Mercurial > repos > iuc > ucsc_netsyntenic

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 303002db06287fb25306020c4391626842f52162
author iuc
date Sun, 22 Sep 2024 07:25:52 +0000
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e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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1 <tool id="ucsc_netsyntenic" name="netSyntenic" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT">
e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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2 <description>
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3 Add synteny info to a net
e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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4 </description>
e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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5 <macros>
e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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6 <token name="@TOOL_VERSION@">469</token>
e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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7 </macros>
e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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8 <xrefs>
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9 <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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10 </xrefs>
e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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11 <requirements>
e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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12 <requirement type="package" version="@TOOL_VERSION@">ucsc-netsyntenic</requirement>
e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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13 </requirements>
e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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14 <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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15 <command detect_errors="exit_code"><![CDATA[
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16 netSyntenic
e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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17 '$in_net'
e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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18 '$out'
e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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19 ]]></command>
e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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20 <inputs>
e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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21 <param name="in_net" format="ucsc.net" type="data" label="Input net" />
e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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22 </inputs>
e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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23 <outputs>
e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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24 <data name="out" format="ucsc.net" />
e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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25 </outputs>
e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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26 <tests>
e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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27 <test expect_num_outputs="1">
e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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28 <param name="in_net" value="input1.ucsc.net" />
e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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29 <output name="out" file="out1.ucsc.net"/>
e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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30 </test>
e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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31 </tests>
e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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32 <help><![CDATA[
e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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33 **What it does**
e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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34
1
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35 `netSyntenic`_ is a tool to add synteny info to a net. See details of `net format`_.
4c97f2468645 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 303002db06287fb25306020c4391626842f52162
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36
4c97f2468645 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 303002db06287fb25306020c4391626842f52162
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37 For implementation details see netSyntenic's `source code`_.
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e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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38
e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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39 .. _netSyntenic: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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40 .. _net format: https://genome.ucsc.edu/goldenPath/help/net.html
1
4c97f2468645 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 303002db06287fb25306020c4391626842f52162
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41 .. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/mouseStuff/netSyntenic/netSyntenic.c
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e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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42 ]]> </help>
e5cc5dc2c848 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
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43 <citations>
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44 <citation type="doi">10.1093/bib/bbs038</citation>
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45 </citations>
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46 </tool>