Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml @ 27:6f8ea4b9a2c4 draft
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
author | peterjc |
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date | Wed, 09 Sep 2020 15:32:17 +0000 |
parents | 6f386c5dc4fb |
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"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
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1 <tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
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> |
4c4a0da938ff
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6 </macros> |
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7 <expand macro="preamble" /> |
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8 <command detect_errors="aggressive"> |
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"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
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9 blastdbcmd |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
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10 @DBCMD_OPTS@ |
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"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
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11 -info -out "$info" |
5 | 12 </command> |
13 <inputs> | |
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14 <expand macro="input_conditional_choose_db_type" /> |
5 | 15 </inputs> |
16 <outputs> | |
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"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
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17 <data name="info" format="txt" label="@ON_DBCMD_OPTS@ info" /> |
5 | 18 </outputs> |
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19 <tests> |
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20 <test> |
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21 <param name="db_opts|db_type" value="prot" /> |
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"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
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22 <param name="db_opts|db_origin|database" value="four_human_proteins" /> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
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23 <output name="info" file="four_human_proteins.dbinfo.txt" ftype="txt" compare="contains" /> |
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24 </test> |
c16c30e9ad5b
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25 <test> |
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26 <param name="db_opts|db_type" value="nucl" /> |
27
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"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
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27 <param name="db_opts|db_origin|database" value="three_human_mRNA" /> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
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28 <output name="info" file="three_human_mRNA.dbinfo.txt" ftype="txt" compare="contains" /> |
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29 </test> |
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30 <test> |
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peterjc
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31 <param name="db_opts|db_type" value="nucl" /> |
27
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"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
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32 <param name="db_opts|db_origin|database" value="rhodopsin_nucs" /> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
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33 <output name="info" file="rhodopsin_nucs.dbinfo.txt" ftype="txt" compare="contains" /> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
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34 </test> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
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35 <test> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
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36 <param name="db_opts|db_type" value="nucl" /> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
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37 <param name="db_opts|db_origin|database" value="three_human_mRNA,rhodopsin_nucs" /> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
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38 <output name="info" file="three_human_mRNA_and_rhodopsin_nucs.dbinfo.txt" ftype="txt" compare="contains" /> |
20
3034ce97dd33
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peterjc
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39 </test> |
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40 </tests> |
5 | 41 <help> |
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42 |
5 | 43 **What it does** |
44 | |
45 Calls the NCBI BLAST+ blastdbcmd command line tool with the -info | |
46 switch to give summary information about a BLAST database, such as | |
47 the size (number of sequences and total length) and date. | |
48 | |
49 ------- | |
50 | |
51 **References** | |
52 | |
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53 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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54 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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55 |
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56 @REFERENCES@ |
5 | 57 </help> |
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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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58 <expand macro="blast_citations" /> |
5 | 59 </tool> |