Mercurial > repos > bgruening > diamond
comparison diamond_makedb.xml @ 1:df7738595640 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
author | bgruening |
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date | Mon, 06 Feb 2017 07:08:25 -0500 |
parents | 98037ef3d2a9 |
children | 64be1ac21109 |
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0:98037ef3d2a9 | 1:df7738595640 |
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1 <tool id="bg_diamond_makedb" name="Diamond makedb" version="0.6.13"> | 1 <tool id="bg_diamond_makedb" name="Diamond makedb" version="@VERSION@"> |
2 <description>Build database from a FASTA file</description> | 2 <description>Build database from a FASTA file</description> |
3 <requirements> | 3 <macros> |
4 <requirement type="package" version="0.6.13">diamond</requirement> | 4 <import>macros.xml</import> |
5 </requirements> | 5 </macros> |
6 | |
7 <expand macro="requirements" /> | |
8 <expand macro="stdio" /> | |
9 <expand macro="version_command" /> | |
10 | |
6 <command> | 11 <command> |
7 <!-- DB has two files, *.dmnd and *.tx --> | 12 <!-- DB has two files, *.dmnd and *.tx --> |
8 <![CDATA[ | 13 <![CDATA[ |
9 diamond makedb | 14 diamond makedb |
10 --threads "\${GALAXY_SLOTS:-12}" | 15 --threads "\${GALAXY_SLOTS:-12}" |
11 --in $infile | 16 --in '$infile' |
12 --db ./database | 17 --db ./database |
13 && | |
14 mv ./database.dmnd $outfile | |
15 ]]> | 18 ]]> |
16 </command> | 19 </command> |
20 | |
17 <inputs> | 21 <inputs> |
18 <param name="infile" type="data" format="fasta" label="Input reference file in FASTA format" /> | 22 <param name="infile" type="data" format="fasta" label="Input reference file in FASTA format" /> |
19 </inputs> | 23 </inputs> |
20 | 24 |
21 <outputs> | 25 <outputs> |
22 <data format="diamond_database" name="outfile" label="Diamond database ${on_string}"/> | 26 <data format="dmnd" name="outfile" from_work_dir="database.dmnd" label="${tool.name} on ${on_string}"/> |
23 </outputs> | 27 </outputs> |
28 | |
24 <tests> | 29 <tests> |
25 <test> | 30 <test> |
26 <param name="infile" value="protein.fasta" ftype="fasta"/> | 31 <param name="infile" value="db.fasta" ftype="fasta"/> |
27 <output name="outfile" file="diamond_makedb_result1.dmnd" ftpye="diamond_database"/> | 32 <output name="outfile" value="db.dmnd"/> |
28 </test> | 33 </test> |
29 </tests> | 34 </tests> |
35 | |
30 <help> | 36 <help> |
31 <![CDATA[ | 37 <![CDATA[ |
32 | 38 |
33 .. class:: infomark | 39 .. class:: infomark |
34 | 40 |
35 **What it does** | 41 **What it does** |
36 | 42 |
37 DIAMOND_ is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. | 43 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 | 44 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 | 45 about 80-90% of all matches that BLASTX finds, with an e-value of at most 1e-5. In sensitive mode, DIAMOND is about 2,500 |
40 times faster than BLASTX, finding more than 94% of all matches. | 46 times faster than BLASTX, finding more than 94% of all matches. |
41 | 47 |
42 .. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/ | 48 .. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/ |
43 | 49 |
44 | 50 |
45 ]]> | 51 ]]> |
46 </help> | 52 </help> |
47 <citations> | 53 |
48 <citation type="doi">10.1038/nmeth.3176</citation> | 54 <expand macro="citations" /> |
49 </citations> | |
50 </tool> | 55 </tool> |