Mercurial > repos > iuc > ucsc_chainsort

annotate chainsort.xml @ 2:c0300333731b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainsort commit 82eef3f0884d3912fb2c3876242c1f10c3fe13b8
author iuc
date Sat, 28 Sep 2024 16:24:55 +0000
parents 754d04fba5b9
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7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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1 <tool id="ucsc_chainsort" name="chainSort" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT">
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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2 <description>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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3 Sort chains
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4 </description>
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5 <macros>
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c0300333731b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainsort commit 82eef3f0884d3912fb2c3876242c1f10c3fe13b8
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6 <token name="@TOOL_VERSION@">469</token>
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7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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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>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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10 </xrefs>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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11 <requirements>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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12 <requirement type="package" version="@TOOL_VERSION@">ucsc-chainsort</requirement>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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13 </requirements>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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14 <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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15 <command detect_errors="exit_code"><![CDATA[
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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16 chainSort
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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17 '$in_chain'
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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18 $sort_by
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19 '$out'
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20 ]]></command>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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21 <inputs>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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22 <param name="in_chain" format="chain" type="data" label="Chain dataset" />
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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23 <param name="sort_by" type="select" label="Sort">
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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24 <option value="" selected="true">by score</option>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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25 <option value="-target">on target start</option>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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26 <option value="-query">on query start</option>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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27 </param>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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28 </inputs>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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29 <outputs>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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30 <data name="out" format="chain" />
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="in_chain" value="input.chain" />
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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35 <output name="out" file="sorted_score.chain" />
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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36 </test>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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37 <test>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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38 <param name="in_chain" value="input.chain" />
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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39 <param name="sort_by" value="-query" />
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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40 <output name="out" file="sorted_query.chain" />
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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41 </test>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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42 </tests>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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43 <help><![CDATA[
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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44 **What it does**
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45
1
754d04fba5b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainsort commit 303002db06287fb25306020c4391626842f52162
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46 `chainSort`_ is a tool to sort `chains`_.
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47
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
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48 Note this tool loads all chains into memory, so it is not suitable for large datasets. Instead, run chainSort on multiple small dataset, followed by chainMergeSort.
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49
1
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50 For implementation details see chainSort's `source code`_.
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51
0
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52 .. _chainSort: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
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53 .. _chains: https://genome.ucsc.edu/goldenPath/help/chain.html
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54 .. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/mouseStuff/chainSort/chainSort.c
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55 ]]> </help>
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56 <citations>
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57 <citation type="doi">10.1093/bib/bbs038</citation>
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58 </citations>
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59 </tool>