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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_nettoaxt commit ceabe93bfa87e7736841c5a165cd00593a52881f
author iuc
date Thu, 19 Sep 2024 17:13:14 +0000
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1 <tool id="ucsc_nettoaxt" name="netToAxt" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT">
2 <description>
3 Convert net (and chain) to axt format
4 </description>
5 <macros>
6 <token name="@TOOL_VERSION@">469</token>
7 </macros>
8 <xrefs>
9 <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
10 </xrefs>
11 <requirements>
12 <requirement type="package" version="@TOOL_VERSION@">ucsc-nettoaxt</requirement>
13 </requirements>
14 <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
15 <command detect_errors="exit_code"><![CDATA[
16 netToAxt
17 '$in_net'
18 '$in_chain'
19 '$in_target'
20 '$in_query'
21 '$out'
22 $qChain
23 #if str($maxGap)
24 -maxGap=$maxGap
25 #end if
26 $noSplit
27 ]]></command>
28 <inputs>
29 <param name="in_net" format="ucsc.net" type="data" label="Net dataset" />
30 <param name="in_chain" format="chain" type="data" label="Chain dataset" />
31 <param name="in_target" format="twobit" type="data" label="Dataset with target sequence" />
32 <param name="in_query" format="twobit" type="data" label="Dataset with query sequence" />
33 <param argument="-qChain" type="boolean" optional="true" truevalue="-qChain" falsevalue="" label="Is the net with respect to the query side of chains?" />
34 <param argument="-maxGap" type="integer" optional="true" min="0" label="Maximum size of gap before breaking" help="default 100" />
35 <param argument="-noSplit" type="boolean" optional="true" truevalue="-noSplit" falsevalue="" label="Don't split chain when there is an insertion of another chain" />
36
37 </inputs>
38 <outputs>
39 <data name="out" format="axt" />
40 </outputs>
41 <tests>
42 <test>
43 <param name="in_net" value="hg38.chrM.mm39.chrM.ucsc.net" />
44 <param name="in_chain" value="hg38.chrM.mm39.chrM.chain" />
45 <param name="in_target" value="hg38.chrM.twobit" />
46 <param name="in_query" value="mm39.chrM.twobit" />
47 <output name="out" file="out.axt" />
48 </test>
49 </tests>
50 <help><![CDATA[
51 **What it does**
52
53 `netToAxt`_ is a tool from the UCSC suite to convert dataset from `ucsc.net`_ format (and `alignment chains`_) to `axt`_ format.
54
55 For implementation details see netToAxt's `source code`_.
56
57 .. _netToAxt: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
58 .. _ucsc.net: https://genome.ucsc.edu/goldenPath/help/net.html
59 .. _alignment chains: https://genome.ucsc.edu/goldenPath/help/chain.html
60 .. _axt: https://genome.ucsc.edu/goldenPath/help/axt.html
61 .. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/mouseStuff/netToAxt/netToAxt.c
62 ]]> </help>
63 <citations>
64 <citation type="doi">10.1093/bib/bbs038</citation>
65 </citations>
66 </tool>