annotate abundance-dist-single.xml @ 10:65b382bf9b7c draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997

<tool id="khmer_abundance_distribution_single" name="khmer: Abundance Distribution (all-in-one)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>
        Calculate abundance distribution of k-mers
    </description>
    <macros>
        <token name="@BINARY@">abundance-dist-single.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@
@TABLEPARAMS@
${zero}
${bigcount}
#if $save_countgraph
    --savegraph=${optional_output_countgraph}
#end if
--squash
@THREADS@
${input_sequence_filename}
${output_histogram_filename}

]]>
    </command>
    <inputs>
        <expand macro="input_sequence_filename" />
        <param argument="--savegraph" name="save_countgraph" type="boolean" label="Save the k-mer countgraph to a file"
            help="" />
        <expand macro="input_zero" />
        <expand macro="input_bigcount" />
        <expand macro="tableinputs" />
    </inputs>
    <outputs>
        <data name="optional_output_countgraph" format="oxlicg" label="${tool.name} on ${on_string}: k-mer countgraph">
            <filter>save_countgraph == True</filter>
        </data>
        <expand macro="abundance-histogram-output" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input_sequence_filename" value="test-abund-read-2.fa" />
            <param name="type" value="specific" />
            <param name="tablesize_specific" value="1e7" />
            <param name="n_tables" value="2" />
            <param name="ksize" value="17" />
            <param name="no_zero" value="false" />
            <output name="output_histogram_filename" ftype="csv">
                <assert_contents>
                    <has_text text="1,96,96,0.98" />
                    <has_text text="1001,2,98,1.0" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="2">
            <param name="input_sequence_filename" value="test-abund-read-2.fq.gz" />
            <param name="type" value="specific" />
            <param name="tablesize_specific" value="1e7" />
            <param name="n_tables" value="2" />
            <param name="ksize" value="17" />
            <param name="no_zero" value="false" />
            <param name="bigcount" value="false" />
            <param name="save_countgraph" value="true"/>
            <output name="output_histogram_filename" ftype="csv">
                <assert_contents>
                    <has_text text="1,96,96,0.98" />
                    <has_text text="255,2,98,1.0" />
                </assert_contents>
            </output>
            <output name="optional_output_countgraph">
                <assert_contents>
                    <has_size size="1k"/>
                </assert_contents>
            </output>
        </test>

    </tests>
    <help><![CDATA[
Calculate the abundance distribution of k-mers from a single sequence file.

Note that with `-b` this script is constant memory; in exchange,
k-mer counts will stop at 255. The memory usage of this script with
`-b` will be about 1.15x the product of the `-x` and
`-N` numbers.

@ABUNDANCE_HISTOGRAM_OUTPUT_HELP@

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