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comparison complementBed.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 <![CDATA[
9 complementBed 10 complementBed
10 -d $distance 11 -i "$input"
11 -g genome 12 -g "$genome"
12 &gt; $output 13 > "$output"
14 ]]>
13 </command> 15 </command>
14 <inputs> 16 <inputs>
15 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/> 17 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/>
16 <expand macro="genome" /> 18 <expand macro="genome" />
17 </inputs> 19 </inputs>
18 <outputs> 20 <outputs>
19 <data format_source="inputA" name="output" metadata_source="inputA" label="Complemen of ${inputA.name}"/> 21 <data format_source="input" name="output" metadata_source="input" label="Complemen of ${input.name}"/>
20 </outputs> 22 </outputs>
23 <tests>
24 <test>
25 <param name="input" value="a.bed" ftype="bed" />
26 <param name="genome" value="mm9_chr1.len" />
27 <output name="output" file="complementBed_result1.bed" ftype="bed" />
28 </test>
29 </tests>
21 <help> 30 <help>
22 31 <![CDATA[
23 **What it does** 32 **What it does**
24 33
25 bedtools complement returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file. 34 bedtools complement returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file.
26 35
27 .. image:: $PATH_TO_IMAGES/complement-glyph.png 36 .. image:: $PATH_TO_IMAGES/complement-glyph.png
28 37
29 @REFERENCES@ 38 @REFERENCES@
39 ]]>
30 </help> 40 </help>
31 <expand macro="citations" /> 41 <expand macro="citations" />
32 </tool> 42 </tool>