<tool id="drep_compare" name="dRep compare" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" python_template_version="3.5">
    <description>compare a list of genomes</description>
    <expand macro="biotools" />
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
@PREPARE_GENOMES@
dRep compare outdir
@GENOMES@
@COMPARISON_CLUSTERING_OPTIONS@
@WARNING_OPTIONS@
    ]]></command>
    <inputs>
        <expand macro="genomes"/>
        <expand macro="comparison_clustering_options"/>
        <expand macro="warning_options"/>
        <expand macro="select_outputs"/>
    </inputs>
    <outputs>
        <expand macro="common_outputs" />
    </outputs>
    <tests>
        <test expect_num_outputs="4">
            <expand macro="test_string_inputs"/>
            <expand macro="test_default_comparison_clustering_options"/>
            <expand macro="test_default_warning_options"/>
            <expand macro="test_default_select_outputs"/>
            <expand macro="test_log_output">
                <has_text text="dRep compare finished" />
            </expand>
        </test>
        <test expect_num_outputs="4">
            <expand macro="test_integer_inputs"/>
            <expand macro="test_default_comparison_clustering_options"/>
            <expand macro="test_default_warning_options"/>
            <expand macro="test_default_select_outputs"/>
            <expand macro="test_log_output">
                <has_text text="dRep compare finished" />
            </expand>
        </test>
    </tests>
    <help><![CDATA[
**dRep compare**

`dRep <https://drep.readthedocs.io/en/latest/overview.html>`_ performs rapid pair-wise comparison of genome sets.

`dRep compare <https://drep.readthedocs.io/en/latest/overview.html#genome-comparison>`_ can rapidly and accurately compare a list of genomes in a pair-wise manner. This allows identification of groups of organisms that share similar DNA content in terms of Average Nucleotide Identity (ANI).

dRep performs this in two steps:

  - first with a rapid primary algorithm (Mash)
  - second with a more sensitive algorithm (ANIm).

We can't just use Mash because, while incredibly fast, it is not robust to genome incompletenss (see `Choosing parameters <https://drep.readthedocs.io/en/latest/choosing_parameters.html>`_ and `Module Descriptions <https://drep.readthedocs.io/en/latest/module_descriptions.html>`_) and only provides an “estimate” of ANI. ANIm is robust to genome incompleteness and is more accurate, but too slow to perform pair-wise comparisons of longer genome lists.

dRep first compares all genomes using Mash, and then only runs the secondary algorithm (ANIm or gANI) on sets of genomes that have at least 90% Mash ANI. This results in a great decrease in the number of (slow) secondary comparisons that need to be run while maintaining the sensitivity of ANIm.


**INPUTS**

  - Genome sets in fasta format.


**OUTPUTS**

  - `Figures <https://drep.readthedocs.io/en/latest/example_output.html#figures>`_ that show the relationship of the Genome inputs.
  - `Warnings <https://drep.readthedocs.io/en/latest/example_output.html#warnings>`_ report two things: de-replicated genome similarity and secondary clusters that were almost different.


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