Mercurial > repos > bgruening > bedtools_test_bag

comparison flankbed.xml @ 12:c782e0edc4f1 draft default tip

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author bgruening
date Thu, 19 Jun 2014 10:12:00 -0400
parents e526617a6bb9
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11:e526617a6bb9 12:c782e0edc4f1
1 <tool id="bedtools_flankbed" name="FlankBed" version="0.2.0"> 1 <tool id="bedtools_flankbed" name="FlankBed" version="@WRAPPER_VERSION@.0">
2 <description></description> 2 <description></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" />
9 flankBed 9 flankBed
10 $pct 10 $pct
11 $strand 11 $strand
12 -g $genome 12 -g $genome
13 -i $inputA 13 -i $inputA
14
15 #if $addition.addition_select == 'b':
16 -b $addition.b
17 #else:
18 -l $addition.l
19 -r $addition.r
20 #end if
21
14 &gt; $output 22 &gt; $output
15 #if $addition.addition_select == 'b':
16 -b $addition.b
17 #else:
18 -l $addition.l
19 -r $addition.r
20 #end if
21 </command> 23 </command>
22 <inputs> 24 <inputs>
23 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/> 25 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
24 <expand macro="genome" /> 26 <expand macro="genome" />
25 <param name="pct" type="boolean" checked="false" truevalue="-pct" falsevalue="" label="Define -l and -r as a fraction of the feature’s length" help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”" /> 27 <param name="pct" type="boolean" checked="false" truevalue="-pct" falsevalue="" label="Define -l and -r as a fraction of the feature’s length" help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”" />
26 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Define -l and -r based on strand" help="For example. if used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate" /> 28 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Define -l and -r based on strand" help="For example. if used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate" />
27 <expand macro="addition" /> 29 <expand macro="addition" />
28
29
30 </inputs> 30 </inputs>
31 <outputs> 31 <outputs>
32 <data format="bed" name="output" label=""/> 32 <data format="bed" name="output" label=""/>
33 </outputs> 33 </outputs>
34 <help> 34 <help>