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comparison sortBed.xml @ 4:315929597efb draft

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author iuc
date Wed, 07 Jan 2015 12:45:05 -0500
parents 7511823bdea1
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3:190a747ddaa8 4:315929597efb
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>
9 sortBed -i $input $option &gt; $output 9 <![CDATA[
10 sortBed
11 -i $input
12 $option
13 > $output
14 ]]>
10 </command> 15 </command>
11 <inputs> 16 <inputs>
12 <param format="bed" name="input" type="data" label="Sort the following BED file"/> 17 <param format="bed" name="input" type="data" label="Sort the following BED file"/>
13 <param name="option" type="select" label="Sort by"> 18 <param name="option" type="select" label="Sort by">
14 <!-- sort -k 1,1 -k2,2 -n a.bed --> 19 <!-- sort -k 1,1 -k2,2 -n a.bed -->
19 <option value="-chrThenSizeD">chromosome, then by feature size (desc).</option> 24 <option value="-chrThenSizeD">chromosome, then by feature size (desc).</option>
20 <option value="-chrThenScoreA">chromosome, then by score (asc).</option> 25 <option value="-chrThenScoreA">chromosome, then by score (asc).</option>
21 <option value="-chrThenScoreD">chromosome, then by score (desc).</option> 26 <option value="-chrThenScoreD">chromosome, then by score (desc).</option>
22 </param> 27 </param>
23 </inputs> 28 </inputs>
24
25 <outputs> 29 <outputs>
26 <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/> 30 <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/>
27 </outputs> 31 </outputs>
28 32 <tests>
33 <test>
34 <param name="input" value="sortBed1.bed" ftype="bed" />
35 <param name="option" value="" />
36 <output name="output" file="sortBed_result1.bed" ftype="bed" />
37 </test>
38 </tests>
29 <help> 39 <help>
30 40 <![CDATA[
31 **What it does** 41 **What it does**
32 42
33 Sorts a feature file by chromosome and other criteria. 43 Sorts a feature file by chromosome and other criteria.
34 44
35 45
38 It should be noted that sortBed is merely a convenience utility, as the UNIX sort utility 48 It should be noted that sortBed is merely a convenience utility, as the UNIX sort utility
39 will sort BED files more quickly while using less memory. For example, UNIX sort will sort a BED file 49 will sort BED files more quickly while using less memory. For example, UNIX sort will sort a BED file
40 by chromosome then by start position in the following manner: sort -k 1,1 -k2,2 -n a.bed 50 by chromosome then by start position in the following manner: sort -k 1,1 -k2,2 -n a.bed
41 51
42 @REFERENCES@ 52 @REFERENCES@
43 53 ]]>
44 </help> 54 </help>
45 <expand macro="citations" /> 55 <expand macro="citations" />
46 </tool> 56 </tool>