mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 13:50:20 +08:00
64 lines
2.3 KiB
XML
64 lines
2.3 KiB
XML
<tool id="Extract genomic DNA2" name="Extract genomic DNA">
|
|
<description>using coordinates from UNassembled genomes</description>
|
|
<command interpreter="python">twoBitToFa_wrapper.py $input $out_file1 $input_chromCol $input_startCol $input_endCol $input_strandCol $dbkey "/depot/data2/galaxy/twobit.loc"</command>
|
|
<inputs>
|
|
<param format="interval" name="input" type="data" label="Fetch sequences corresponding to Query"/>
|
|
</inputs>
|
|
<outputs>
|
|
<data format="fasta" name="out_file1" />
|
|
</outputs>
|
|
<tests>
|
|
<test>
|
|
<param name="input" value="droPer1.bed" dbkey="droPer1" ftype="bed" />
|
|
<output name="out_file1" file="droPer1.dat" />
|
|
</test>
|
|
</tests>
|
|
<help>
|
|
|
|
.. class:: warningmark
|
|
|
|
Make sure that the genome build is specified for the interval dataset you are extracting sequences for (click the pencil icon if it is not specified).
|
|
|
|
.. class:: infomark
|
|
|
|
Why do we have two sequence extractors?
|
|
|
|
* **Extract genomic DNA using coordinates from ASSEMBLED genomes** - will work for most cases when your intervals are located on assembled chromosomes (i.e., chr1, chrX, etc.)
|
|
* **Extract genomic DNA using coordinates from UNassembled genomes** (this tool) - is designed to work on partially assembled or unassembled genomes when your intervals are located in contigs or scaffolds rather than assembled chromosomes (i.e., super_1 etc.)
|
|
|
|
These two tools will be merged in the future.
|
|
|
|
-----
|
|
|
|
**What it does**
|
|
|
|
This tool uses coordinate, strand, and build information to fetch genomic DNAs in FASTA format.
|
|
|
|
-----
|
|
|
|
**Example**
|
|
|
|
Input dataset::
|
|
|
|
super_1 127475281 127475310 NM_000230 0 +
|
|
super_1 127485994 127486166 NM_000230 0 +
|
|
super_1 127486011 127486166 D49487 0 +
|
|
|
|
Fetch genomic DNAs of the above data::
|
|
|
|
>super_1:127475281-127475310
|
|
GTAGGAATCGCAGCGCCAGCGGTTGCAAG
|
|
>super_1:127485994-127486166
|
|
GCCCAAGAAGCCCATCCTGGGAAGGAAAATGCATTGGGGAACCCTGTGCG
|
|
GATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATC
|
|
CAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAG
|
|
GATCAATGACATTTCACACACG
|
|
>super_1:127486011-127486166
|
|
TGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGG
|
|
CCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGA
|
|
CACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCAC
|
|
ACACG
|
|
|
|
</help>
|
|
</tool>
|