Mercurial > repos > iuc > bedtools
comparison getfastaBed.xml @ 43:07e8b80f278c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
| author | iuc |
|---|---|
| date | Fri, 01 Apr 2022 19:02:51 +0000 |
| parents | 841fb4dc3ab3 |
| children | 64e2edfe7a2c |
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| 42:841fb4dc3ab3 | 43:07e8b80f278c |
|---|---|
| 89 <param name="tab" value="False" /> | 89 <param name="tab" value="False" /> |
| 90 <param name="split" value="False" /> | 90 <param name="split" value="False" /> |
| 91 <param name="nameOnly" value="True" /> | 91 <param name="nameOnly" value="True" /> |
| 92 <output name="output" file="getfastaBed_result4.bed" ftype="fasta" /> | 92 <output name="output" file="getfastaBed_result4.bed" ftype="fasta" /> |
| 93 </test> | 93 </test> |
| 94 <test> | |
| 95 <param name="input" value="nucBed2.bed" ftype="bed" /> | |
| 96 <param name="fasta_source_selector" value="preloaded"/> | |
| 97 <param name="fasta_id" value="testid" /> | |
| 98 <param name="tab" value="False" /> | |
| 99 <param name="split" value="False" /> | |
| 100 <param name="nameOnly" value="True" /> | |
| 101 <output name="output" file="getfastaBed_result4.bed" ftype="fasta" /> | |
| 102 </test> | |
| 94 </tests> | 103 </tests> |
| 95 <help><![CDATA[ | 104 <help><![CDATA[ |
| 96 **What it does** | 105 **What it does** |
| 97 | 106 |
| 98 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>”. | 107 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>”. |