Mercurial > repos > iuc > bedtools
comparison sortBed.xml @ 34:dde39ba9c031 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
author | iuc |
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date | Mon, 29 Apr 2019 05:55:48 -0400 |
parents | 4f7a5ccd2ae9 |
children | ce3c7f062223 |
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33:87ee588b3d45 | 34:dde39ba9c031 |
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1 <tool id="bedtools_sortbed" name="bedtools SortBED" version="@WRAPPER_VERSION@"> | 1 <tool id="bedtools_sortbed" name="bedtools SortBED" version="@TOOL_VERSION@"> |
2 <description>order the intervals</description> | 2 <description>order the intervals</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
7 <expand macro="stdio" /> | 7 <expand macro="stdio" /> |
8 <command> | 8 <command><![CDATA[ |
9 <![CDATA[ | 9 sortBed |
10 sortBed | 10 -i '$input' |
11 -i '$input' | 11 $option |
12 $option | 12 > '$output' |
13 > '$output' | 13 ]]></command> |
14 ]]> | |
15 </command> | |
16 <inputs> | 14 <inputs> |
17 <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="Sort the following @STD_BEDTOOLS_INPUT_LABEL@ file"/> | 15 <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="Sort the following @STD_BEDTOOLS_INPUT_LABEL@ file" /> |
18 <param name="option" type="select" label="Sort by"> | 16 <param name="option" type="select" label="Sort by"> |
19 <!-- sort -k 1,1 -k2,2 -n a.bed --> | 17 <!-- sort -k 1,1 -k2,2 -n a.bed --> |
20 <option value="">chromosome, then by start position (asc)</option> | 18 <option value="">chromosome, then by start position (asc)</option> |
21 <option value="-sizeA">feature size in ascending order.</option> | 19 <option value="-sizeA">feature size in ascending order.</option> |
22 <option value="-sizeD">feature size in descending order.</option> | 20 <option value="-sizeD">feature size in descending order.</option> |
25 <option value="-chrThenScoreA">chromosome, then by score (asc).</option> | 23 <option value="-chrThenScoreA">chromosome, then by score (asc).</option> |
26 <option value="-chrThenScoreD">chromosome, then by score (desc).</option> | 24 <option value="-chrThenScoreD">chromosome, then by score (desc).</option> |
27 </param> | 25 </param> |
28 </inputs> | 26 </inputs> |
29 <outputs> | 27 <outputs> |
30 <data format_source="input" name="output" metadata_source="input" label="SortBed on ${input.name}"/> | 28 <data name="output" format_source="input" metadata_source="input" label="SortBed on ${input.name}"/> |
31 </outputs> | 29 </outputs> |
32 <tests> | 30 <tests> |
33 <test> | 31 <test> |
34 <param name="input" value="sortBed1.bed" ftype="bed" /> | 32 <param name="input" value="sortBed1.bed" ftype="bed" /> |
35 <param name="option" value="" /> | 33 <param name="option" value="" /> |
36 <output name="output" file="sortBed_result1.bed" ftype="bed" /> | 34 <output name="output" file="sortBed_result1.bed" ftype="bed" /> |
37 </test> | 35 </test> |
38 </tests> | 36 </tests> |
39 <help> | 37 <help><![CDATA[ |
40 <![CDATA[ | |
41 **What it does** | 38 **What it does** |
42 | 39 |
43 Sorts a feature file by chromosome and other criteria. | 40 Sorts a feature file by chromosome and other criteria. |
44 | 41 |
45 | 42 |
48 It should be noted that sortBed is merely a convenience utility, as the UNIX sort utility | 45 It should be noted that sortBed is merely a convenience utility, as the UNIX sort utility |
49 will sort BED files more quickly while using less memory. For example, UNIX sort will sort a BED file | 46 will sort BED files more quickly while using less memory. For example, UNIX sort will sort a BED file |
50 by chromosome then by start position in the following manner: sort -k 1,1 -k2,2 -n a.bed | 47 by chromosome then by start position in the following manner: sort -k 1,1 -k2,2 -n a.bed |
51 | 48 |
52 @REFERENCES@ | 49 @REFERENCES@ |
53 ]]> | 50 ]]></help> |
54 </help> | |
55 <expand macro="citations" /> | 51 <expand macro="citations" /> |
56 </tool> | 52 </tool> |