view flankBed.xml @ 32:4f7a5ccd2ae9 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
author iuc
date Tue, 11 Dec 2018 14:01:26 -0500
parents db1841942d2b
children dde39ba9c031
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<tool id="bedtools_flankbed" name="bedtools FlankBed" version="@WRAPPER_VERSION@">
    <description>create new intervals from the flanks of existing intervals</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        flankBed
        $pct
        $strand
        -g @GENOME_FILE@
        -i '$input'

        #if $addition.addition_select == 'b':
            -b $addition.b
        #else:
            -l $addition.l
            -r $addition.r
        #end if
        > '$output'
]]>
    </command>
    <inputs>
        <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ 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”. (-pct)" />
        <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue=""
            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. (-s)" />
        <expand macro="addition" />
    </inputs>
    <outputs>
        <data metadata_source="input" format_source="input" name="output" />
    </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"/>
            <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"/>
            <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>