Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/blastxml_to_tabular.xml @ 11:4c4a0da938ff draft
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
Supports $GALAXY_SLOTS.
Includes more tests and heavy use of macros.
author | peterjc |
---|---|
date | Thu, 05 Dec 2013 06:55:59 -0500 |
parents | 70e7dcbf6573 |
children | 623f727cdff1 |
rev | line source |
---|---|
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
10
diff
changeset
|
1 <tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.0.22"> |
3
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
2 <description>Convert BLAST XML output to tabular</description> |
10
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
8
diff
changeset
|
3 <version_command interpreter="python">blastxml_to_tabular.py --version</version_command> |
3
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
4 <command interpreter="python"> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
5 blastxml_to_tabular.py $blastxml_file $tabular_file $out_format |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
6 </command> |
8
1f546099212f
Uploaded v0.0.17, default to extended 24 column tabular output (rather than standard 12 column output). This should avoid many cases of repeated BLAST jobs being run due to later needing the extra columns.
peterjc
parents:
3
diff
changeset
|
7 <stdio> |
1f546099212f
Uploaded v0.0.17, default to extended 24 column tabular output (rather than standard 12 column output). This should avoid many cases of repeated BLAST jobs being run due to later needing the extra columns.
peterjc
parents:
3
diff
changeset
|
8 <!-- Anything other than zero is an error --> |
1f546099212f
Uploaded v0.0.17, default to extended 24 column tabular output (rather than standard 12 column output). This should avoid many cases of repeated BLAST jobs being run due to later needing the extra columns.
peterjc
parents:
3
diff
changeset
|
9 <exit_code range="1:" /> |
1f546099212f
Uploaded v0.0.17, default to extended 24 column tabular output (rather than standard 12 column output). This should avoid many cases of repeated BLAST jobs being run due to later needing the extra columns.
peterjc
parents:
3
diff
changeset
|
10 <exit_code range=":-1" /> |
1f546099212f
Uploaded v0.0.17, default to extended 24 column tabular output (rather than standard 12 column output). This should avoid many cases of repeated BLAST jobs being run due to later needing the extra columns.
peterjc
parents:
3
diff
changeset
|
11 </stdio> |
3
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
12 <inputs> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
13 <param name="blastxml_file" type="data" format="blastxml" label="BLAST results as XML"/> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
14 <param name="out_format" type="select" label="Output format"> |
8
1f546099212f
Uploaded v0.0.17, default to extended 24 column tabular output (rather than standard 12 column output). This should avoid many cases of repeated BLAST jobs being run due to later needing the extra columns.
peterjc
parents:
3
diff
changeset
|
15 <option value="std">Tabular (standard 12 columns)</option> |
1f546099212f
Uploaded v0.0.17, default to extended 24 column tabular output (rather than standard 12 column output). This should avoid many cases of repeated BLAST jobs being run due to later needing the extra columns.
peterjc
parents:
3
diff
changeset
|
16 <option value="ext" selected="True">Tabular (extended 24 columns)</option> |
3
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
17 </param> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
18 </inputs> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
19 <outputs> |
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
10
diff
changeset
|
20 <data name="tabular_file" format="tabular" label="$blastxml_file.display_name (as tabular)" /> |
3
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
21 </outputs> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
22 <requirements> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
23 </requirements> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
24 <tests> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
25 <test> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
26 <param name="blastxml_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
27 <param name="out_format" value="std" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
28 <!-- Note this has some white space differences from the actual blastp output blast_four_human_vs_rhodopsin.tabluar --> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
29 <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_converted.tabular" ftype="tabular" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
30 </test> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
31 <test> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
32 <param name="blastxml_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
33 <param name="out_format" value="ext" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
34 <!-- Note this has some white space differences from the actual blastp output blast_four_human_vs_rhodopsin_22c.tabluar --> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
35 <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_converted_ext.tabular" ftype="tabular" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
36 </test> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
37 <test> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
38 <param name="blastxml_file" value="blastp_sample.xml" ftype="blastxml" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
39 <param name="out_format" value="std" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
40 <!-- Note this has some white space differences from the actual blastp output --> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
41 <output name="tabular_file" file="blastp_sample_converted.tabular" ftype="tabular" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
42 </test> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
43 <test> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
44 <param name="blastxml_file" value="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
45 <param name="out_format" value="std" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
46 <!-- Note this has some white space differences from the actual blastx output --> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
47 <output name="tabular_file" file="blastx_rhodopsin_vs_four_human_converted.tabular" ftype="tabular" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
48 </test> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
49 <test> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
50 <param name="blastxml_file" value="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
51 <param name="out_format" value="ext" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
52 <!-- Note this has some white space and XXXX masking differences from the actual blastx output --> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
53 <output name="tabular_file" file="blastx_rhodopsin_vs_four_human_converted_ext.tabular" ftype="tabular" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
54 </test> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
55 <test> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
56 <param name="blastxml_file" value="blastx_sample.xml" ftype="blastxml" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
57 <param name="out_format" value="std" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
58 <!-- Note this has some white space differences from the actual blastx output --> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
59 <output name="tabular_file" file="blastx_sample_converted.tabular" ftype="tabular" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
60 </test> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
61 <test> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
62 <param name="blastxml_file" value="blastp_human_vs_pdb_seg_no.xml" ftype="blastxml" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
63 <param name="out_format" value="std" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
64 <!-- Note this has some white space differences from the actual blastp output --> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
65 <output name="tabular_file" file="blastp_human_vs_pdb_seg_no_converted_std.tabular" ftype="tabular" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
66 </test> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
67 <test> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
68 <param name="blastxml_file" value="blastp_human_vs_pdb_seg_no.xml" ftype="blastxml" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
69 <param name="out_format" value="ext" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
70 <!-- Note this has some white space differences from the actual blastp output --> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
71 <output name="tabular_file" file="blastp_human_vs_pdb_seg_no_converted_ext.tabular" ftype="tabular" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
72 </test> |
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
10
diff
changeset
|
73 <test> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
10
diff
changeset
|
74 <param name="blastxml_file" value="blastn_arabidopsis.xml" ftype="blastxml" /> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
10
diff
changeset
|
75 <param name="out_format" value="std" /> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
10
diff
changeset
|
76 <output name="tabular_file" file="blastn_arabidopsis.standard.tabular" ftype="tabular" /> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
10
diff
changeset
|
77 </test> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
10
diff
changeset
|
78 <test> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
10
diff
changeset
|
79 <param name="blastxml_file" value="blastn_arabidopsis.xml" ftype="blastxml" /> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
10
diff
changeset
|
80 <param name="out_format" value="ext" /> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
10
diff
changeset
|
81 <output name="tabular_file" file="blastn_arabidopsis.extended.tabular" ftype="tabular" /> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
10
diff
changeset
|
82 </test> |
3
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
83 </tests> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
84 <help> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
85 |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
86 **What it does** |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
87 |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
88 NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
89 formats including tabular and a more detailed XML format. A complex workflow |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
90 may need both the XML and the tabular output - but running BLAST twice is |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
91 slow and wasteful. |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
92 |
8
1f546099212f
Uploaded v0.0.17, default to extended 24 column tabular output (rather than standard 12 column output). This should avoid many cases of repeated BLAST jobs being run due to later needing the extra columns.
peterjc
parents:
3
diff
changeset
|
93 This tool takes the BLAST XML output and can convert it into the |
3
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
94 standard 12 column tabular equivalent: |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
95 |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
96 ====== ========= ============================================ |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
97 Column NCBI name Description |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
98 ------ --------- -------------------------------------------- |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
99 1 qseqid Query Seq-id (ID of your sequence) |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
100 2 sseqid Subject Seq-id (ID of the database hit) |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
101 3 pident Percentage of identical matches |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
102 4 length Alignment length |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
103 5 mismatch Number of mismatches |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
104 6 gapopen Number of gap openings |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
105 7 qstart Start of alignment in query |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
106 8 qend End of alignment in query |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
107 9 sstart Start of alignment in subject (database hit) |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
108 10 send End of alignment in subject (database hit) |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
109 11 evalue Expectation value (E-value) |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
110 12 bitscore Bit score |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
111 ====== ========= ============================================ |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
112 |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
113 The BLAST+ tools can optionally output additional columns of information, |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
114 but this takes longer to calculate. Most (but not all) of these columns are |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
115 included by selecting the extended tabular output. The extra columns are |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
116 included *after* the standard 12 columns. This is so that you can write |
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
10
diff
changeset
|
117 workflow filtering steps that accept either the 12 or 25 column tabular |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
10
diff
changeset
|
118 BLAST output. This tool now uses this extended 25 column output by default. |
3
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
119 |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
120 ====== ============= =========================================== |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
121 Column NCBI name Description |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
122 ------ ------------- ------------------------------------------- |
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
10
diff
changeset
|
123 13 sallseqid All subject Seq-id(s), separated by ';' |
3
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
124 14 score Raw score |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
125 15 nident Number of identical matches |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
126 16 positive Number of positive-scoring matches |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
127 17 gaps Total number of gaps |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
128 18 ppos Percentage of positive-scoring matches |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
129 19 qframe Query frame |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
130 20 sframe Subject frame |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
131 21 qseq Aligned part of query sequence |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
132 22 sseq Aligned part of subject sequence |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
133 23 qlen Query sequence length |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
134 24 slen Subject sequence length |
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
10
diff
changeset
|
135 25 salltitles All subject title(s), separated by '<>' |
3
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
136 ====== ============= =========================================== |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
137 |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
138 Beware that the XML file (and thus the conversion) and the tabular output |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
139 direct from BLAST+ may differ in the presence of XXXX masking on regions |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
140 low complexity (columns 21 and 22), and thus also calculated figures like |
8
1f546099212f
Uploaded v0.0.17, default to extended 24 column tabular output (rather than standard 12 column output). This should avoid many cases of repeated BLAST jobs being run due to later needing the extra columns.
peterjc
parents:
3
diff
changeset
|
141 the percentage identity (column 3). |
3
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
142 |
10
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
8
diff
changeset
|
143 **References** |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
8
diff
changeset
|
144 |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
8
diff
changeset
|
145 If you use this Galaxy tool in work leading to a scientific publication please |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
8
diff
changeset
|
146 cite: |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
8
diff
changeset
|
147 |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
8
diff
changeset
|
148 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
8
diff
changeset
|
149 Galaxy tools and workflows for sequence analysis with applications |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
8
diff
changeset
|
150 in molecular plant pathology. PeerJ 1:e167 |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
8
diff
changeset
|
151 http://dx.doi.org/10.7717/peerj.167 |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
8
diff
changeset
|
152 |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
8
diff
changeset
|
153 This wrapper is available to install into other Galaxy Instances via the Galaxy |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
8
diff
changeset
|
154 Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus |
3
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
155 </help> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
156 </tool> |