view flankBed.xml @ 45:a1a923cd89e8 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit d1ee301a39e9830693eedb6ca089456081540f28

<tool id="bedtools_flankbed" name="bedtools FlankBed" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
    <description>create new intervals from the flanks of existing intervals</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools" />
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command><![CDATA[
flankBed
$pct
$strand
@GENOME_FILE@
-i '$input'

#if $addition.addition_select == 'b':
    -b $addition.b
#else:
    -l $addition.l
    -r $addition.r
#end if
> '$output'
    ]]></command>
    <inputs>
        <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
        <expand macro="input_conditional_genome_file" />
        <param argument="-pct" type="boolean" truevalue="-pct" falsevalue="" checked="false"
            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" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false"
            label="Define -l and -r based on strand"
            help="For example, if used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate" />
        <expand macro="addition" />
    </inputs>
    <outputs>
        <data name="output" format_source="input" metadata_source="input" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="a.bed" ftype="bed" />
            <param name="genome_file_opts_selector" value="hist" />
            <param name="genome" value="mm9_chr1.len" ftype="tabular"/>
            <param name="addition_select" value="b"/>
            <param name="b" value="5"/>
            <output name="output" file="flankBed_result1.bed" ftype="bed" />
        </test>
        <test>
            <param name="input" value="a.bed" ftype="bed" />
            <param name="genome_file_opts_selector" value="hist" />
            <param name="genome" value="mm9_chr1.len" ftype="tabular"/>
            <param name="addition_select" value="lr"/>
            <param name="l" value="2"/>
            <param name="r" value="3"/>
            <output name="output" file="flankBed_result2.bed" ftype="bed" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

bedtools flank will optionally create flanking intervals whose size is user-specified fraction of the original interval.

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

.. class:: warningmark

In order to prevent creating intervals that violate chromosome boundaries, bedTools flank requires a bedTool genome file defining the length of each chromosome or contig. . This should be a two column tabular file with the chromosome name in the first column and the END coordinate of the chromosome in the second column.

If you need this data for any genome that is at UCSC (http://genome.ucsc.edu), it can be extracted from the Table Browser with the "Get Data: UCSC Main" tool. Set "group" to "All Tables", "table" to "chromInfo", and "output format" to "all fields from selected table".

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