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comparison diamond_makedb.xml @ 0:98037ef3d2a9 draft

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author bgruening
date Sun, 08 Feb 2015 10:05:26 -0500
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children df7738595640
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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>