|
0
|
1 <tool id="bg_diamond_makedb" name="Diamond makedb" version="0.6.13">
|
|
|
2 <description>Build database from a FASTA file</description>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="package" version="0.6.13">diamond</requirement>
|
|
|
5 </requirements>
|
|
|
6 <command>
|
|
|
7 <!-- DB has two files, *.dmnd and *.tx -->
|
|
|
8 <![CDATA[
|
|
|
9 diamond makedb
|
|
|
10 --threads "\${GALAXY_SLOTS:-12}"
|
|
|
11 --in $infile
|
|
|
12 --db ./database
|
|
|
13 &&
|
|
|
14 mv ./database.dmnd $outfile
|
|
|
15 ]]>
|
|
|
16 </command>
|
|
|
17 <inputs>
|
|
|
18 <param name="infile" type="data" format="fasta" label="Input reference file in FASTA format" />
|
|
|
19 </inputs>
|
|
|
20
|
|
|
21 <outputs>
|
|
|
22 <data format="diamond_database" name="outfile" label="Diamond database ${on_string}"/>
|
|
|
23 </outputs>
|
|
|
24 <tests>
|
|
|
25 <test>
|
|
|
26 <param name="infile" value="protein.fasta" ftype="fasta"/>
|
|
|
27 <output name="outfile" file="diamond_makedb_result1.dmnd" ftpye="diamond_database"/>
|
|
|
28 </test>
|
|
|
29 </tests>
|
|
|
30 <help>
|
|
|
31 <![CDATA[
|
|
|
32
|
|
|
33 .. class:: infomark
|
|
|
34
|
|
|
35 **What it does**
|
|
|
36
|
|
|
37 DIAMOND_ is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.
|
|
|
38 On Illumina reads of length 100-150bp, in fast mode, DIAMOND is about 20,000 times faster than BLASTX, while reporting
|
|
|
39 about 80-90% of all matches that BLASTX finds, with an e-value of at most 1e-5. In sensitive mode, DIAMOND ist about 2,500
|
|
|
40 times faster than BLASTX, finding more than 94% of all matches.
|
|
|
41
|
|
|
42 .. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/
|
|
|
43
|
|
|
44
|
|
|
45 ]]>
|
|
|
46 </help>
|
|
|
47 <citations>
|
|
|
48 <citation type="doi">10.1038/nmeth.3176</citation>
|
|
|
49 </citations>
|
|
|
50 </tool>
|
