<tool id="khmer_abundance_distribution" name="khmer: Abundance Distribution" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>
        Calculate abundance distribution of k-mers using pre-made k-mer countgraphs
    </description>
    <macros>
        <token name="@BINARY@">abundance-dist.py</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version" />
    <command><![CDATA[
set -u &&
@BINARY@
--squash
${zero}
${bigcount}
${input_countgraph_filename}
${input_sequence_filename}
${output_histogram_filename}
]]>
    </command>
    <inputs>
        <expand macro="input_countgraph_filename" />
        <expand macro="input_sequence_filename" />
        <expand macro="input_zero" />
        <expand macro="input_bigcount" />
    </inputs>
    <outputs>
        <expand macro="abundance-histogram-output" />
    </outputs>
    <tests>
        <test>
            <param name="input_sequence_filename" value="test-abund-read-2.fa" />
            <param name="input_countgraph_filename" value="test-abund-read-2.oxlicg" ftype="oxlicg" />
            <param name="zero" value="false" />
            <output name="output_histogram_filename">
                <assert_contents>
                    <has_text text="1,96,96,0.98" />
                    <has_text text="1001,2,98,1.0" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input_sequence_filename" value="test-abund-read-2.fa.gz" />
            <param name="input_countgraph_filename" value="test-abund-read-2.oxlicg" ftype="oxlicg" />
            <param name="zero" value="false" />
            <param name="bigcount" value="false" />
            <output name="output_histogram_filename">
                <assert_contents>
                    <has_text text="1,96,96,0.98" />
                    <has_text text="255,2,98,1.0" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
Calculate abundance distribution of the k-mers in the sequence file using a
pre-made k-mer countgraph.

@ABUNDANCE_HISTOGRAM_OUTPUT_HELP@

@HELP_FOOTER@
]]>
    </help>
    <citations>
        <expand macro="software-citation" />
        <expand macro="counting-citation" />
    </citations>
</tool>