Mercurial > repos > iuc > bedops_sortbed

annotate sort-bed.xml @ 1:4de6dea7d80f draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://bedops.readthedocs.io/ commit 8b3e6e5354e485ab1068ef5605bcce2e7523376f
author iuc
date Mon, 14 Apr 2025 18:35:14 +0000
parents e0ca90448989
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
1 <tool id="bedops-sort-bed" name="bedops sort-bed" version="@TOOL_VERSION@" profile="22.01">
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
2 <macros>
1
4de6dea7d80f planemo upload for repository https://bedops.readthedocs.io/ commit 8b3e6e5354e485ab1068ef5605bcce2e7523376f
iuc
parents: 0
diff changeset
3 <token name="@TOOL_VERSION@">2.4.42</token>
0
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
4 </macros>
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
5 <requirements>
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
6 <requirement type="package" version="@TOOL_VERSION@">bedops</requirement>
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
7 </requirements>
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
8 <command><![CDATA[
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
9 sort-bed
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
10 --max-mem "\${GALAXY_MEMORY_MB:-1024}M"
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
11 --tmpdir "\${_GALAXY_JOB_TMP_DIR:-.}"
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
12 $unique
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
13 $duplicates
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
14 #for file in $inputs:
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
15 '$file'
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
16 #end for
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
17 > '$output'
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
18 ]]></command>
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
19 <inputs>
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
20 <param name="inputs" type="data" format="bed" multiple="true"/>
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
21 <param argument="--unique" type="boolean" truevalue="--unique" falsevalue="" label="Output only unique elements?"/>
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
22 <param argument="--duplicates" type="boolean" truevalue="--duplicates" falsevalue="" label="Output only duplicate elements?"/>
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
23 </inputs>
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
24 <outputs>
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
25 <data name="output" format_source="inputs" label="$tool.name: sorted output"/>
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
26 </outputs>
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
27 <tests>
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
28 <test>
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
29 <param name="inputs" value="unsorted.bed" ftype="bed"/>
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
30 <output name="output" value="sorted_simpled.bed"/>
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
31 </test>
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
32 <test>
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
33 <param name="inputs" value="unsorted.bed" ftype="bed"/>
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
34 <param name="unique" value="true"/>
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
35 <output name="output" value="sorted_unique.bed"/>
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
36 </test>
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
37 <test>
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
38 <param name="inputs" value="unsorted.bed" ftype="bed"/>
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
39 <param name="duplicates" value="true"/>
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
40 <output name="output" value="sorted_duplicates.bed"/>
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
41 </test>
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
42 </tests>
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
43 <help><![CDATA[
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
44 What this tool does
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
45 ===================
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
46
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
47 The sort-bed utility sorts BED files of any size, even larger than system memory. BED files that are in lexicographic-chromosome order allow BEDOPS utilities to work efficiently with data from any species without software modifications. Further, sorted files can be traversed very quickly.
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
48
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
49 Sorted BED order is defined first by lexicographic chromosome order, then ascending integer start coordinate order, and finally by ascending integer end coordinate order. To make the sort order unambiguous, a lexicographical sort is applied on fourth and subsequent columns, where present in the input BED dataset.
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
50
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
51
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
52 Input
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
53 =====
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
54
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
55 The sort-bed utility requires one or more three-column BED file(s). Support for common headers (such as UCSC BED track headers) is included, although headers will be stripped from the output.
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
56
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
57
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
58 Output
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
59 ======
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
60
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
61 Sort order is defined by a lexicographical sort on chromosome name, a numerical sort on start coordinates, a numerical sort on stop coordinates where there are start matches, and finally a lexicographical sort on the remainder of the BED element (if additional columns are present). Additional options may be specified to print only unique or duplicate elements.
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
62 ]]></help>
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
63 <citations>
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
64 <citation type="doi">https://doi.org/10.1093/bioinformatics/bts277</citation>
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
65 </citations>
e0ca90448989 planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca
iuc
parents:
diff changeset
66 </tool>