Mercurial > repos > iuc > ucsc_maftoaxt

comparison maftoaxt.xml @ 1:df00da62178e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt commit 303002db06287fb25306020c4391626842f52162
author iuc
date Sun, 22 Sep 2024 07:24:57 +0000
parents d1f6d417813d
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0:d1f6d417813d 1:df00da62178e
1 <tool id="maftoaxt" name="mafToAxt" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT"> 1 <tool id="maftoaxt" name="mafToAxt" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT">
2 <description> 2 <description>
3 Convert file from MAF to axt format 3 Convert file from MAF to axt format
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <token name="@TOOL_VERSION@">377</token> 6 <token name="@TOOL_VERSION@">469</token>
7 </macros> 7 </macros>
8 <xrefs> 8 <xrefs>
9 <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref> 9 <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
10 </xrefs> 10 </xrefs>
11 <requirements> 11 <requirements>
23 '$querySeq' 23 '$querySeq'
24 '$out' 24 '$out'
25 $stripDb 25 $stripDb
26 ]]></command> 26 ]]></command>
27 <inputs> 27 <inputs>
28 <param name="in_maf" format="maf" type="data" label="maf file" /> 28 <param name="in_maf" format="maf" type="data" label="MAF dataset" />
29 29
30 <conditional name="tar_seq"> 30 <conditional name="tar_seq">
31 <param name="tarSeq" type="select" label="Select target sequence" optional="false" help="Which sequence from the MAF file should be used as the target sequence. "> 31 <param name="tarSeq" type="select" label="Select target sequence" optional="false" help="Which sequence from the MAF file should be used as the target sequence. ">
32 <option value="" selected="true">Use the first sequence of the block as the target</option> 32 <option value="" selected="true">Use the first sequence of the block as the target</option>
33 <option value="customTar">Specify the target sequence by name</option> 33 <option value="customTar">Specify the target sequence by name</option>
60 </test> 60 </test>
61 </tests> 61 </tests>
62 <help><![CDATA[ 62 <help><![CDATA[
63 **What it does** 63 **What it does**
64 64
65 `mafToAxt`_ is a tool to convert maf dataset to axt format. Depending on parameters and the number of alignments in the MAF file this can be a full conversion or data extraction. 65 `mafToAxt`_ is a tool to convert `MAF`_ dataset to `axt`_ format. Depending on parameters and the number of alignments in the MAF file this can be a full conversion or data extraction.
66
67 For implementation details see mafToAxt's `source code`_.
66 68
67 .. _mafToAxt: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt 69 .. _mafToAxt: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
70 .. _axt: https://genome.ucsc.edu/goldenPath/help/axt.html
71 .. _MAF: https://genome.ucsc.edu/FAQ/FAQformat.html#format5
72 .. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/mouseStuff/mafToAxt/mafToAxt.c
68 ]]> </help> 73 ]]> </help>
69 <citations> 74 <citations>
70 <citation type="doi">10.1093/bib/bbs038</citation> 75 <citation type="doi">10.1093/bib/bbs038</citation>
71 </citations> 76 </citations>
72 </tool> 77 </tool>