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add chainnet tool from ucsc/kent (#6284)
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| name: ucsc_chainnet | ||
| owner: iuc | ||
| description: Make alignment nets out of chains | ||
| long_description: | ||
| homepage_url: http://hgdownload.cse.ucsc.edu/admin/exe/ | ||
| remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet | ||
| type: unrestricted | ||
| categories: | ||
| - Sequence Analysis |
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| <tool id="ucsc_chainnet" name="chainNet" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT"> | ||
| <description> | ||
| make alignment nets out of alignment 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-chainnet</requirement> | ||
| </requirements> | ||
| <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command> | ||
| <command detect_errors="exit_code"><![CDATA[ | ||
| chainNet | ||
| '$in_chain' | ||
| #if str( $target_reference_index_source.target_reference_index_source_selector ) == "history": | ||
| '${target_reference_index_source.in_tar_ref_index}' | ||
| #else: | ||
| '$target_reference_index_source.tar_ref_index_file.fields.path' | ||
| #end if | ||
| #if str( $query_reference_index_source.query_reference_index_source_selector ) == "history": | ||
| '${query_reference_index_source.in_que_ref_index}' | ||
| #else: | ||
| '$query_reference_index_source.que_ref_index_file.fields.path' | ||
| #end if | ||
| '$targetNet' | ||
| '$queryNet' | ||
| #if str($minSpace) | ||
| -minSpace=$minSpace | ||
| #end if | ||
| #if str($minFill) | ||
| -minFill=$minFill | ||
| #end if | ||
| #if str($minScore) | ||
| -minScore=$minScore | ||
| #end if | ||
| $inclHap | ||
| #if str($verbose) | ||
| -verbose=$verbose | ||
| #end if | ||
| ]]></command> | ||
| <inputs> | ||
| <param name="in_chain" format="chain" type="data" label="Chain dataset" help="Select chain dataset" /> | ||
|
|
||
| <conditional name="target_reference_index_source"> | ||
| <param name="target_reference_index_source_selector" type="select" label="Choose the source for the target reference genome index"> | ||
| <option value="cached">Built-in</option> | ||
| <option value="history">From history</option> | ||
| </param> | ||
| <when value="cached"> | ||
| <param name="tar_ref_index_file" type="select" label="Using reference genome index"> | ||
| <options from_data_table="fasta_indexes" /> | ||
| </param> | ||
| </when> | ||
| <when value="history"> | ||
| <param name="in_tar_ref_index" format="tabular" type="data" label="Dataset with chrom sizes for target sequence. Typically a '.fai' file." /> | ||
| </when> | ||
| </conditional> | ||
|
|
||
| <conditional name="query_reference_index_source"> | ||
| <param name="query_reference_index_source_selector" type="select" label="Choose the source for the query reference genome index"> | ||
| <option value="cached">Built-in</option> | ||
| <option value="history">From history</option> | ||
| </param> | ||
| <when value="cached"> | ||
| <param name="que_ref_index_file" type="select" label="Using reference genome index"> | ||
| <options from_data_table="fasta_indexes" /> | ||
| </param> | ||
| </when> | ||
| <when value="history"> | ||
| <param name="in_que_ref_index" format="tabular" type="data" label="Dataset with chrom sizes for query sequence. Typically a '.fai' file." /> | ||
| </when> | ||
| </conditional> | ||
|
|
||
| <param argument="-minSpace" type="integer" optional="true" min="0" label="Minimum gap size to fill" help="default 25" /> | ||
| <param argument="-minFill" type="integer" optional="true" min="0" label="Minimum fill to record" help="default half of minSpace" /> | ||
| <param argument="-minScore" type="integer" optional="true" label="Minimum chain score to consider" help="default 2000" /> | ||
| <param argument="-inclHap" type="boolean" optional="true" truevalue="-inclHap" falsevalue="" label="Include query sequences name in the form *_hap*|*_alt*. Normally these are excluded from nets as being haplotype pseudochromosomes." /> | ||
| <param argument="-verbose" type="integer" optional="true" label="Verbosity" help="default 1" /> | ||
|
|
||
| </inputs> | ||
| <outputs> | ||
| <data name="targetNet" format="ucsc.net" label="${tool.name} on ${on_string}: target.net"/> | ||
| <data name="queryNet" format="ucsc.net" label="${tool.name} on ${on_string}: query.net" /> | ||
| </outputs> | ||
| <tests> | ||
| <test expect_num_outputs="2"> | ||
| <param name="in_chain" value="input.chain" /> | ||
| <conditional name="target_reference_index_source"> | ||
| <param name="target_reference_index_source_selector" value="history" /> | ||
| <param name="in_tar_ref_index" value="hg38.chr20.chunk.fasta.fai"/> | ||
| </conditional> | ||
| <conditional name="query_reference_index_source"> | ||
| <param name="query_reference_index_source_selector" value="history" /> | ||
| <param name="in_que_ref_index" value="mm39.chr2.chunk.fasta.fai"/> | ||
| </conditional> | ||
| <output name="targetNet" file="target.net"/> | ||
| <output name="queryNet" file="query.net"/> | ||
| </test> | ||
| <test expect_num_outputs="2"> | ||
| <param name="in_chain" value="input.chain" /> | ||
| <conditional name="target_reference_index_source"> | ||
| <param name="target_reference_index_source_selector" value="cached" /> | ||
| <param name="tar_ref_index_file" value="hg38.chr20.chunk"/> | ||
| </conditional> | ||
| <conditional name="query_reference_index_source"> | ||
| <param name="query_reference_index_source_selector" value="cached" /> | ||
| <param name="que_ref_index_file" value="mm39.chr2.chunk"/> | ||
| </conditional> | ||
| <output name="targetNet" file="target.net"/> | ||
| <output name="queryNet" file="query.net"/> | ||
| </test> | ||
| <test expect_num_outputs="2"> | ||
| <param name="in_chain" value="input.chain" /> | ||
| <param name="minScore" value="1200" /> | ||
| <conditional name="target_reference_index_source"> | ||
| <param name="target_reference_index_source_selector" value="cached" /> | ||
| <param name="tar_ref_index_file" value="hg38.chr20.chunk"/> | ||
| </conditional> | ||
| <conditional name="query_reference_index_source"> | ||
| <param name="query_reference_index_source_selector" value="history" /> | ||
| <param name="in_que_ref_index" value="mm39.chr2.chunk.fasta.fai"/> | ||
| </conditional> | ||
| <output name="targetNet" file="target.1200.net"/> | ||
| <output name="queryNet" file="query.1200.net"/> | ||
| </test> | ||
| </tests> | ||
| <help><![CDATA[ | ||
| **What it does** | ||
| `chainNet`_ is a tool that makes alignment nets out of `alignment chains`_. | ||
| It outputs two files in the `ucsc.net`_ format -- one for the target sequence and one for the query sequence. | ||
| For implementation details see ChainNet's `source code`_. | ||
| .. _chainNet: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt | ||
| .. _ucsc.net: https://genome.ucsc.edu/goldenPath/help/net.html | ||
| .. _alignment chains: https://genome.ucsc.edu/goldenPath/help/chain.html | ||
| .. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/mouseStuff/chainNet/chainNet.c | ||
| ]]> </help> | ||
| <citations> | ||
| <citation type="doi">10.1093/bib/bbs038</citation> | ||
| </citations> | ||
| </tool> |
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|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| hg38.chr20.chunk hg38 hg38.chr20.chunk ${__HERE__}/hg38.chr20.chunk.fasta.fai | ||
| mm39.chr2.chunk mm39 mm39.chr2.chunk ${__HERE__}/mm39.chr2.chunk.fasta.fai |
1 change: 1 addition & 0 deletions
1
tools/ucsc_tools/ucsc_chainnet/test-data/hg38.chr20.chunk.fasta.fai
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| hg38.chr20:10004760-11615810 1611050 30 1611050 1611051 |
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| @@ -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 |
1 change: 1 addition & 0 deletions
1
tools/ucsc_tools/ucsc_chainnet/test-data/mm39.chr2.chunk.fasta.fai
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| mm39.chr2:136351215-137822786 1471571 31 1471571 1471572 |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,25 @@ | ||
| ##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 mm39.chr2:136351215-137822786 1471571 | ||
| fill 42266 172 hg38.chr20:10004760-11615810 + 49202 176 id 13 score 4568 ali 172 | ||
| fill 87101 168 hg38.chr20:10004760-11615810 + 87669 167 id 7 score 6916 ali 167 | ||
| fill 87751 136 hg38.chr20:10004760-11615810 + 84589 137 id 6 score 6961 ali 136 | ||
| fill 158262 69 hg38.chr20:10004760-11615810 + 148667 69 id 15 score 2152 ali 68 | ||
| fill 189050 37 hg38.chr20:10004760-11615810 + 195952 38 id 20 score 1248 ali 36 | ||
| fill 189780 50 hg38.chr20:10004760-11615810 + 195854 50 id 18 score 1336 ali 50 | ||
| fill 244295 318 hg38.chr20:10004760-11615810 - 266744 261 id 3 score 13332 ali 256 | ||
| gap 244343 47 hg38.chr20:10004760-11615810 - 266919 70 | ||
| fill 258580 88 hg38.chr20:10004760-11615810 + 288132 88 id 9 score 5958 ali 88 | ||
| fill 260289 312 hg38.chr20:10004760-11615810 + 288278 276 id 4 score 9256 ali 268 | ||
| fill 260754 161 hg38.chr20:10004760-11615810 + 288114 161 id 5 score 8091 ali 161 | ||
| fill 364812 49 hg38.chr20:10004760-11615810 + 398052 55 id 19 score 1280 ali 48 | ||
| fill 409807 23 hg38.chr20:10004760-11615810 + 469454 23 id 16 score 1838 ali 23 | ||
| fill 516292 70 hg38.chr20:10004760-11615810 + 580524 105 id 22 score 1201 ali 70 | ||
| fill 546215 130 hg38.chr20:10004760-11615810 + 600994 130 id 8 score 5978 ali 130 | ||
| fill 579921 120 hg38.chr20:10004760-11615810 + 640387 120 id 14 score 3681 ali 120 | ||
| fill 722616 101 hg38.chr20:10004760-11615810 + 796556 102 id 10 score 5873 ali 101 | ||
| fill 722717 82 hg38.chr20:10004760-11615810 + 796671 81 id 17 score 1399 ali 73 | ||
| fill 821044 1970 hg38.chr20:10004760-11615810 - 879848 2177 id 2 score 64329 ali 1889 | ||
| fill 824476 150 hg38.chr20:10004760-11615810 - 890884 148 id 11 score 5421 ali 148 | ||
| fill 1062631 89 hg38.chr20:10004760-11615810 + 1121156 98 id 21 score 1208 ali 87 | ||
| fill 1342678 120 hg38.chr20:10004760-11615810 + 1425778 120 id 12 score 4864 ali 120 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 mm39.chr2:136351215-137822786 1471571 | ||
| fill 42266 172 hg38.chr20:10004760-11615810 + 49202 176 id 13 score 4568 ali 172 | ||
| fill 87101 168 hg38.chr20:10004760-11615810 + 87669 167 id 7 score 6916 ali 167 | ||
| fill 87751 136 hg38.chr20:10004760-11615810 + 84589 137 id 6 score 6961 ali 136 | ||
| fill 158262 69 hg38.chr20:10004760-11615810 + 148667 69 id 15 score 2152 ali 68 | ||
| fill 244295 318 hg38.chr20:10004760-11615810 - 266744 261 id 3 score 13332 ali 256 | ||
| gap 244343 47 hg38.chr20:10004760-11615810 - 266919 70 | ||
| fill 258580 88 hg38.chr20:10004760-11615810 + 288132 88 id 9 score 5958 ali 88 | ||
| fill 260289 312 hg38.chr20:10004760-11615810 + 288278 276 id 4 score 9256 ali 268 | ||
| fill 260754 161 hg38.chr20:10004760-11615810 + 288114 161 id 5 score 8091 ali 161 | ||
| fill 546215 130 hg38.chr20:10004760-11615810 + 600994 130 id 8 score 5978 ali 130 | ||
| fill 579921 120 hg38.chr20:10004760-11615810 + 640387 120 id 14 score 3681 ali 120 | ||
| fill 722616 101 hg38.chr20:10004760-11615810 + 796556 102 id 10 score 5873 ali 101 | ||
| fill 821044 1970 hg38.chr20:10004760-11615810 - 879848 2177 id 2 score 64329 ali 1889 | ||
| fill 824476 150 hg38.chr20:10004760-11615810 - 890884 148 id 11 score 5421 ali 148 | ||
| fill 1342678 120 hg38.chr20:10004760-11615810 + 1425778 120 id 12 score 4864 ali 120 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| ##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 195854 50 mm39.chr2:136351215-137822786 + 189780 50 id 18 score 1336 ali 50 | ||
| fill 195952 38 mm39.chr2:136351215-137822786 + 189050 37 id 20 score 1248 ali 36 | ||
| 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 398052 55 mm39.chr2:136351215-137822786 + 364812 49 id 19 score 1280 ali 48 | ||
| fill 469454 23 mm39.chr2:136351215-137822786 + 409807 23 id 16 score 1838 ali 23 | ||
| fill 580524 105 mm39.chr2:136351215-137822786 + 516292 70 id 22 score 1201 ali 70 | ||
| 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 796671 81 mm39.chr2:136351215-137822786 + 722717 82 id 17 score 1399 ali 73 | ||
| 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 1121156 98 mm39.chr2:136351215-137822786 + 1062631 89 id 21 score 1208 ali 87 | ||
| fill 1425778 120 mm39.chr2:136351215-137822786 + 1342678 120 id 12 score 4864 ali 120 |
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