Mercurial > repos > iuc > ucsc_netsyntenic
annotate netsyntenic.xml @ 0:e5cc5dc2c848 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
| author | iuc |
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| date | Wed, 04 Sep 2024 10:32:21 +0000 |
| parents | |
| children | 4c97f2468645 |
| rev | line source |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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1 <tool id="ucsc_netsyntenic" name="netSyntenic" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT"> |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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2 <description> |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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3 Add synteny info to a net |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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4 </description> |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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5 <macros> |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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6 <token name="@TOOL_VERSION@">469</token> |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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7 </macros> |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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8 <xrefs> |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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9 <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref> |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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10 </xrefs> |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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11 <requirements> |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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12 <requirement type="package" version="@TOOL_VERSION@">ucsc-netsyntenic</requirement> |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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13 </requirements> |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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14 <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command> |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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15 <command detect_errors="exit_code"><![CDATA[ |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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16 netSyntenic |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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17 '$in_net' |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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18 '$out' |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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19 ]]></command> |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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20 <inputs> |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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21 <param name="in_net" format="ucsc.net" type="data" label="Input net" /> |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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22 </inputs> |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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23 <outputs> |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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24 <data name="out" format="ucsc.net" /> |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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25 </outputs> |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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26 <tests> |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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27 <test expect_num_outputs="1"> |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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28 <param name="in_net" value="input1.ucsc.net" /> |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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29 <output name="out" file="out1.ucsc.net"/> |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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30 </test> |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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31 </tests> |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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32 <help><![CDATA[ |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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33 **What it does** |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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34 |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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35 `netSyntenic`_ is a tool to add synteny info to a net. See details of `net format`. |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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36 |
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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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37 .. _netSyntenic: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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38 .. _net format: https://genome.ucsc.edu/goldenPath/help/net.html |
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e5cc5dc2c848
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic commit 731f04b7f59bd92cc68ad1c7565ae35960e75645
iuc
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39 ]]> </help> |
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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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40 <citations> |
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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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41 <citation type="doi">10.1093/bib/bbs038</citation> |
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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 </citations> |
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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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43 </tool> |