Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml @ 19:7f3c448e119b draft
v0.1.07 - fix macro problem in blastxml_to_tabular.xml, reenable .loc tests
| author | peterjc |
|---|---|
| date | Thu, 19 Nov 2015 06:30:35 -0500 |
| parents | 697f40151eaf |
| children | 3034ce97dd33 |
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|---|---|
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697f40151eaf
v0.1.05 - Update citation information now GigaScience paper is out
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1 <tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="@WRAPPER_VERSION@"> |
| 5 | 2 <description>Show BLAST database information from blastdbcmd</description> |
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4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
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3 <macros> |
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4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
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4 <token name="@BINARY@">blastdbcmd</token> |
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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
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5 <import>ncbi_macros.xml</import> |
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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
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6 </macros> |
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c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
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7 <expand macro="preamble" /> |
| 5 | 8 <command> |
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9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
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9 blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path}" -info -out "$info" |
| 5 | 10 </command> |
| 11 <inputs> | |
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4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
10
diff
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12 <expand macro="input_conditional_choose_db_type" /> |
| 5 | 13 </inputs> |
| 14 <outputs> | |
| 15 <data name="info" format="txt" label="${db_opts.database.fields.name} info" /> | |
| 16 </outputs> | |
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c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
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17 <tests> |
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c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
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18 <test> |
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c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
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19 <param name="db_opts|db_type" value="prot" /> |
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c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
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20 <param name="db_opts|database" value="four_human_proteins" /> |
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c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
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21 <output name="info" file="four_human_proteins.dbinfo.txt" ftype="txt" lines_diff="4" /> |
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c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
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22 </test> |
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c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
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23 <test> |
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c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
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24 <param name="db_opts|db_type" value="nucl" /> |
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c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
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25 <param name="db_opts|database" value="three_human_mRNA" /> |
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c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
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26 <output name="info" file="three_human_mRNA.dbinfo.txt" ftype="txt" lines_diff="4" /> |
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c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
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27 </test> |
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c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
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28 </tests> |
| 5 | 29 <help> |
| 30 | |
| 31 **What it does** | |
| 32 | |
| 33 Calls the NCBI BLAST+ blastdbcmd command line tool with the -info | |
| 34 switch to give summary information about a BLAST database, such as | |
| 35 the size (number of sequences and total length) and date. | |
| 36 | |
| 37 ------- | |
| 38 | |
| 39 **References** | |
| 40 | |
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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
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41 If you use this Galaxy tool in work leading to a scientific publication please |
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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.
peterjc
parents:
9
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42 cite the following papers: |
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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.
peterjc
parents:
9
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changeset
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43 |
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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:
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44 @REFERENCES@ |
| 5 | 45 </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.
peterjc
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46 <expand macro="blast_citations" /> |
| 5 | 47 </tool> |