comparison linksBed.xml @ 34:dde39ba9c031 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95

33:87ee588b3d45

<tool id="bedtools_links" name="bedtools LinksBed" version="@WRAPPER_VERSION@">
    <description>create a HTML page of links to UCSC locations</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        bedtools links
            -base "${basename}"
            -org "${org}"
            -db "${db}"
            -i "${input}"
            > "${output}"
]]>
    </command>
    <inputs>
        <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
        <param name="basename" type="text" value="http://genome.ucsc.edu"
            label="The 'basename' for the UCSC genome browser" />
        <param name="org" type="text" value="human" label="Organism name" help="e.g. mouse, human (-org)" />
        <param name="db" type="text" value="hg19" label="The genome build" help="(-db)"/>
    </inputs>
    <outputs>
        <data name="output" format="html" />
    </outputs>
    <tests>

            <param name="org" value="mouse" />
            <param name="db" value="mm9" />
            <output name="output" file="linksBed_result2.html" lines_diff="2" ftype="html" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

Creates an HTML file with links to an instance of the UCSC Genome Browser for all features / intervals in a file. This is useful for cases when one wants to manually inspect through a large set of annotations or features.

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

34:dde39ba9c031

<tool id="bedtools_links" name="bedtools LinksBed" version="@TOOL_VERSION@">
    <description>create a HTML page of links to UCSC locations</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command><![CDATA[
bedtools links
-base '${basename}'
-org '${org}'
-db '${db}'
-i '${input}'
> '${output}'
    ]]></command>
    <inputs>
        <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
        <param name="basename" argument="-base" type="text" value="http://genome.ucsc.edu"
            label="The 'basename' for the UCSC genome browser" />
        <param argument="-org" type="text" value="human" label="Organism name" help="E.g. mouse, human" />
        <param argument="-db" type="text" value="hg19" label="The genome build" />
    </inputs>
    <outputs>
        <data name="output" format="html" />
    </outputs>
    <tests>

            <param name="org" value="mouse" />
            <param name="db" value="mm9" />
            <output name="output" file="linksBed_result2.html" lines_diff="2" ftype="html" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Creates an HTML file with links to an instance of the UCSC Genome Browser for all features / intervals in a file. This is useful for cases when one wants to manually inspect through a large set of annotations or features.

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