Mercurial > repos > iuc > bedtools
annotate getfastaBed.xml @ 7:8e6b7c3597a8 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7
| author | iuc |
|---|---|
| date | Mon, 18 Jul 2016 14:06:15 -0400 |
| parents | 607c0576c6ab |
| children | c78cf6fe3018 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="bedtools_getfastabed" name="GetFastaBed" version="@WRAPPER_VERSION@.0"> |
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607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
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2 <description>use intervals to extract sequences from a FASTA file</description> |
| 0 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 1 | 9 <![CDATA[ |
| 0 | 10 bedtools getfasta |
| 11 $name | |
| 12 $tab | |
| 13 $strand | |
| 14 $split | |
| 15 -fi $fasta | |
| 1 | 16 -bed $input |
| 0 | 17 -fo $output |
| 1 | 18 ]]> |
| 0 | 19 </command> |
| 20 <inputs> | |
| 1 | 21 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file" /> |
| 0 | 22 <param format="fasta" name="fasta" type="data" label="Fasta file" /> |
| 1 | 23 <param name="name" type="boolean" checked="false" truevalue="-name" falsevalue="" |
| 24 label="Use the 'name' column in the BED file for the FASTA headers in the output FASTA file" | |
| 25 help="(-name)" /> | |
| 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" /> | |
| 0 | 33 </inputs> |
| 34 <outputs> | |
| 1 | 35 <data format="fasta" name="output"> |
| 36 <change_format> | |
| 37 <when input="tab" value="-tab" format="tabular" /> | |
| 38 </change_format> | |
| 39 </data> | |
| 0 | 40 </outputs> |
| 1 | 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> | |
| 0 | 57 <help> |
| 1 | 58 <![CDATA[ |
| 0 | 59 **What it does** |
| 60 | |
| 1 | 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>:<start>-<end>”. |
| 0 | 62 |
| 63 .. image:: $PATH_TO_IMAGES/getfasta-glyph.png | |
| 64 | |
| 65 .. class:: warningmark | |
| 66 | |
| 67 1. The headers in the input FASTA file must exactly match the chromosome column in the BED file. | |
| 68 | |
| 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. | |
| 70 | |
| 71 @REFERENCES@ | |
| 1 | 72 ]]> |
| 0 | 73 </help> |
| 74 <expand macro="citations" /> | |
| 75 </tool> |