<?xml version="1.0"?>
<tool id="circos_wiggle_to_stacked" name="Circos: Stack bigWigs as Histogram" version="@WRAPPER_VERSION@">
    <description>reformats for use in Circos stacked histogram plots</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
    </expand>
    <edam_topics>
        <edam_topic>topic_0797</edam_topic>
        <edam_topic>topic_0092</edam_topic>
    </edam_topics>
    <edam_operations>
        <edam_operation>operation_0335</edam_operation>
    </edam_operations>
    <command detect_errors="exit_code"><![CDATA[
python
    '$__tool_directory__/stack-histogram.py'
    #for i in $input
        '$i'
    #end for
    > '$output'
    ]]></command>
    <inputs>
        <param name="input" type="data" format="bigwig" label="BigWig files" multiple="True" help="These MUST have identical chromosomes and intervals, within their datasets. This tool is incredibly, intentionally naïve, and will crash if there are missing ranges in some bigwig files. This feels like a reasonable assumption to make (simplifies processing) at the expense of theoretical correctness, given that when you are stacking histograms they're probably coming from the same upstream pipeline with the same settings (i.e. step/width/etc.)"/>
    </inputs>
    <outputs>
        <data name="output" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="scatter/1.bw,scatter/1.bw,scatter/1.bw" ftype="bigwig" />
            <output name="output" file="scatter/1.multi.out" ftype="tabular" />
        </test>
    </tests>
    <help><![CDATA[
Converts standard bigWig files into a format appropriate for Circos stacked histogram plots

If you need to process bedgraph, please convert those to bigwig first.
    ]]></help>
    <expand macro="citations" />
</tool>