annotate sort-bed.xml @ 0:baeee32175e8 draft default tip

planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca

<tool id="bedops-sort-bed" name="bedops sort-bed" version="@TOOL_VERSION@" profile="22.01">
    <macros>
        <token name="@TOOL_VERSION@">2.4.41</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">bedops</requirement>
    </requirements>
    <command><![CDATA[
sort-bed 
--max-mem "\${GALAXY_MEMORY_MB:-1024}M"
--tmpdir "\${_GALAXY_JOB_TMP_DIR:-.}"
$unique
$duplicates
#for file in $inputs:
    '$file'
#end for
> '$output'
    ]]></command>
    <inputs>
        <param name="inputs" type="data" format="bed" multiple="true"/>
        <param argument="--unique" type="boolean" truevalue="--unique" falsevalue="" label="Output only unique elements?"/>
        <param argument="--duplicates" type="boolean" truevalue="--duplicates" falsevalue="" label="Output only duplicate elements?"/>
    </inputs>
    <outputs>
        <data name="output" format_source="inputs" label="$tool.name: sorted output"/>
    </outputs>
    <tests>
        <test>
            <param name="inputs" value="unsorted.bed" ftype="bed"/>
            <output name="output" value="sorted_simpled.bed"/>
        </test>
        <test>
            <param name="inputs" value="unsorted.bed" ftype="bed"/>
            <param name="unique" value="true"/>
            <output name="output" value="sorted_unique.bed"/>
        </test>
        <test>
            <param name="inputs" value="unsorted.bed" ftype="bed"/>
            <param name="duplicates" value="true"/>
            <output name="output" value="sorted_duplicates.bed"/>
        </test>
    </tests>
    <help><![CDATA[
What this tool does
===================

The sort-bed utility sorts BED files of any size, even larger than system memory. BED files that are in lexicographic-chromosome order allow BEDOPS utilities to work efficiently with data from any species without software modifications. Further, sorted files can be traversed very quickly.

Sorted BED order is defined first by lexicographic chromosome order, then ascending integer start coordinate order, and finally by ascending integer end coordinate order. To make the sort order unambiguous, a lexicographical sort is applied on fourth and subsequent columns, where present in the input BED dataset.


Input
=====

The sort-bed utility requires one or more three-column BED file(s). Support for common headers (such as UCSC BED track headers) is included, although headers will be stripped from the output.


Output
======

Sort order is defined by a lexicographical sort on chromosome name, a numerical sort on start coordinates, a numerical sort on stop coordinates where there are start matches, and finally a lexicographical sort on the remainder of the BED element (if additional columns are present). Additional options may be specified to print only unique or duplicate elements.
    ]]></help>
    <citations>
        <citation type="doi">https://doi.org/10.1093/bioinformatics/bts277</citation>
    </citations>
</tool>