Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml @ 15:c16c30e9ad5b draft
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
author | peterjc |
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date | Sun, 05 Jul 2015 10:37:27 -0400 |
parents | 2fe07f50a41e |
children | b5f1f599d1fb |
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1 <tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.1.03"> |
5 | 2 <description>Show BLAST database information from blastdbcmd</description> |
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3 <macros> |
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4 <token name="@BINARY@">blastdbcmd</token> |
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5 <import>ncbi_macros.xml</import> |
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6 </macros> |
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7 <expand macro="preamble" /> |
5 | 8 <command> |
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Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
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9 blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path}" -info -out "$info" |
5 | 10 </command> |
11 <inputs> | |
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12 <expand macro="input_conditional_choose_db_type" /> |
5 | 13 </inputs> |
14 <outputs> | |
15 <data name="info" format="txt" label="${db_opts.database.fields.name} info" /> | |
16 </outputs> | |
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17 <tests> |
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18 <!-- Disable for ToolShed where *.loc tests not yet supported |
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19 See https://github.com/peterjc/galaxy_blast/issues/53 |
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20 <test> |
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21 <param name="db_opts|db_type" value="prot" /> |
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22 <param name="db_opts|database" value="four_human_proteins" /> |
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23 <output name="info" file="four_human_proteins.dbinfo.txt" ftype="txt" lines_diff="4" /> |
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24 </test> |
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25 <test> |
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26 <param name="db_opts|db_type" value="nucl" /> |
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27 <param name="db_opts|database" value="three_human_mRNA" /> |
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28 <output name="info" file="three_human_mRNA.dbinfo.txt" ftype="txt" lines_diff="4" /> |
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29 </test> |
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30 --> |
c16c30e9ad5b
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31 </tests> |
5 | 32 <help> |
33 | |
34 **What it does** | |
35 | |
36 Calls the NCBI BLAST+ blastdbcmd command line tool with the -info | |
37 switch to give summary information about a BLAST database, such as | |
38 the size (number of sequences and total length) and date. | |
39 | |
40 ------- | |
41 | |
42 **References** | |
43 | |
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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.
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44 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.
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45 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
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46 |
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47 @REFERENCES@ |
5 | 48 </help> |
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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.
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49 <expand macro="blast_citations" /> |
5 | 50 </tool> |