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planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_xml_to_tabular commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
author dfornika
date Mon, 09 Sep 2019 17:17:09 -0400
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1 <tool id="blast_xml_to_tabular" name="BLAST XML to tabular" version="1.1.0">
2 <description>Convert BLAST XML output to tabular</description>
3 <command detect_errors="exit_code">
4 <![CDATA[
5 '$__tool_directory__/blast_xml_to_tabular.py'
6 '${blastxml_file}'
7 '${tabular_file}'
8 '${out_format}'
9 ]]>
10 </command>
11 <inputs>
12 <param name="blastxml_file" type="data" format="blastxml" label="BLAST results as XML"/>
13 <param name="out_format" type="select" label="Output format">
14 <option value="std" selected="True">Tabular (standard 12 columns)</option>
15 <option value="ext">Tabular (extended 24 columns)</option>
16 <option value="ext+">Tabular (extended 26 columns)</option>
17 </param>
18 </inputs>
19 <outputs>
20 <data name="tabular_file" format="tabular" label="BLAST results: data $blastxml_file.hid as tabular" />
21 </outputs>
22 <help>
23
24 .. class:: infomark
25
26 **What it does**
27
28 NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of
29 formats including tabular and a more detailed XML format. A complex workflow
30 may need both the XML and the tabular output - but running BLAST twice is
31 slow and wasteful.
32
33 This tool takes the BLAST XML output and by default converts it into the
34 standard 12 column tabular equivalent:
35
36 ====== ========= ============================================
37 Column NCBI name Description
38 ------ --------- --------------------------------------------
39 1 qseqid Query Seq-id (ID of your sequence)
40 2 sseqid Subject Seq-id (ID of the database hit)
41 3 pident Percentage of identical matches
42 4 length Alignment length
43 5 mismatch Number of mismatches
44 6 gapopen Number of gap openings
45 7 qstart Start of alignment in query
46 8 qend End of alignment in query
47 9 sstart Start of alignment in subject (database hit)
48 10 send End of alignment in subject (database hit)
49 11 evalue Expectation value (E-value)
50 12 bitscore Bit score
51 ====== ========= ============================================
52
53 The BLAST+ tools can optionally output additional columns of information,
54 but this takes longer to calculate. Most (but not all) of these columns are
55 included by selecting the extended tabular output. The extra columns are
56 included *after* the standard 12 columns. This is so that you can write
57 workflow filtering steps that accept either the 12 or 24 column tabular
58 BLAST output.
59
60 ====== ============= ===========================================
61 Column NCBI name Description
62 ------ ------------- -------------------------------------------
63 13 sallseqid All subject Seq-id(s), separated by a ';'
64 14 score Raw score
65 15 nident Number of identical matches
66 16 positive Number of positive-scoring matches
67 17 gaps Total number of gaps
68 18 ppos Percentage of positive-scoring matches
69 19 qframe Query frame
70 20 sframe Subject frame
71 21 qseq Aligned part of query sequence
72 22 sseq Aligned part of subject sequence
73 23 qlen Query sequence length
74 24 slen Subject sequence length
75 ====== ============= ===========================================
76
77 Very slight modifications were made to the "BLAST XML to tabular" tool that
78 ships with Galaxy to output two more column columns:
79
80 ====== ============= ===========================================
81 Column NCBI name Description
82 ------ ------------- -------------------------------------------
83 25 pcov Percentage coverage
84 26 sallseqdescr All subject Seq-descr(s), separated by a ','
85 ====== ============= ===========================================
86
87 ----
88
89 .. class:: infomark
90
91 This is a slightly modified version of a tool that ships with Galaxy.
92 If the 12 or 24 columns formats are desired, use the original tool.
93
94 .. class:: warningmark
95
96 Beware that the XML file (and thus the conversion) and the tabular output
97 direct from BLAST+ may differ in the presence of XXXX masking on regions
98 low complexity (columns 21 and 22), and thus also calculated figures like
99 the percentage identity (column 3).
100
101 </help>
102 </tool>