annotate slopBed.xml @ 24:33c3ddea63c5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 09721a12bdd393441b162056316241aba3895a4f

<tool id="bedtools_slopbed" name="SlopBed" version="@WRAPPER_VERSION@.0">
    <description>adjust the size of intervals</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        bedtools slop
        $pct
        $strand
        -g @GENOME_FILE@
        -i '$inputA'
        #if $addition.addition_select == 'b':
            -b $addition.b
        #else:
            -l $addition.l
            -r $addition.r
        #end if
        $header
        > '$output'
]]>
    </command>
    <inputs>
        <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
        <expand macro="input_conditional_genome_file" />
        <param name="pct" type="boolean" checked="false" truevalue="-pct" falsevalue=""
            label="Define -l and -r as a fraction of the feature’s length"
            help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”" />
        <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue=""
            label="Define -l and -r based on strand"
            help="If used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate" />
        <expand macro="addition" />
        <expand macro="print_header" />
    </inputs>
    <outputs>
        <data format="bed" name="output"/>
    </outputs>
    <tests>
        <test>
            <param name="inputA" value="a.bed" ftype="bed" />
            <param name="genome_file_opts_selector" value="hist" />
            <param name="genome" value="mm9_chr1.len" ftype="bed" />
            <param name="addition_select" value="b" />
            <param name="b" value="5" />
            <output name="output" file="slopBed_result1.bed" ftype="bed" />
        </test>
        <test>
            <param name="inputA" value="a.bed" ftype="bed" />
            <param name="genome_file_opts_selector" value="hist" />
            <param name="genome" value="mm9_chr1.len" ftype="bed" />
            <param name="addition_select" value="lr" />
            <param name="l" value="2" />
            <param name="r" value="3" />
            <output name="output" file="slopBed_result2.bed" ftype="bed" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

bedtools slop will increase the size of each feature in a feature file by a user-defined number of bases. While something like this could be done with an awk '{OFS="\t" print $1,$2-&lt;slop>,$3+&lt;slop>}', bedtools slop will restrict the resizing to the size of the chromosome (i.e. no start &lt; 0 and no end > chromosome size).

.. image:: $PATH_TO_IMAGES/slop-glyph.png

.. class:: warningmark

In order to prevent the extension of intervals beyond chromosome boundaries, bedtools slop requires a genome file defining the length of each chromosome or contig.
@REFERENCES@
]]>
    </help>
    <expand macro="citations" />
</tool>