Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml @ 14:2fe07f50a41e draft
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
author | peterjc |
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date | Mon, 01 Dec 2014 05:59:16 -0500 |
parents | 623f727cdff1 |
children | c16c30e9ad5b |
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2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
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diff
changeset
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1 <tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.1.01"> |
5 | 2 <description>Show BLAST database information from blastdbcmd</description> |
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
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3 <macros> |
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
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4 <token name="@BINARY@">blastdbcmd</token> |
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
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5 <import>ncbi_macros.xml</import> |
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
|
6 </macros> |
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
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7 <expand macro="requirements" /> |
5 | 8 <command> |
9
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
5
diff
changeset
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9 blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path}" -info -out "$info" |
5 | 10 </command> |
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
10
diff
changeset
|
11 <expand macro="stdio" /> |
5 | 12 <inputs> |
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
10
diff
changeset
|
13 <expand macro="input_conditional_choose_db_type" /> |
5 | 14 </inputs> |
15 <outputs> | |
16 <data name="info" format="txt" label="${db_opts.database.fields.name} info" /> | |
17 </outputs> | |
18 <help> | |
19 | |
20 **What it does** | |
21 | |
22 Calls the NCBI BLAST+ blastdbcmd command line tool with the -info | |
23 switch to give summary information about a BLAST database, such as | |
24 the size (number of sequences and total length) and date. | |
25 | |
26 ------- | |
27 | |
28 **References** | |
29 | |
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:
9
diff
changeset
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30 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:
9
diff
changeset
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31 cite the following papers: |
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:
9
diff
changeset
|
32 |
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
|
33 @REFERENCES@ |
5 | 34 </help> |
14
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
35 <expand macro="blast_citations" /> |
5 | 36 </tool> |