Mercurial > repos > iuc > ucsc_chainsort

annotate chainsort.xml @ 0:7e2d89cef769 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
2 <description>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
3 Sort chains
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
4 </description>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
5 <macros>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
6 <token name="@TOOL_VERSION@">455</token>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
7 </macros>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
8 <xrefs>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
10 </xrefs>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
11 <requirements>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
13 </requirements>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
16 chainSort
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
17 '$in_chain'
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
18 $sort_by
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
19 '$out'
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
20 ]]></command>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
21 <inputs>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
27 </param>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
28 </inputs>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
29 <outputs>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
31 </outputs>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
32 <tests>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
33 <test>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
36 </test>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
37 <test>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
41 </test>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
42 </tests>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
43 <help><![CDATA[
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
44 **What it does**
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
45
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
46 `chainSort`_ is a tool to sort chains.
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
47
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
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.
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
49
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
50 .. _chainSort: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
51 ]]> </help>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
52 <citations>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
53 <citation type="doi">10.1093/bib/bbs038</citation>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
54 </citations>
7e2d89cef769 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
iuc
parents:
diff changeset
55 </tool>