<tool id="bedtools_bedtoigv" name="bedtools BED to IGV" version="@TOOL_VERSION@">
    <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 name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="Create IGV batch script for this @STD_BEDTOOLS_INPUT_LABEL@ 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 argument="-clps" type="boolean" truevalue="-clps" falsevalue="" label="Collapse the aligned reads prior to taking a snapshot?"/>
        <param argument="-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 argument="-slop" type="integer" min="0" value="0" label="Number of flanking base pairs on the left and right of the image."/>
        <param argument="-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 name="output" format="txt" 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 @STD_BEDTOOLS_INPUT_LABEL@ 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>