<tool id="crossmap_wig" name="CrossMap Wig" version="@WRAPPER_VERSION@">
    <description>Convert genome coordinates or annotation files between genome assemblies</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
CrossMap.py wig
'${chain_source.input_chain}'
'${input}'
output
    ]]></command>

    <inputs>
        <param name="input" type="data" format="wig" label="Wiggle file"/>

        <expand macro="chain" />
    </inputs>

    <outputs>
        <data name="output" format="bigwig" label="${tool.name} on ${on_string}" from_work_dir="output.bw" />
        <data name="output2" format="bedgraph" label="${tool.name} (bedgraph) on ${on_string}" from_work_dir="output.sorted.bgr" />
    </outputs>

    <tests>
    <!-- WIG - Doesn't understand fixedStep -->
        <test>
            <param name="input" value="test_wig_01_input_a.wig" ftype="wig"/>
            <param name="index_source" value="history"/>
            <param name="input_chain" value="aToB.over.chain" ftype="csv"/>

            <output name="output" file="test_wig_01_output_a.bw"/>
            <output name="output2" file="test_wig_01_output_a.sorted.bgr"/>
        </test>

        <test><!-- cached reference genome -->
            <param name="input" value="test_wig_01_input_a.wig" ftype="wig" dbkey="hg18" />
            <param name="index_source" value="cached"/>

            <output name="output" file="test_wig_01_output_a.bw"/>
            <output name="output2" file="test_wig_01_output_a.sorted.bgr"/>
        </test>
    </tests>
    <help><![CDATA[
@HELP_GENERAL@

Wig
---

Input wiggle data can be in variableStep (for data with irregular
intervals) or fixedStep (for data with regular intervals). Regardless of
the input, the output will always in bedGraph format. bedGraph format is
similar to wiggle format and can be converted into BigWig format using UCSC
wigToBigWig tool. We export files in bedGraph because it is usually much
smaller than file in wiggle format, and more importantly, CrossMap
internally transforms wiggle into bedGraph to increase running speed.
    ]]></help>

    <citations>
        <citation type="doi">10.1093/bioinformatics/btt730</citation>
    </citations>
</tool>