view randomBed.xml @ 40:a68aa6c1204a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 29bd1be4655cd26052095a49a8e188d2572b703b"

<tool id="bedtools_randombed" name="bedtools RandomBed" version="@TOOL_VERSION@" profile="@PROFILE@">
    <description>generate random intervals in a genome</description>
    <expand macro="bio_tools" />
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command><![CDATA[
bedtools random
-g @GENOME_FILE@
-l $length
-n $intervals
#if str($seed.seed_choose) == "True":
    -seed $seed.seed
#end if
> '$output'
    ]]></command>
    <inputs>
        <expand macro="input_conditional_genome_file" />
        <param name="length" argument="-l" type="integer" value="100" label="The length of the intervals to generate" />
        <param name="intervals" argument="-n" type="integer" value="1000000" label="The number of intervals to generate" />
        <expand macro="seed" />
    </inputs>
    <outputs>
        <data name="output" format="bed" />
    </outputs>
    <tests>
        <test>
            <param name="genome_file_opts_selector" value="hist" />
            <param name="genome" value="mm9_chr1.len" />
            <param name="seed_choose" value="False" />
            <param name="length" value="5" />
            <param name="intervals" value="3" />
            <output name="output">
                <assert_contents>
                    <has_text_matching expression="chr1" />
                    <has_n_columns n="6" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

bedtools random will generate a random set of intervals in BED6 format. One can specify both the number (-n) and the size (-l) of the intervals that should be generated.

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