Mercurial > repos > iuc > ucsc_netsyntenic
changeset 0:d2039064b27d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
| author | iuc |
|---|---|
| date | Wed, 04 Sep 2024 10:32:30 +0000 |
| parents | |
| children | a28010c3ac9b |
| files | netsyntenic.xml test-data/input1.ucsc.net test-data/out1.ucsc.net |
| diffstat | 3 files changed, 2025 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/netsyntenic.xml Wed Sep 04 10:32:30 2024 +0000 @@ -0,0 +1,43 @@ +<tool id="ucsc_netsyntenic" name="netSyntenic" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT"> + <description> + Add synteny info to a net + </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-netsyntenic</requirement> + </requirements> + <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command> + <command detect_errors="exit_code"><![CDATA[ + netSyntenic + '$in_net' + '$out' + ]]></command> + <inputs> + <param name="in_net" format="ucsc.net" type="data" label="Input net" /> + </inputs> + <outputs> + <data name="out" format="ucsc.net" /> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="in_net" value="input1.ucsc.net" /> + <output name="out" file="out1.ucsc.net"/> + </test> + </tests> + <help><![CDATA[ +**What it does** + +`netSyntenic`_ is a tool to add synteny info to a net. See details of `net format`. + +.. _netSyntenic: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt +.. _net format: https://genome.ucsc.edu/goldenPath/help/net.html + ]]> </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/input1.ucsc.net Wed Sep 04 10:32:30 2024 +0000 @@ -0,0 +1,991 @@ +##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 0 1582298 mm39.chr2:136351215-137822786 + 0 1469837 id 1 score 19768454 ali 703298 + gap 624 34 mm39.chr2:136351215-137822786 + 756 0 + gap 1118 244 mm39.chr2:136351215-137822786 + 1154 131 + gap 1378 44 mm39.chr2:136351215-137822786 + 1301 0 + gap 1445 35 mm39.chr2:136351215-137822786 + 1315 0 + gap 1554 65 mm39.chr2:136351215-137822786 + 1382 0 + gap 2551 32 mm39.chr2:136351215-137822786 + 2297 0 + gap 2982 16019 mm39.chr2:136351215-137822786 + 2686 10041 + gap 20356 36 mm39.chr2:136351215-137822786 + 14299 0 + gap 20578 3032 mm39.chr2:136351215-137822786 + 14468 4563 + gap 24210 31 mm39.chr2:136351215-137822786 + 19623 0 + gap 24309 39 mm39.chr2:136351215-137822786 + 19672 0 + gap 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