annotate binlinks.xml @ 5:a64dc31ab7f2 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 39a0176dab234a07118a79ac44ca7d79469d3b91"

<?xml version="1.0"?>
<tool id="circos_binlinks" name="Circos: Link Density Track" version="@WRAPPER_VERSION@">
    <description>reduce links to a density plot</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
binlinks
    -bin_size $bin_size
    #if str($link_end) != '':
        -link_end '$link_end'
    #end if

    #if str($output_style) != '':
        -output_style $output_style
    #end if

    $num
    $log
    $normalize

    < '$linksfile' | sed 's/ /\t/g' > '$outfile'

    ]]></command>
    <inputs>
        <param name="bin_size" type="integer" label="Bin Size" min="0" value="1000000"/>
        <param name="linksfile" type="data" format="tabular" label="Links file" help="This should be a 6 column (or 7 with additional k=v pairs) tabular file of link data."/>

        <param name="link_end" type="select" label="Link End Behaviour" help="Controls which end(s) of the link are processed for each bin. The start of the link is considered to be the end defined by the first link line, and the link end is defined by the second link line. For example, if -link_end=start then a bin will contain the sum (or number if -num is used) of links that start at that bin. If -link_end==end then links that end at that bin will be used. Finally, -link_end=both will make the bin value reflect the total outgoing and incoming links. (from the Circos Manual)">
            <option value="" selected="True">Default</option>
            <option value="0">Start</option>
            <option value="1">End</option>
            <option value="2">Both</option>
        </param>

        <param name="output_style" type="select" label="Output Style" help="Controls which end(s) of the link are processed for each bin. The start of the link is considered to be the end defined by the first link line, and the link end is defined by the second link line. For example, if -link_end=start then a bin will contain the sum (or number if -num is used) of links that start at that bin. If -link_end==end then links that end at that bin will be used. Finally, -link_end=both will make the bin value reflect the total outgoing and incoming links. (from the Circos Manual)">
            <option value="" selected="True">Default</option>
            <option value="0">Link density</option>
            <option value="1">Link density for largest contribution</option>
            <option value="2">Link density for each target chromosome</option>
            <option value="3">Link density for each target chromosome (stacked histogram)</option>
        </param>

        <param name="num" type="boolean" truevalue="-num" falsevalue="" label="Use number of links rather than sum of ends" help="If the end of a link spans bins, each bin will contain a +1 contribution from the link. In other words, the sum of bin values may be larger than the number of links. (from the Circos Manual)"/>
        <param name="log" type="boolean" truevalue="-log" falsevalue="" label="Calculate log10 of the values."/>
        <param name="normalize" type="boolean" truevalue="-normalize" falsevalue="" label="Normalize" help="This only works when you select 'stacked histograms' in the 'Output Style' section."/>
        <!--<param name="color_by_chr" type="boolean" truevalue="yes" falsevalue="no" label="" "/>-->
    </inputs>
    <outputs>
        <data name="outfile" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="linksfile" value="binlinks/1.tab" ftype="tabular" />
            <param name="bin_size" value="1000000" />
            <output name="outfile" file="binlinks/1.out" ftype="tabular" />
        </test>
    </tests>
    <help><![CDATA[
From the `official documentation <http://circos.ca/documentation/tutorials/utilities/density_tracks/>`__

    The purpose of this script is to generate data for histogram and highlight tracks that stores the number, size and consensus position of links. All chromosomes in the input link file are divided into bins (controlled by -bin_size), and link statistics are calculated on a bin-by-bin basis.
    ]]></help>
    <expand macro="citations" />
</tool>