<?xml version="1.0"?>
<tool id="circos_bundlelinks" name="Circos: Bundle Links" version="@WRAPPER_VERSION@">
    <description>reduce numbers of links in datasets before plotting</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <edam_topics>
        <edam_topic>topic_0797</edam_topic>
        <edam_topic>topic_0092</edam_topic>
    </edam_topics>
    <edam_operations>
        <edam_operation>operation_3436</edam_operation>
    </edam_operations>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
bundlelinks
    #if $max_gap:
        -max_gap $max_gap
    #end if

    -min_bundle_membership $min_bundle_membership

    #if $min_bundle_extent
    -min_bundle_extent $min_bundle_extent
    #end if

    #if $min_bundle_size
    -min_bundle_size $min_bundle_size
    #end if

    #if $min_bundle_identity
    -min_bundle_identity $min_bundle_identity
    #end if

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

    ]]></command>
    <inputs>
        <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="max_gap" type="integer" min="1" optional="true" label="Max Gap" help="Adjacent links are merged into bundles if their start/end coordinates are sufficiently close. Given two links L1 and L2, they are merged into a bundle if: chr( L1 ) == chr( L2 ) AND distance( start(L1), start(L2) ) &lt;= max_gap AND distance( end(L1), end(L2) ) &lt;= max_gap. If a link does not have any acceptable adjacent neighbouring links, it forms a single-link bundle."/>
        <param name="min_bundle_membership" type="integer" value="0" min="0" label="Minimum Bundle Membership" help="The minimum number of links required in a bundle for the bundle to be accepted"/>

        <param name="min_bundle_extent"   type="integer" optional="true" min="0" label="Minimum Bundle Extent"   help="Extent cutoff for a bundle. The extent of a bundle is the end-start value for its start and end. The minimum is taken, so the cutoff test is `min( end1-start1, end2-start2 ) &gt;? cutoff`"/>
        <param name="min_bundle_size"     type="integer" optional="true" min="0" label="Minimum Bundle Size"     help="Size cutoff for a bundle. The size of a bundle is the total size of merged link coordinates for the bundle. There is a separate size for the bundle start (composed of merged link ends that form the bundle start) and bundle end. The minimum is taken, so the cutoff test is `min( size(merged link for start), size(merged link for end) ) &gt;? cutoff`"/>
        <param name="min_bundle_identity" type="float" optional="true"  min="0" max="1" label="Minimum Bundle Identity" help="This parameter filters bundles based on the bundle identity, which is defined as `identity = bundle_size / bundle_extent`. Identity of both ends of the bundle are evaluated independently and the minimum is taken `min( identity(start), identity(end) ) &gt;? cutoff`"/>
    </inputs>
    <outputs>
        <data name="outfile" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="linksfile" value="bundlelinks/1.tab" ftype="tabular" />
            <param name="max_gap" value="1000000" />
            <param name="min_bundle_membership" value="0" />
            <output name="outfile" file="bundlelinks/1.out" ftype="tabular" />
        </test>
    </tests>
    <help><![CDATA[
From the `official documentation <http://circos.ca/documentation/tutorials/utilities/bundling_links/lesson>`__

    The purpose of the bundlelinks tool is to reduce the number of links in a dataset by merging (or bundling) adjacent links together. By merging links, you can distill a visually complex representation into one which effectively summarizes the link structure of your data. A bundle is encoded as a new link with a single start and end position, which are formed by the boundaries of the merged links. Bundles are best shown using the ribbon feature.




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