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comparison getfastaBed.xml @ 1:82aac94b06c3 draft

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author iuc
date Thu, 08 Jan 2015 14:25:51 -0500
parents b8348686a0b9
children 607c0576c6ab
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0:b8348686a0b9 1:82aac94b06c3
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 bedtools getfasta 10 bedtools getfasta
10 $name 11 $name
11 $tab 12 $tab
12 $strand 13 $strand
13 $split 14 $split
14 -fi $fasta 15 -fi $fasta
15 -bed $inputA 16 -bed $input
16 -fo $output 17 -fo $output
18 ]]>
17 </command> 19 </command>
18 <inputs> 20 <inputs>
19 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file" /> 21 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file" />
20 <param format="fasta" name="fasta" type="data" label="Fasta file" /> 22 <param format="fasta" name="fasta" type="data" label="Fasta file" />
21 <param name="name" type="boolean" checked="false" truevalue="-name" falsevalue="" label="Use the “name” column in the BED file for the FASTA headers in the output FASTA file" /> 23 <param name="name" type="boolean" checked="false" truevalue="-name" falsevalue=""
22 <param name="tab" type="boolean" checked="false" truevalue="-tab" falsevalue="" label="Report extract sequences in a tab-delimited format instead of in FASTA format" /> 24 label="Use the 'name' column in the BED file for the FASTA headers in the output FASTA file"
23 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Force strandedness" help="If the feature occupies the antisense strand, the sequence will be reverse complemented." /> 25 help="(-name)" />
24 <param name="split" type="boolean" checked="false" truevalue="-split" falsevalue="" label="Given BED12 input, extract and concatenate the sequences from the BED 'blocks' (e.g., exons)" /> 26 <param name="tab" type="boolean" checked="false" truevalue="-tab" falsevalue=""
27 label="Report extract sequences in a tab-delimited format instead of in FASTA format"
28 help="(-tab)" />
29 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue=""
30 label="Force strandedness"
31 help="If the feature occupies the antisense strand, the sequence will be reverse complemented. (-s)" />
32 <expand macro="split" />
25 </inputs> 33 </inputs>
26 <outputs> 34 <outputs>
27 <data format="fasta" name="output" /> 35 <data format="fasta" name="output">
36 <change_format>
37 <when input="tab" value="-tab" format="tabular" />
38 </change_format>
39 </data>
28 </outputs> 40 </outputs>
41 <tests>
42 <test>
43 <param name="input" value="nucBed1.bed" ftype="bed" />
44 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
45 <param name="tab" value="False" />
46 <param name="split" value="False" />
47 <output name="output" file="getfastaBed_result1.bed" ftype="fasta" />
48 </test>
49 <test>
50 <param name="input" value="nucBed1.bed" ftype="bed" />
51 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
52 <param name="tab" value="True" />
53 <param name="split" value="False" />
54 <output name="output" file="getfastaBed_result2.tabular" ftype="tabular" />
55 </test>
56 </tests>
29 <help> 57 <help>
58 <![CDATA[
30 **What it does** 59 **What it does**
31 60
32 bedtools getfasta will extract the sequence defined by the coordinates in a BED interval and create a new FASTA entry in the output file for each extracted sequence. By default, the FASTA header for each extracted sequence will be formatted as follows: “&lt;chrom>:&lt;start>-&lt;end>”. 61 bedtools getfasta will extract the sequence defined by the coordinates in a BED interval and create a new FASTA entry in the output file for each extracted sequence. By default, the FASTA header for each extracted sequence will be formatted as follows: “>chrom>:&lt;start>-&lt;end>”.
33 62
34 .. image:: $PATH_TO_IMAGES/getfasta-glyph.png 63 .. image:: $PATH_TO_IMAGES/getfasta-glyph.png
35 64
36 .. class:: warningmark 65 .. class:: warningmark
37 66
38 1. The headers in the input FASTA file must exactly match the chromosome column in the BED file. 67 1. The headers in the input FASTA file must exactly match the chromosome column in the BED file.
39 68
40 2. You can use the UNIX fold command to set the line width of the FASTA output. For example, fold -w 60 will make each line of the FASTA file have at most 60 nucleotides for easy viewing. 69 2. You can use the UNIX fold command to set the line width of the FASTA output. For example, fold -w 60 will make each line of the FASTA file have at most 60 nucleotides for easy viewing.
41 70
42 @REFERENCES@ 71 @REFERENCES@
72 ]]>
43 </help> 73 </help>
44 <expand macro="citations" /> 74 <expand macro="citations" />
45 </tool> 75 </tool>