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comparison mapBed.xml @ 2:457b09031d57 draft

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Uploaded
author iuc
date Tue, 19 May 2015 07:05:36 -0400
parents 82aac94b06c3
children 2cd7e321d259
comparison
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1:82aac94b06c3 2:457b09031d57
1 <tool id="bedtools_map" name="MapBed" version="@WRAPPER_VERSION@.0"> 1 <tool id="bedtools_map" name="MapBed" version="@WRAPPER_VERSION@.1">
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 <![CDATA[ 9 <![CDATA[
10 bedtools map 10 bedtools map
11 -a "${inputA}" 11 -a "${inputA}"
12 -b "${inputB}" 12 -b "${inputB}"
13 $strand 13 $strand
14 -o $operation 14 @C_AND_O_ARGUMENT@
15 -c "${cols}"
16 -f $overlap 15 -f $overlap
17 $reciprocal 16 $reciprocal
18 $split 17 $split
19 $header 18 $header
20 #if $genome.genome_choose == "-g" : 19 #if $genome.genome_choose == "-g" :
24 ]]> 23 ]]>
25 </command> 24 </command>
26 <inputs> 25 <inputs>
27 <param format="bam,bed,vcf,gff,gff3" name="inputA" type="data" label="File A (BAM/BED/VCF/GFF)" /> 26 <param format="bam,bed,vcf,gff,gff3" name="inputA" type="data" label="File A (BAM/BED/VCF/GFF)" />
28 <param format="bam,bed,gff,vcf,gff3" name="inputB" type="data" label="File B (BAM/BED/VCF/GFF)" /> 27 <param format="bam,bed,gff,vcf,gff3" name="inputB" type="data" label="File B (BAM/BED/VCF/GFF)" />
29 <expand macro="choose_columns" />
30 <expand macro="overlap" /> 28 <expand macro="overlap" />
31 <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue="" 29 <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue=""
32 label="Require reciprocal overlap" 30 label="Require reciprocal overlap"
33 help="If set, the overlap between the BAM alignment and the BED interval must affect the above fraction of both the alignment and the BED interval. (-r)" /> 31 help="If set, the overlap between the BAM alignment and the BED interval must affect the above fraction of both the alignment and the BED interval. (-r)" />
34 <expand macro="strand2" /> 32 <expand macro="strand2" />
35 <expand macro="choose_operations"> 33 <expand macro="c_and_o_argument" />
36 <expand macro="math_options" />
37 <expand macro="additional_math_options" />
38 </expand>
39 <expand macro="split" /> 34 <expand macro="split" />
40 <expand macro="print_header" /> 35 <expand macro="print_header" />
41 <conditional name="genome"> 36 <conditional name="genome">
42 <param name="genome_choose" type="boolean" checked="false" truevalue="-g" falsevalue="" 37 <param name="genome_choose" type="boolean" checked="false" truevalue="-g" falsevalue=""
43 label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage." help="(-g)" /> 38 label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage." help="(-g)" />
51 </outputs> 46 </outputs>
52 <tests> 47 <tests>
53 <test> 48 <test>
54 <param name="inputA" value="mapBed1.bed" ftype="bed" /> 49 <param name="inputA" value="mapBed1.bed" ftype="bed" />
55 <param name="inputB" value="mapBed2.bed" ftype="bed" /> 50 <param name="inputB" value="mapBed2.bed" ftype="bed" />
56 <param name="cols" value="5" /> 51 <repeat name="c_and_o_argument_repeat">
57 <param name="operation" value="mean" /> 52 <param name="cols" value="5" />
53 <param name="operation" value="mean" />
54 </repeat>
58 <output name="output" file="mapBed_result1.bed" ftype="bed" /> 55 <output name="output" file="mapBed_result1.bed" ftype="bed" />
59 </test> 56 </test>
60 <test> 57 <test>
61 <param name="inputA" value="mapBed1.bed" ftype="bed" /> 58 <param name="inputA" value="mapBed1.bed" ftype="bed" />
62 <param name="inputB" value="mapBed2.bed" ftype="bed" /> 59 <param name="inputB" value="mapBed2.bed" ftype="bed" />
63 <param name="cols" value="5" /> 60 <repeat name="c_and_o_argument_repeat">
64 <param name="operation" value="collapse" /> 61 <param name="col" value="5" />
62 <param name="operation" value="collapse" />
63 </repeat>
65 <output name="output" file="mapBed_result2.bed" ftype="bed" /> 64 <output name="output" file="mapBed_result2.bed" ftype="bed" />
66 </test> 65 </test>
67 <test> 66 <test>
68 <param name="inputA" value="mapBed1.bed" ftype="bed" /> 67 <param name="inputA" value="mapBed1.bed" ftype="bed" />
69 <param name="inputB" value="mapBed2.bed" ftype="bed" /> 68 <param name="inputB" value="mapBed2.bed" ftype="bed" />
70 <param name="cols" value="5" /> 69 <repeat name="c_and_o_argument_repeat">
71 <param name="operation" value="collapse" /> 70 <param name="cols" value="5" />
71 <param name="operation" value="collapse" />
72 </repeat>
72 <param name="strand" value="-S" /> 73 <param name="strand" value="-S" />
73 <output name="output" file="mapBed_result3.bed" ftype="bed" /> 74 <output name="output" file="mapBed_result3.bed" ftype="bed" />
74 </test> 75 </test>
75 <test> 76 <test>
76 <param name="inputA" value="mapBed1.bed" ftype="bed" /> 77 <param name="inputA" value="mapBed1.bed" ftype="bed" />
77 <param name="inputB" value="mapBed2.bed" ftype="bed" /> 78 <param name="inputB" value="mapBed2.bed" ftype="bed" />
78 <param name="cols" value="5" /> 79 <repeat name="c_and_o_argument_repeat">
79 <param name="operation" value="collapse" /> 80 <param name="cols" value="5" />
81 <param name="operation" value="collapse" />
82 </repeat>
80 <param name="strand" value="-s" /> 83 <param name="strand" value="-s" />
81 <output name="output" file="mapBed_result4.bed" ftype="bed" /> 84 <output name="output" file="mapBed_result4.bed" ftype="bed" />
82 </test> 85 </test>
83 </tests> 86 </tests>
84 <help> 87 <help>