annotate gemini_windower.xml @ 8:406d3552beca draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd

<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">
    <description>Compute sliding window statistics from variants</description>
    <expand macro="bio_tools"/>
    <macros>
        <import>gemini_macros.xml</import>
        <token name="@BINARY@">windower</token>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
<![CDATA[
        gemini @BINARY@
            -w $w
            -s $s
            -t $window_analysis
            -o $operation
            '$infile'
            > '$outfile'
]]>
    </command>
    <inputs>
        <expand macro="infile" />

        <param argument="-t" name="window_analysis" type="select"
        label="The type of window analysis requested?" help="">
            <option value="nucl_div">(nucl_div)</option>
            <option value="hwe">(hwe)</option>
        </param>

        <param argument="-o" name="operation" type="select"
        label="The operation that should be applied to the -t values" help="">
            <option value="mean">mean</option>
            <option value="median">median</option>
            <option value="min">min</option>
            <option value="max">max</option>
            <option value="collapse">collapse</option>
        </param>

        <param argument="-w" name="w" type="integer" value="10000" min="2"
        label="Window size in bp" help="" />
        <param argument="-s" name="s" type="integer" value="1000" min="0"
        label="Step size for sliding the window in bp" help="Specify 0 here for sliding by one full window size" />
    </inputs>
    <outputs>
        <data name="outfile" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
            <param name="w" value="50000" />
            <param name="s" value="50000000" />
            <param name="window_analysis" value="nucl_div" />
            <param name="operation" value="mean" />
            <output name="outfile" file="gemini_windower_template.tabular" compare="re_match" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Compute variation metrics across genomic windows.

**Examples**

Compute the average nucleotide diversity for all variants found in non-overlapping, 50Kb windows::

 -w 50000 
 -s 0 
 -t nucl_div 
 -o mean

Compute the average nucleotide diversity for all variants found in 50Kb windows that overlap by 40kb::

 -w 50000
 -s 10000
 -t nucl_div
 -o mean 

Compute the max value for HWE statistics for all variants in 10kb windows every 100kb along the genome::

 -w 10000
 -s 100000
 -t hwe
 -o max

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