Mercurial > repos > iuc > ucsc_netchainsubset

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netchainsubset commit 203061071dae562277de62b43680fc9bae853f35
author iuc
date Wed, 14 Jan 2026 09:16:58 +0000
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6d5ab8d81db2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netchainsubset commit 203061071dae562277de62b43680fc9bae853f35
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1 <tool id="ucsc_netchainsubset" name="netChainSubset" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT">
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2 <description>
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3 Create chain file with subset of chains that appear in the net
6d5ab8d81db2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netchainsubset commit 203061071dae562277de62b43680fc9bae853f35
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4 </description>
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5 <macros>
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6 <token name="@TOOL_VERSION@">482</token>
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7 </macros>
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8 <xrefs>
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9 <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
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10 </xrefs>
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11 <requirements>
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12 <requirement type="package" version="@TOOL_VERSION@">ucsc-netchainsubset</requirement>
6d5ab8d81db2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netchainsubset commit 203061071dae562277de62b43680fc9bae853f35
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13 </requirements>
6d5ab8d81db2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netchainsubset commit 203061071dae562277de62b43680fc9bae853f35
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14 <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
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15 <command detect_errors="exit_code"><![CDATA[
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16 netChainSubset
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17 '$in_net'
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18 '$in_chain'
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19 '$out'
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20 $splitOnInsert
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21 $wholeChains
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22 $skipMissing
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23 ]]></command>
6d5ab8d81db2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netchainsubset commit 203061071dae562277de62b43680fc9bae853f35
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24 <inputs>
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25 <param name="in_net" format="ucsc.net" type="data" label="net dataset" help="" />
6d5ab8d81db2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netchainsubset commit 203061071dae562277de62b43680fc9bae853f35
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26 <param name="in_chain" format="chain" type="data" label="chain dataset" help="" />
6d5ab8d81db2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netchainsubset commit 203061071dae562277de62b43680fc9bae853f35
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27 <param argument="-splitOnInsert" type="boolean" optional="true" truevalue="-splitOnInsert" falsevalue="" label="Split on insert" help="Split chain when get an insertion of another chain." />
6d5ab8d81db2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netchainsubset commit 203061071dae562277de62b43680fc9bae853f35
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28 <param argument="-wholeChains" type="boolean" optional="true" truevalue="-wholeChains" falsevalue="" label="Whole chains" help="Write entire chain references by net, don't split when a high-level net is encoundered. This is useful when nets have been filtered." />
6d5ab8d81db2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netchainsubset commit 203061071dae562277de62b43680fc9bae853f35
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29 <param argument="-skipMissing" type="boolean" optional="true" truevalue="-skipMissing" falsevalue="" label="Skip missing chains" help="Skip chains that are not found instead of generating an error. Useful if chains have been filtered." />
6d5ab8d81db2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netchainsubset commit 203061071dae562277de62b43680fc9bae853f35
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30 </inputs>
6d5ab8d81db2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netchainsubset commit 203061071dae562277de62b43680fc9bae853f35
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31 <outputs>
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32 <data name="out" format="chain" />
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33 </outputs>
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34 <tests>
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35 <test expect_num_outputs="1">
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36 <param name="in_net" value="target.net" />
6d5ab8d81db2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netchainsubset commit 203061071dae562277de62b43680fc9bae853f35
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37 <param name="in_chain" value="in.chain" />
6d5ab8d81db2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netchainsubset commit 203061071dae562277de62b43680fc9bae853f35
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38 <output name="out" file="out.chain" />
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39 </test>
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40 </tests>
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41 <help><![CDATA[
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42 **What it does**
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43
6d5ab8d81db2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netchainsubset commit 203061071dae562277de62b43680fc9bae853f35
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44 `netChainSubset`_ is a tool to create a `chain`_ file with subset of chains that appear in the net.
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45 This process creates so called `liftOver`_ file used to convert coordinates between asesemblies.
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46
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47 For implementation details see netChainSubset's `source code`_.
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48
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49 .. _netChainSubset: https://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER
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50 .. _net: https://genome.ucsc.edu/goldenPath/help/net.html
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51 .. _chain: https://genome.ucsc.edu/goldenPath/help/chain.html
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52 .. _liftOver: https://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Liftover
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53 .. _source code: https://github.com/ucscGenomeBrowser/kent/blob/151a59e4e7526124ff096019c6c4052f0a900711/src/hg/mouseStuff/netChainSubset/netChainSubset.c
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54 ]]> </help>
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55 <citations>
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56 <citation type="doi">10.1093/bib/bbs038</citation>
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57 </citations>
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58 </tool>