligned reads prior to taking a snapshot?"/>
        <param name="name" type="boolean" truevalue="-name" falsevalue="" label="Use the name field (column 4) for each image's filename." help="Default is to use chr:start-pos."/>
        <param name="slop" type="integer" min="0" value="0" label="Number of flanking base pairs on the left and right of the image."/>
        <param name="img" type="select" label="Select the type of image to be created.">
            <option value="png">png</option>
            <option value="eps">eps</option>
            <option value="svg">svg</option>
        </param>
    </inputs>
    <outputs>
        <data format="txt" name="output" metadata_source="input" label="BED to IGV on ${input.name}"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="bed12.bed" ftype="bed" />
            <output name="output" file="igv_bed_script.txt" ftype="txt" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

Creates a batch script to create IGV images at each interval defined in a BED/GFF/VCF file.

**Notes**

(1)  The resulting script is meant to be run from within IGV.
(2)  It is assumed that prior to running the script, you've loaded the proper genome and tracks.

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