Mercurial > repos > iuc > ucsc_chainsort
comparison chainsort.xml @ 0:7e2d89cef769 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
| author | iuc |
|---|---|
| date | Mon, 26 Aug 2024 13:54:15 +0000 |
| parents | |
| children | 754d04fba5b9 |
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| -1:000000000000 | 0:7e2d89cef769 |
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| 1 <tool id="ucsc_chainsort" name="chainSort" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT"> | |
| 2 <description> | |
| 3 Sort chains | |
| 4 </description> | |
| 5 <macros> | |
| 6 <token name="@TOOL_VERSION@">455</token> | |
| 7 </macros> | |
| 8 <xrefs> | |
| 9 <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref> | |
| 10 </xrefs> | |
| 11 <requirements> | |
| 12 <requirement type="package" version="@TOOL_VERSION@">ucsc-chainsort</requirement> | |
| 13 </requirements> | |
| 14 <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command> | |
| 15 <command detect_errors="exit_code"><![CDATA[ | |
| 16 chainSort | |
| 17 '$in_chain' | |
| 18 $sort_by | |
| 19 '$out' | |
| 20 ]]></command> | |
| 21 <inputs> | |
| 22 <param name="in_chain" format="chain" type="data" label="Chain dataset" /> | |
| 23 <param name="sort_by" type="select" label="Sort"> | |
| 24 <option value="" selected="true">by score</option> | |
| 25 <option value="-target">on target start</option> | |
| 26 <option value="-query">on query start</option> | |
| 27 </param> | |
| 28 </inputs> | |
| 29 <outputs> | |
| 30 <data name="out" format="chain" /> | |
| 31 </outputs> | |
| 32 <tests> | |
| 33 <test> | |
| 34 <param name="in_chain" value="input.chain" /> | |
| 35 <output name="out" file="sorted_score.chain" /> | |
| 36 </test> | |
| 37 <test> | |
| 38 <param name="in_chain" value="input.chain" /> | |
| 39 <param name="sort_by" value="-query" /> | |
| 40 <output name="out" file="sorted_query.chain" /> | |
| 41 </test> | |
| 42 </tests> | |
| 43 <help><![CDATA[ | |
| 44 **What it does** | |
| 45 | |
| 46 `chainSort`_ is a tool to sort chains. | |
| 47 | |
| 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. | |
| 49 | |
| 50 .. _chainSort: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt | |
| 51 ]]> </help> | |
| 52 <citations> | |
| 53 <citation type="doi">10.1093/bib/bbs038</citation> | |
| 54 </citations> | |
| 55 </tool> |