root/galaxy-central/tools/ncbi_blast_plus/blastxml_to_tabular.xml

リビジョン 2, 1.1 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.0.1">
2    <description>Convert BLAST XML output to tabular</description>
3    <command interpreter="python">
4      blastxml_to_tabular.py $blastxml_file $tabular_file
5    </command>
6    <inputs>
7        <param name="blastxml_file" type="data" format="blastxml" label="BLAST results as XML"/>
8    </inputs>
9    <outputs>
10        <data name="tabular_file" format="tabular" label="BLAST results as tabular" />
11    </outputs>
12    <requirements>
13    </requirements>
14    <tests>
15    </tests>
16    <help>
17   
18**What it does**
19
20NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of formats including
21tabular and a more detailed XML format. A complex workflow may need both the XML and the
22tabular output.
23
24This tool takes the BLAST XML output and converts it into the 12 column tabular equivalent:
25
261. Id of your sequence
272. GI of the database hit
283. % identity
294. Alignment length
305. # mismatches
316. # gaps
327. Start position in your sequence
338. End position in your sequence
349. Start position in database hit
3510. End position in database hit
3611. E-value
3712. Bit score
38
39
40    </help>
41</tool>
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。