Mercurial > repos > iuc > ucsc_nettoaxt

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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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46187b2b5d56 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_nettoaxt commit ceabe93bfa87e7736841c5a165cd00593a52881f
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1 <tool id="ucsc_nettoaxt" name="netToAxt" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT">
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2 <description>
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3 Convert net (and chain) to axt format
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4 </description>
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5 <macros>
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6 <token name="@TOOL_VERSION@">469</token>
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7 </macros>
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8 <xrefs>
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9 <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
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10 </xrefs>
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11 <requirements>
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12 <requirement type="package" version="@TOOL_VERSION@">ucsc-nettoaxt</requirement>
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13 </requirements>
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14 <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
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15 <command detect_errors="exit_code"><![CDATA[
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16 netToAxt
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17 '$in_net'
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18 '$in_chain'
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19 '$in_target'
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20 '$in_query'
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21 '$out'
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22 $qChain
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23 #if str($maxGap)
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24 -maxGap=$maxGap
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25 #end if
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26 $noSplit
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27 ]]></command>
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28 <inputs>
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29 <param name="in_net" format="ucsc.net" type="data" label="Net dataset" />
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30 <param name="in_chain" format="chain" type="data" label="Chain dataset" />
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31 <param name="in_target" format="twobit" type="data" label="Dataset with target sequence" />
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32 <param name="in_query" format="twobit" type="data" label="Dataset with query sequence" />
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33 <param argument="-qChain" type="boolean" optional="true" truevalue="-qChain" falsevalue="" label="Is the net with respect to the query side of chains?" />
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34 <param argument="-maxGap" type="integer" optional="true" min="0" label="Maximum size of gap before breaking" help="default 100" />
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35 <param argument="-noSplit" type="boolean" optional="true" truevalue="-noSplit" falsevalue="" label="Don't split chain when there is an insertion of another chain" />
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36
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37 </inputs>
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38 <outputs>
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39 <data name="out" format="axt" />
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40 </outputs>
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41 <tests>
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42 <test>
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43 <param name="in_net" value="hg38.chrM.mm39.chrM.ucsc.net" />
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44 <param name="in_chain" value="hg38.chrM.mm39.chrM.chain" />
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45 <param name="in_target" value="hg38.chrM.twobit" />
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46 <param name="in_query" value="mm39.chrM.twobit" />
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47 <output name="out" file="out.axt" />
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48 </test>
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49 </tests>
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50 <help><![CDATA[
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51 **What it does**
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52
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53 `netToAxt`_ is a tool from the UCSC suite to convert dataset from `ucsc.net`_ format (and `alignment chains`_) to `axt`_ format.
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54
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55 For implementation details see netToAxt's `source code`_.
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56
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57 .. _netToAxt: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
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58 .. _ucsc.net: https://genome.ucsc.edu/goldenPath/help/net.html
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59 .. _alignment chains: https://genome.ucsc.edu/goldenPath/help/chain.html
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60 .. _axt: https://genome.ucsc.edu/goldenPath/help/axt.html
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61 .. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/mouseStuff/netToAxt/netToAxt.c
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62 ]]> </help>
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63 <citations>
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64 <citation type="doi">10.1093/bib/bbs038</citation>
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65 </citations>
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66 </tool>