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annotate bundlelinks.xml @ 2:014a21767ac4 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
author iuc
date Tue, 17 Sep 2019 16:54:57 -0400
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children df7356989ac1
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014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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1 <?xml version="1.0"?>
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2 <tool id="circos_bundlelinks" name="Circos: Bundle Links" version="@WRAPPER_VERSION@">
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3 <description>reduce numbers of links in datasets before plotting</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 bundlelinks
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10 #if $max_gap:
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11 -max_gap $max_gap
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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12 #end if
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014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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14 -min_bundle_membership $min_bundle_membership
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16 #if $min_bundle_extent
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17 -min_bundle_extent $min_bundle_extent
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18 #end if
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20 #if $min_bundle_size
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21 -min_bundle_size $min_bundle_size
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22 #end if
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24 #if $min_bundle_identity
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25 -min_bundle_identity $min_bundle_identity
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26 #end if
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28 < '$linksfile' | sed 's/ /\t/g' > '$outfile'
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30 ]]></command>
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31 <inputs>
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32 <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."/>
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33 <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."/>
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34 <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"/>
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35
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36 <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`"/>
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37 <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`"/>
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38 <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`"/>
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39 </inputs>
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40 <outputs>
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41 <data name="outfile" format="tabular" />
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42 </outputs>
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43 <tests>
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44 <test>
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45 <param name="linksfile" value="bundlelinks/1.tab" ftype="tabular" />
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46 <param name="max_gap" value="1000000" />
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47 <param name="min_bundle_membership" value="0" />
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48 <output name="outfile" file="bundlelinks/1.out" ftype="tabular" />
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49 </test>
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50 </tests>
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51 <help><![CDATA[
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52 From the `official documentation <http://circos.ca/documentation/tutorials/utilities/bundling_links/lesson>`__
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53
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54 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.
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59 ]]></help>
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60 <expand macro="citations" />
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61 </tool>