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comparison flankBed.xml @ 32:b0d5e752c0c5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
author iuc
date Tue, 05 Sep 2017 09:51:56 -0400
parents c0fbce5dc84a
children ac2040a5e6ff
comparison
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31:cb98f29aa1dc 32:b0d5e752c0c5
1 <tool id="bedtools_flankbed" name="FlankBed" version="@WRAPPER_VERSION@.0"> 1 <tool id="bedtools_flankbed" name="FlankBed" version="@WRAPPER_VERSION@.1">
2 <description>create new intervals from the flanks of existing intervals</description> 2 <description>create new intervals from the flanks of existing 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" />
8 <command> 8 <command>
9 <![CDATA[ 9 <![CDATA[
10 flankBed 10 flankBed
11 $pct 11 $pct
12 $strand 12 $strand
13 -g $genome 13 -g @GENOME_FILE@
14 -i '$input' 14 -i '$input'
15 15
16 #if $addition.addition_select == 'b': 16 #if $addition.addition_select == 'b':
17 -b $addition.b 17 -b $addition.b
18 #else: 18 #else:
22 > '$output' 22 > '$output'
23 ]]> 23 ]]>
24 </command> 24 </command>
25 <inputs> 25 <inputs>
26 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/> 26 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/>
27 <expand macro="genome" /> 27 <expand macro="input_conditional_genome_file" />
28 <param name="pct" type="boolean" checked="false" truevalue="-pct" falsevalue="" 28 <param name="pct" type="boolean" checked="false" truevalue="-pct" falsevalue=""
29 label="Define -l and -r as a fraction of the feature’s length" 29 label="Define -l and -r as a fraction of the feature’s length"
30 help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”. (-pct)" /> 30 help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”. (-pct)" />
31 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" 31 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue=""
32 label="Define -l and -r based on strand" 32 label="Define -l and -r based on strand"
37 <data metadata_source="input" format_source="input" name="output" /> 37 <data metadata_source="input" format_source="input" name="output" />
38 </outputs> 38 </outputs>
39 <tests> 39 <tests>
40 <test> 40 <test>
41 <param name="input" value="a.bed" ftype="bed" /> 41 <param name="input" value="a.bed" ftype="bed" />
42 <param name="genome_file_opts_selector" value="hist" />
42 <param name="genome" value="mm9_chr1.len"/> 43 <param name="genome" value="mm9_chr1.len"/>
43 <param name="addition_select" value="b"/> 44 <param name="addition_select" value="b"/>
44 <param name="b" value="5"/> 45 <param name="b" value="5"/>
45 <output name="output" file="flankBed_result1.bed" ftype="bed" /> 46 <output name="output" file="flankBed_result1.bed" ftype="bed" />
46 </test> 47 </test>
47 <test> 48 <test>
48 <param name="input" value="a.bed" ftype="bed" /> 49 <param name="input" value="a.bed" ftype="bed" />
50 <param name="genome_file_opts_selector" value="hist" />
49 <param name="genome" value="mm9_chr1.len"/> 51 <param name="genome" value="mm9_chr1.len"/>
50 <param name="addition_select" value="lr"/> 52 <param name="addition_select" value="lr"/>
51 <param name="l" value="2"/> 53 <param name="l" value="2"/>
52 <param name="r" value="3"/> 54 <param name="r" value="3"/>
53 <output name="output" file="flankBed_result2.bed" ftype="bed" /> 55 <output name="output" file="flankBed_result2.bed" ftype="bed" />