Mercurial > repos > iuc > circos
comparison bundlelinks.xml @ 2:890ef899a3d7 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
| author | iuc |
|---|---|
| date | Tue, 17 Sep 2019 16:54:24 -0400 |
| parents | |
| children | 74146c252453 |
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| 1:95664f8de269 | 2:890ef899a3d7 |
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| 1 <?xml version="1.0"?> | |
| 2 <tool id="circos_bundlelinks" name="Circos: Bundle Links" version="@WRAPPER_VERSION@"> | |
| 3 <description>reduce numbers of links in datasets before plotting</description> | |
| 4 <macros> | |
| 5 <import>macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="requirements" /> | |
| 8 <command detect_errors="exit_code"><![CDATA[ | |
| 9 bundlelinks | |
| 10 #if $max_gap: | |
| 11 -max_gap $max_gap | |
| 12 #end if | |
| 13 | |
| 14 -min_bundle_membership $min_bundle_membership | |
| 15 | |
| 16 #if $min_bundle_extent | |
| 17 -min_bundle_extent $min_bundle_extent | |
| 18 #end if | |
| 19 | |
| 20 #if $min_bundle_size | |
| 21 -min_bundle_size $min_bundle_size | |
| 22 #end if | |
| 23 | |
| 24 #if $min_bundle_identity | |
| 25 -min_bundle_identity $min_bundle_identity | |
| 26 #end if | |
| 27 | |
| 28 < '$linksfile' | sed 's/ /\t/g' > '$outfile' | |
| 29 | |
| 30 ]]></command> | |
| 31 <inputs> | |
| 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."/> | |
| 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) ) <= max_gap AND distance( end(L1), end(L2) ) <= max_gap. If a link does not have any acceptable adjacent neighbouring links, it forms a single-link bundle."/> | |
| 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"/> | |
| 35 | |
| 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 ) >? cutoff`"/> | |
| 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) ) >? cutoff`"/> | |
| 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) ) >? cutoff`"/> | |
| 39 </inputs> | |
| 40 <outputs> | |
| 41 <data name="outfile" format="tabular" /> | |
| 42 </outputs> | |
| 43 <tests> | |
| 44 <test> | |
| 45 <param name="linksfile" value="bundlelinks/1.tab" ftype="tabular" /> | |
| 46 <param name="max_gap" value="1000000" /> | |
| 47 <param name="min_bundle_membership" value="0" /> | |
| 48 <output name="outfile" file="bundlelinks/1.out" ftype="tabular" /> | |
| 49 </test> | |
| 50 </tests> | |
| 51 <help><![CDATA[ | |
| 52 From the `official documentation <http://circos.ca/documentation/tutorials/utilities/bundling_links/lesson>`__ | |
| 53 | |
| 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. | |
| 55 | |
| 56 | |
| 57 | |
| 58 | |
| 59 ]]></help> | |
| 60 <expand macro="citations" /> | |
| 61 </tool> |