Mercurial > repos > iuc > ucsc_netchainsubset
changeset 0:6d5ab8d81db2 draft default tip
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 |
| parents | |
| children | |
| files | netchainsubset.xml test-data/in.chain test-data/out.chain test-data/target.net |
| diffstat | 4 files changed, 346 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/netchainsubset.xml Wed Jan 14 09:16:58 2026 +0000 @@ -0,0 +1,58 @@ +<tool id="ucsc_netchainsubset" name="netChainSubset" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT"> + <description> + Create chain file with subset of chains that appear in the net + </description> + <macros> + <token name="@TOOL_VERSION@">482</token> + </macros> + <xrefs> + <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref> + </xrefs> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">ucsc-netchainsubset</requirement> + </requirements> + <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command> + <command detect_errors="exit_code"><![CDATA[ + netChainSubset + '$in_net' + '$in_chain' + '$out' + $splitOnInsert + $wholeChains + $skipMissing + ]]></command> + <inputs> + <param name="in_net" format="ucsc.net" type="data" label="net dataset" help="" /> + <param name="in_chain" format="chain" type="data" label="chain dataset" help="" /> + <param argument="-splitOnInsert" type="boolean" optional="true" truevalue="-splitOnInsert" falsevalue="" label="Split on insert" help="Split chain when get an insertion of another chain." /> + <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." /> + <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." /> + </inputs> + <outputs> + <data name="out" format="chain" /> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="in_net" value="target.net" /> + <param name="in_chain" value="in.chain" /> + <output name="out" file="out.chain" /> + </test> + </tests> + <help><![CDATA[ +**What it does** + +`netChainSubset`_ is a tool to create a `chain`_ file with subset of chains that appear in the net. +This process creates so called `liftOver`_ file used to convert coordinates between asesemblies. + +For implementation details see netChainSubset's `source code`_. + +.. _netChainSubset: https://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER +.. _net: https://genome.ucsc.edu/goldenPath/help/net.html +.. _chain: https://genome.ucsc.edu/goldenPath/help/chain.html +.. _liftOver: https://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Liftover +.. _source code: https://github.com/ucscGenomeBrowser/kent/blob/151a59e4e7526124ff096019c6c4052f0a900711/src/hg/mouseStuff/netChainSubset/netChainSubset.c + ]]> </help> + <citations> + <citation type="doi">10.1093/bib/bbs038</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/in.chain Wed Jan 14 09:16:58 2026 +0000 @@ -0,0 +1,159 @@ +##matrix=axtChain 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91 +##gapPenalties=axtChain O=400 E=30 +chain 64329 hg38.chr20:10004760-11615810 1611050 + 879848 882025 mm39.chr2:136351215-137822786 1471571 - 648557 650527 2 +24 0 1 +52 12 0 +46 0 6 +24 1 0 +63 0 1 +6 0 9 +78 14 0 +25 0 4 +14 4 0 +4 19 0 +12 9 0 +43 77 0 +19 2 0 +37 2 0 +61 1 0 +16 0 4 +74 0 7 +51 1 0 +30 17 0 +18 1 0 +28 0 2 +125 0 13 +8 0 14 +8 0 3 +88 5 0 +35 0 1 +5 0 1 +6 0 7 +21 0 1 +27 4 0 +64 10 0 +46 2 0 +42 1 0 +54 0 1 +12 1 0 +115 3 0 +10 0 1 +27 1 0 +20 1 0 +42 21 0 +20 2 0 +50 11 0 +8 27 0 +45 1 0 +26 11 0 +5 3 0 +28 2 0 +34 1 0 +24 0 2 +39 1 0 +29 3 0 +68 17 0 +4 0 3 +29 + +chain 13332 hg38.chr20:10004760-11615810 1611050 + 266744 267005 mm39.chr2:136351215-137822786 1471571 - 1226958 1227276 3 +17 0 14 +111 2 0 +42 3 0 +39 0 47 +31 0 1 +16 + +chain 9256 hg38.chr20:10004760-11615810 1611050 + 288278 288554 mm39.chr2:136351215-137822786 1471571 + 260289 260601 4 +34 8 0 +38 0 2 +9 0 17 +11 0 24 +15 0 1 +161 + +chain 8091 hg38.chr20:10004760-11615810 1611050 + 288114 288275 mm39.chr2:136351215-137822786 1471571 + 260754 260915 5 +161 + +chain 6961 hg38.chr20:10004760-11615810 1611050 + 84589 84726 mm39.chr2:136351215-137822786 1471571 + 87751 87887 6 +83 1 0 +53 + +chain 6916 hg38.chr20:10004760-11615810 1611050 + 87669 87836 mm39.chr2:136351215-137822786 1471571 + 87101 87269 7 +58 0 1 +109 + +chain 5978 hg38.chr20:10004760-11615810 1611050 + 600994 601124 mm39.chr2:136351215-137822786 1471571 + 546215 546345 8 +130 + +chain 5958 hg38.chr20:10004760-11615810 1611050 + 288132 288220 mm39.chr2:136351215-137822786 1471571 + 258580 258668 9 +88 + +chain 5873 hg38.chr20:10004760-11615810 1611050 + 796556 796658 mm39.chr2:136351215-137822786 1471571 + 722616 722717 10 +31 1 0 +70 + +chain 5421 hg38.chr20:10004760-11615810 1611050 + 890884 891032 mm39.chr2:136351215-137822786 1471571 - 646945 647095 11 +25 0 2 +123 + +chain 4864 hg38.chr20:10004760-11615810 1611050 + 1425778 1425898 mm39.chr2:136351215-137822786 1471571 + 1342678 1342798 12 +120 + +chain 4568 hg38.chr20:10004760-11615810 1611050 + 49202 49378 mm39.chr2:136351215-137822786 1471571 + 42266 42438 13 +99 4 0 +73 + +chain 3681 hg38.chr20:10004760-11615810 1611050 + 640387 640507 mm39.chr2:136351215-137822786 1471571 + 579921 580041 14 +120 + +chain 2152 hg38.chr20:10004760-11615810 1611050 + 148667 148736 mm39.chr2:136351215-137822786 1471571 + 158262 158331 15 +10 1 0 +38 0 1 +20 + +chain 1838 hg38.chr20:10004760-11615810 1611050 + 469454 469477 mm39.chr2:136351215-137822786 1471571 + 409807 409830 16 +23 + +chain 1399 hg38.chr20:10004760-11615810 1611050 + 796671 796752 mm39.chr2:136351215-137822786 1471571 + 722717 722799 17 +30 5 0 +8 3 0 +27 0 9 +8 + +chain 1336 hg38.chr20:10004760-11615810 1611050 + 195854 195904 mm39.chr2:136351215-137822786 1471571 + 189780 189830 18 +50 + +chain 1280 hg38.chr20:10004760-11615810 1611050 + 398052 398107 mm39.chr2:136351215-137822786 1471571 + 364812 364861 19 +11 1 0 +7 0 1 +15 6 0 +15 + +chain 1248 hg38.chr20:10004760-11615810 1611050 + 195952 195990 mm39.chr2:136351215-137822786 1471571 + 189050 189087 20 +22 2 0 +5 0 1 +9 + +chain 1208 hg38.chr20:10004760-11615810 1611050 + 1121156 1121254 mm39.chr2:136351215-137822786 1471571 + 1062631 1062720 21 +9 0 1 +12 7 0 +12 4 0 +13 0 1 +41 + +chain 1201 hg38.chr20:10004760-11615810 1611050 + 580524 580629 mm39.chr2:136351215-137822786 1471571 + 516292 516362 22 +14 3 0 +16 19 0 +19 13 0 +21 + +chain 1170 hg38.chr20:10004760-11615810 1611050 + 806859 806881 mm39.chr2:136351215-137822786 1471571 + 737566 737588 23 +22 + +chain 1030 hg38.chr20:10004760-11615810 1611050 + 1532147 1532161 mm39.chr2:136351215-137822786 1471571 + 1423235 1423249 24 +14 + +chain 1012 hg38.chr20:10004760-11615810 1611050 + 361832 361870 mm39.chr2:136351215-137822786 1471571 + 345076 345108 25 +20 6 0 +12
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.chain Wed Jan 14 09:16:58 2026 +0000 @@ -0,0 +1,111 @@ +##matrix=axtChain 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91 +##gapPenalties=axtChain O=400 E=30 +chain 4568 hg38.chr20:10004760-11615810 1611050 + 49202 49378 mm39.chr2:136351215-137822786 1471571 + 42266 42438 13 +99 4 0 +73 + +chain 6961 hg38.chr20:10004760-11615810 1611050 + 84589 84726 mm39.chr2:136351215-137822786 1471571 + 87751 87887 6 +83 1 0 +53 + +chain 6916 hg38.chr20:10004760-11615810 1611050 + 87669 87836 mm39.chr2:136351215-137822786 1471571 + 87101 87269 7 +58 0 1 +109 + +chain 2152 hg38.chr20:10004760-11615810 1611050 + 148667 148736 mm39.chr2:136351215-137822786 1471571 + 158262 158331 15 +10 1 0 +38 0 1 +20 + +chain 13332 hg38.chr20:10004760-11615810 1611050 + 266744 267005 mm39.chr2:136351215-137822786 1471571 - 1226958 1227276 3 +17 0 14 +111 2 0 +42 3 0 +39 0 47 +31 0 1 +16 + +chain 8091 hg38.chr20:10004760-11615810 1611050 + 288114 288275 mm39.chr2:136351215-137822786 1471571 + 260754 260915 5 +161 + +chain 9256 hg38.chr20:10004760-11615810 1611050 + 288278 288554 mm39.chr2:136351215-137822786 1471571 + 260289 260601 4 +34 8 0 +38 0 2 +9 0 17 +11 0 24 +15 0 1 +161 + +chain 5978 hg38.chr20:10004760-11615810 1611050 + 600994 601124 mm39.chr2:136351215-137822786 1471571 + 546215 546345 8 +130 + +chain 3681 hg38.chr20:10004760-11615810 1611050 + 640387 640507 mm39.chr2:136351215-137822786 1471571 + 579921 580041 14 +120 + +chain 5873 hg38.chr20:10004760-11615810 1611050 + 796556 796658 mm39.chr2:136351215-137822786 1471571 + 722616 722717 10 +31 1 0 +70 + +chain 64329 hg38.chr20:10004760-11615810 1611050 + 879848 882025 mm39.chr2:136351215-137822786 1471571 - 648557 650527 2 +24 0 1 +52 12 0 +46 0 6 +24 1 0 +63 0 1 +6 0 9 +78 14 0 +25 0 4 +14 4 0 +4 19 0 +12 9 0 +43 77 0 +19 2 0 +37 2 0 +61 1 0 +16 0 4 +74 0 7 +51 1 0 +30 17 0 +18 1 0 +28 0 2 +125 0 13 +8 0 14 +8 0 3 +88 5 0 +35 0 1 +5 0 1 +6 0 7 +21 0 1 +27 4 0 +64 10 0 +46 2 0 +42 1 0 +54 0 1 +12 1 0 +115 3 0 +10 0 1 +27 1 0 +20 1 0 +42 21 0 +20 2 0 +50 11 0 +8 27 0 +45 1 0 +26 11 0 +5 3 0 +28 2 0 +34 1 0 +24 0 2 +39 1 0 +29 3 0 +68 17 0 +4 0 3 +29 + +chain 5421 hg38.chr20:10004760-11615810 1611050 + 890884 891032 mm39.chr2:136351215-137822786 1471571 - 646945 647095 11 +25 0 2 +123 + +chain 4864 hg38.chr20:10004760-11615810 1611050 + 1425778 1425898 mm39.chr2:136351215-137822786 1471571 + 1342678 1342798 12 +120 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/target.net Wed Jan 14 09:16:58 2026 +0000 @@ -0,0 +1,18 @@ +##matrix=axtChain 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91 +##gapPenalties=axtChain O=400 E=30 +net hg38.chr20:10004760-11615810 1611050 + fill 49202 176 mm39.chr2:136351215-137822786 + 42266 172 id 13 score 4568 ali 172 + fill 84589 137 mm39.chr2:136351215-137822786 + 87751 136 id 6 score 6961 ali 136 + fill 87669 167 mm39.chr2:136351215-137822786 + 87101 168 id 7 score 6916 ali 167 + fill 148667 69 mm39.chr2:136351215-137822786 + 158262 69 id 15 score 2152 ali 68 + fill 266744 261 mm39.chr2:136351215-137822786 - 244295 318 id 3 score 13332 ali 256 + fill 288114 161 mm39.chr2:136351215-137822786 + 260754 161 id 5 score 8091 ali 161 + fill 288278 276 mm39.chr2:136351215-137822786 + 260289 312 id 4 score 9256 ali 268 + fill 600994 130 mm39.chr2:136351215-137822786 + 546215 130 id 8 score 5978 ali 130 + fill 640387 120 mm39.chr2:136351215-137822786 + 579921 120 id 14 score 3681 ali 120 + fill 796556 102 mm39.chr2:136351215-137822786 + 722616 101 id 10 score 5873 ali 101 + fill 879848 2177 mm39.chr2:136351215-137822786 - 821044 1970 id 2 score 64329 ali 1889 + gap 880298 77 mm39.chr2:136351215-137822786 - 822602 0 + gap 881628 27 mm39.chr2:136351215-137822786 - 821380 0 + fill 890884 148 mm39.chr2:136351215-137822786 - 824476 150 id 11 score 5421 ali 148 + fill 1425778 120 mm39.chr2:136351215-137822786 + 1342678 120 id 12 score 4864 ali 120