<?xml version="1.0"?>
<tool id="circos_interval_to_tile" name="Circos: Interval to Tiles" version="@WRAPPER_VERSION@">
    <description>reformats interval files to prepare for Circos tile plots</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <edam_topics>
        <edam_topic>topic_0797</edam_topic>
        <edam_topic>topic_0092</edam_topic>
    </edam_topics>
    <edam_operations>
        <edam_operation>operation_3434</edam_operation>
    </edam_operations>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
python
#if $ref.ref_source == 'gff3':
    '$__tool_directory__/tiles-from-gff3.py' '$input' '${ref.attr}'
#else
    '$__tool_directory__/tiles-from-bed.py' '$input'
#end if
> '$output'
    ]]></command>
    <inputs>
        <conditional name="ref">
            <param name="ref_source" type="select" label="Data Format">
                <option value="bed" selected="true">BED6+</option>
                <option value="gff3">GFF3</option>
            </param>
            <when value="bed">
                <param name="input" type="data" format="bed" label="BED File (BED6+ only)" />
            </when>
            <when value="gff3">
                <param name="input" type="data" format="gff3" label="GFF3 File" />
                <param name="attr" type="text" label="GFF3 Attribute to pull value from" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output" format="tabular" />
    </outputs>
    <tests>
        <test>
            <conditional name="ref">
                <param name="ref_source" value="bed" />
                <param name="input" value="tiles/1.bed" ftype="bed" />
            </conditional>
            <output name="output" file="tiles/1.out" ftype="tabular" />
        </test>
        <test>
            <conditional name="ref">
                <param name="ref_source" value="gff3" />
                <param name="input" value="tiles/2.gff3" ftype="gff3" />
                <param name="attr" value="Name" />
            </conditional>
            <output name="output" file="tiles/2.out" ftype="tabular" />
        </test>
    </tests>
    <help><![CDATA[
Converts standard BED3+ and GFF3 files into a format appropriate for Circos data tracks, especially tile tracks.

BED3 files do not need conversion, Circos can accept these files directly.
    ]]></help>
    <expand macro="citations" />
</tool>