Mercurial > repos > alermine > nebula
comparison [APliBio]Nebula tools suite/Nebula/IntersectBed/bedtools_intersectBed.xml @ 0:2ec3ba0e9e70 draft
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author | alermine |
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date | Thu, 25 Oct 2012 08:18:25 -0400 |
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-1:000000000000 | 0:2ec3ba0e9e70 |
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1 <tool id="bedtools_intersectBed" name="IntersectBed" version="v2.10.0"> | |
2 <description>Report overlaps between two feature files</description> | |
3 <command>bedtools intersect | |
4 | |
5 $invert $count | |
6 | |
7 -f $min_overlap | |
8 | |
9 #if str($typeA.file_typeA)=="bam" | |
10 -abam $typeA.fileA -b $typeB.fileB > $outbamfile; | |
11 #end if | |
12 | |
13 #if str($typeA.file_typeA)=="bed" | |
14 $report.type_report -a $typeA.fileA -b $typeB.fileB > $outbedfile; | |
15 #end if | |
16 | |
17 #if str($typeA.file_typeA)=="gff" | |
18 $report.type_report -a $typeA.fileA -b $typeB.fileB > $outgfffile; | |
19 #end if | |
20 | |
21 #if str($typeA.file_typeA)=="vcf" | |
22 $report.type_report -a $typeA.fileA -b $typeB.fileB > $outvcffile; | |
23 #end if | |
24 | |
25 </command> | |
26 <inputs> | |
27 | |
28 <conditional name="typeA"> | |
29 <param name="file_typeA" type="select" label="Select the file A type to intersect"> | |
30 <option value="bed">BED (.bed)</option> | |
31 <option value="bam">BAM (.bam)</option> | |
32 <option value="vcf">VCF (.vcf)</option> | |
33 <option value="gff">GFF (.gff)</option> | |
34 </param> | |
35 <when value="bam"> | |
36 <param name="fileA" format="bam" type="data" label="BAM file"/> | |
37 </when> | |
38 <when value="bed"> | |
39 <param name="fileA" format="bed" type="data" label="BED file"/> | |
40 </when> | |
41 <when value="vcf"> | |
42 <param name="fileA" format="vcf" type="data" label="VCF file"/> | |
43 </when> | |
44 <when value="gff"> | |
45 <param name="fileA" format="gff" type="data" label="GFF file"/> | |
46 </when> | |
47 </conditional> | |
48 | |
49 <conditional name="typeB"> | |
50 <param name="file_typeB" type="select" label="Select the file B type to intersect"> | |
51 <option value="bed">BED (.bed)</option> | |
52 <option value="vcf">VCF (.vcf)</option> | |
53 <option value="gff">GFF (.gff)</option> | |
54 </param> | |
55 <when value="bed"> | |
56 <param name="fileB" format="bed" type="data" label="BED file"/> | |
57 </when> | |
58 <when value="vcf"> | |
59 <param name="fileB" format="vcf" type="data" label="VCF file"/> | |
60 </when> | |
61 <when value="gff"> | |
62 <param name="fileB" format="gff" type="data" label="GFF file"/> | |
63 </when> | |
64 </conditional> | |
65 | |
66 <conditional name="report"> | |
67 <param name="type_report" type="select" label="Select the type of report" help="not used if the file A type is BAM"> | |
68 <option value="">write the base-pair overlap between A and B</option> | |
69 <option value="-wa">write the original entry in A for each overlap (-wa)</option> | |
70 <!-- <option value="-wb">-wb : write the original entry in B for each overlap</option> --> | |
71 <option value="-wo">write the original A and B entries plus the number of base pairs of overlap between the two features (-wo)</option> | |
72 <option value="-wao">write the original A and B entries plus the number of base pairs of overlap between the two features (-wao)</option> | |
73 </param> | |
74 <when value=""> | |
75 <!-- do nothing here --> | |
76 </when> | |
77 <when value="-wa"> | |
78 <!-- do nothing here --> | |
79 </when> | |
80 <!-- <when value="-wb"> | |
81 </when> --> | |
82 <when value="-wo"> | |
83 <!-- do nothing here --> | |
84 </when> | |
85 <when value="-wao"> | |
86 <!-- do nothing here --> | |
87 </when> | |
88 </conditional> | |
89 | |
90 <param name="invert" label="Only report those entries in A that have _no overlaps_ with B?" type="boolean" truevalue="-v" falsevalue="" checked="no"/> | |
91 <param name="count" label="For each entry in A, report the number of overlaps with B?" type="boolean" truevalue="-c" falsevalue="" checked="no"/> | |
92 | |
93 <param name="min_overlap" type="float" size="10" value="0.05" label="Minimum overlap required as a fraction of A" help="5% by default" /> | |
94 <param name="file_name" type="text" size="20" value="sample" label="File name (without file extension)"/> | |
95 </inputs> | |
96 | |
97 <outputs> | |
98 <data format="bam" name="outbamfile" label="${file_name}.bam"> | |
99 <filter>typeA['file_typeA']=="bam"</filter> | |
100 </data> | |
101 <data format="bed" name="outbedfile" label="${file_name}.bed"> | |
102 <filter>typeA['file_typeA']=="bed"</filter> | |
103 </data> | |
104 <data format="gff" name="outgfffile" label="${file_name}.gff"> | |
105 <filter>typeA['file_typeA']=="gff"</filter> | |
106 </data> | |
107 <data format="vcf" name="outvcffile" label="${file_name}.vcf"> | |
108 <filter>typeA['file_typeA']=="vcf"</filter> | |
109 </data>--> | |
110 </outputs> | |
111 | |
112 <help> | |
113 **What it does** | |
114 | |
115 This tool use the "intersectBed" function of Bedtools to report overlaps between two feature files. | |
116 | |
117 Note: When intersecting SNPs, make sure the coordinate conform to the UCSC format. | |
118 That is, the start position for each SNP should be SNP position - 1 and the end position should be SNP position. E.g. chr7 10000001 10000002 rs123464 | |
119 | |
120 * Report the base-pair overlap between sequence alignments and genes. | |
121 $ intersectBed -a reads.bed -b genes.bed | |
122 * Report whether each alignment overlaps one or more genes. If not, the alignment is not reported. | |
123 $ intersectBed -a reads.bed -b genes.bed -u | |
124 * Report those alignments that overlap NO genes. Like "grep -v" | |
125 $ intersectBed -a reads.bed -b genes.bed -v | |
126 * Report the number of genes that each alignment overlaps. | |
127 $ intersectBed -a reads.bed -b genes.bed -c | |
128 * Report the entire, original alignment entry for each overlap with a gene. | |
129 $ intersectBed -a reads.bed -b genes.bed -wa | |
130 * Report the entire, original alignment and genes entries for each overlap plus the number of base pairs. Only reads features with overlap are reported. | |
131 $ intersectBed -a reads.bed -b genes.bed -wo | |
132 * Report the entire, original alignment and genes entries for each overlap plus the number of base pairs. However, alignment features w/o overlap are also reported with a NULL gene feature and overlap = 0. | |
133 $ intersectBed -a reads.bed -b genes.bed -wao | |
134 * Only report an overlap with a repeat if it spans at least 50% of the exon. | |
135 $ intersectBed -a exons.bed -b repeatMasker.bed –f 0.50 | |
136 * Only report an overlap if comprises 50% of the structural variant and 50% of the segmental duplication. Thus, it is reciprocally at least a 50% overlap. | |
137 $ intersectBed -a SV.bed -b segmentalDups.bed –f 0.50 -r | |
138 * Read BED A from stdin. For example, find genes that overlap LINEs but not SINEs. | |
139 $ intersectBed -a genes.bed -b LINES.bed | intersectBed -a stdin -b SINEs.bed -v | |
140 * Retain only single-end BAM alignments that overlap exons. | |
141 $ intersectBed -abam reads.bam -b exons.bed > reads.touchingExons.bam | |
142 * Retain only single-end BAM alignments that do not overlap simple sequence repeats. | |
143 $ intersectBed -abam reads.bam -b SSRs.bed -v > reads.noSSRs.bam | |
144 | |
145 ----- | |
146 | |
147 .. class:: infomark | |
148 | |
149 Contact Bruno Zeitouni (bruno.zeitouni@curie.fr) for any questions or concerns about the Galaxy implementation of IntersectBed. | |
150 | |
151 </help> | |
152 | |
153 </tool> |