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comparison sortBed.xml @ 50:df28283b3778 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
author iuc
date Mon, 29 Apr 2019 05:54:22 -0400
parents 2f457890d8c8
children b06c53665eb6
comparison
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49:5074e81a5ce1 50:df28283b3778
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>