Mercurial > repos > iuc > ucsc_chainantirepeat
changeset 0:91674d4623a8 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainantirepeat commit 40350c86093eec2086039bba95b580e8af02da66
| author | iuc |
|---|---|
| date | Sat, 08 Mar 2025 09:24:04 +0000 |
| parents | |
| children | 9f2d2c96a189 |
| files | test-data/hg38.chrM.mm39.chrM.chain test-data/hg38.chrM.twobit test-data/mm39.chrM.twobit test-data/result.chain ucsc_chainantirepeat.xml |
| diffstat | 5 files changed, 362 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hg38.chrM.mm39.chrM.chain Sat Mar 08 09:24:04 2025 +0000 @@ -0,0 +1,150 @@ +##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 673687 hg38.chrM 16569 + 576 16569 mm39.chrM 16299 + 0 15860 1 +19 2 0 +30 1 0 +92 1 0 +11 0 3 +41 2 0 +89 2 0 +80 0 4 +12 7 0 +41 0 2 +114 0 1 +129 0 4 +34 1 0 +29 0 1 +60 0 1 +39 1 0 +118 3 0 +14 0 3 +71 0 1 +31 3 0 +5 0 2 +39 0 6 +16 5 0 +23 0 1 +25 0 3 +37 0 4 +18 4 0 +206 0 1 +37 1 0 +56 2 0 +36 0 7 +84 2 0 +16 0 2 +57 0 2 +7 1 0 +30 2 0 +12 0 1 +20 0 4 +50 1 0 +42 0 1 +272 0 2 +25 2 0 +4 0 1 +74 1 0 +17 0 1 +19 0 3 +72 0 1 +139 1 0 +36 1 0 +10 0 3 +8 0 2 +12 0 1 +19 1 0 +14 0 3 +11 4 0 +1033 1 0 +189 0 1 +271 1 0 +22 1 0 +11 0 2 +83 0 1 +12 1 0 +280 0 3 +19 5 0 +11 0 2 +8 0 3 +14 3 0 +300 3 0 +11 3 0 +17 1 0 +50 6 0 +71 0 1 +56 2 0 +38 0 1 +73 0 3 +16 0 2 +33 1 0 +17 11 0 +1635 0 1 +32 0 1 +15 0 1 +683 22 0 +18 2 0 +26 2 0 +13 1 0 +101 1 0 +7 0 1 +26 0 9 +16 9 0 +1794 0 4 +7 1 0 +10 3 0 +77 0 3 +52 0 3 +13 0 1 +159 0 5 +13 5 0 +165 0 5 +8 5 0 +195 2 0 +7 0 2 +1155 1 0 +80 1 0 +139 1 0 +20 1 0 +23 0 1 +4 0 1 +1307 2 0 +13 0 2 +110 1 0 +10 0 1 +54 0 6 +11 6 0 +68 8 0 +13 0 2 +16 0 6 +33 6 0 +43 0 1 +103 1 0 +23 0 1 +89 3 0 +19 0 3 +10 3 0 +6 2 0 +9 0 2 +323 0 1 +1102 3 0 +12 0 3 +22 0 3 +20 1 0 +35 0 2 +12 2 0 +53 1 0 +8 10 0 +36 10 0 +3 9 0 +19 33 0 +8 44 0 +75 11 0 +6 0 5 +21 6 0 +5 0 1 +11 0 7 +12 1 0 +13 0 1 +136 0 1 +37 0 1 +47
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result.chain Sat Mar 08 09:24:04 2025 +0000 @@ -0,0 +1,151 @@ +##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 673687 hg38.chrM 16569 + 576 16569 mm39.chrM 16299 + 0 15860 1 +19 2 0 +30 1 0 +92 1 0 +11 0 3 +41 2 0 +89 2 0 +80 0 4 +12 7 0 +41 0 2 +114 0 1 +129 0 4 +34 1 0 +29 0 1 +60 0 1 +39 1 0 +118 3 0 +14 0 3 +71 0 1 +31 3 0 +5 0 2 +39 0 6 +16 5 0 +23 0 1 +25 0 3 +37 0 4 +18 4 0 +206 0 1 +37 1 0 +56 2 0 +36 0 7 +84 2 0 +16 0 2 +57 0 2 +7 1 0 +30 2 0 +12 0 1 +20 0 4 +50 1 0 +42 0 1 +272 0 2 +25 2 0 +4 0 1 +74 1 0 +17 0 1 +19 0 3 +72 0 1 +139 1 0 +36 1 0 +10 0 3 +8 0 2 +12 0 1 +19 1 0 +14 0 3 +11 4 0 +1033 1 0 +189 0 1 +271 1 0 +22 1 0 +11 0 2 +83 0 1 +12 1 0 +280 0 3 +19 5 0 +11 0 2 +8 0 3 +14 3 0 +300 3 0 +11 3 0 +17 1 0 +50 6 0 +71 0 1 +56 2 0 +38 0 1 +73 0 3 +16 0 2 +33 1 0 +17 11 0 +1635 0 1 +32 0 1 +15 0 1 +683 22 0 +18 2 0 +26 2 0 +13 1 0 +101 1 0 +7 0 1 +26 0 9 +16 9 0 +1794 0 4 +7 1 0 +10 3 0 +77 0 3 +52 0 3 +13 0 1 +159 0 5 +13 5 0 +165 0 5 +8 5 0 +195 2 0 +7 0 2 +1155 1 0 +80 1 0 +139 1 0 +20 1 0 +23 0 1 +4 0 1 +1307 2 0 +13 0 2 +110 1 0 +10 0 1 +54 0 6 +11 6 0 +68 8 0 +13 0 2 +16 0 6 +33 6 0 +43 0 1 +103 1 0 +23 0 1 +89 3 0 +19 0 3 +10 3 0 +6 2 0 +9 0 2 +323 0 1 +1102 3 0 +12 0 3 +22 0 3 +20 1 0 +35 0 2 +12 2 0 +53 1 0 +8 10 0 +36 10 0 +3 9 0 +19 33 0 +8 44 0 +75 11 0 +6 0 5 +21 6 0 +5 0 1 +11 0 7 +12 1 0 +13 0 1 +136 0 1 +37 0 1 +47 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ucsc_chainantirepeat.xml Sat Mar 08 09:24:04 2025 +0000 @@ -0,0 +1,61 @@ +<tool id="ucsc_chainantirepeat" name="chainAntiRepeat" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT"> + <description> + Remove repeated chains + </description> + <macros> + <token name="@TOOL_VERSION@">469</token> + </macros> + <xrefs> + <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref> + </xrefs> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">ucsc-chainantirepeat</requirement> + </requirements> + <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command> + <command detect_errors="exit_code"><![CDATA[ + chainAntiRepeat + '$in_target' + '$in_query' + '$in_chain' + '$out' + #if $minScore + -minScore='$minScore' + #end if + #if $noCheckScore + -noCheckScore='$noCheckScore' + #end if + ]]></command> + <inputs> + <param name="in_chain" format="chain" type="data" label="Chain dataset" /> + <param name="in_target" format="twobit" type="data" label="Dataset with target sequence" /> + <param name="in_query" format="twobit" type="data" label="Dataset with query sequence" /> + <param argument="-minScore" type="integer" optional="true" label="minimum score (after repeat stuff) to pass" help="Default 5000" /> + <param argument="-noCheckScore" type="integer" optional="true" label="score that will pass without checks (speed tweak)" help="Default 200000" /> + </inputs> + <outputs> + <data name="out" format="chain" /> + </outputs> + <tests> + <test> + <param name="in_chain" value="hg38.chrM.mm39.chrM.chain" /> + <param name="in_target" value="hg38.chrM.twobit" /> + <param name="in_query" value="mm39.chrM.twobit" /> + <output name="out" file="result.chain" /> + </test> + </tests> + <help><![CDATA[ +**What it does** + +`chainAntiRepeat`_ is a tool that gets rid chains that are primarily the results of repeats and degenerate DNA. +The `chain`_ format describes a pairwise alignment that allow gaps in both sequences simultaneously. + +For implementation details see chainAntiRepeat's `source code`_. + +.. _chainAntiRepeat: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt +.. _chain: https://genome.ucsc.edu/goldenPath/help/chain.html +.. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/mouseStuff/chainAntiRepeat/chainAntiRepeat.c + ]]> </help> + <citations> + <citation type="doi">10.1093/bib/bbs038</citation> + </citations> +</tool>