Mercurial > repos > devteam > ncbi_blast_plus

annotate tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml @ 14:db9863278936 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Update README
author peterjc
date Thu, 08 Dec 2016 06:31:03 -0500
parents 4dcc9429d6d2
children c5f20ca77de2
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
856b73016ba1 v0.1.05 - Update citation information now GigaScience paper is out
peterjc
parents: 5
diff changeset
1 <tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="@WRAPPER_VERSION@">
0
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
2 <description>Extract sequence(s) from BLAST database</description>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
3 <macros>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
4 <token name="@BINARY@">blastdbcmd</token>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
5 <import>ncbi_macros.xml</import>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
6 </macros>
3
e98f6bd363ba planemo upload for repository https://github.com/peterjc/galaxy_blast/tools/ncbi_blast_plus commit a567843bb239ee8faec72eb7e52f3b5aa3191631
peterjc
parents: 2
diff changeset
7 <expand macro="preamble" />
0
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
8 <command>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
9 ## The command is a Cheetah template which allows some Python based syntax.
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
10 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
11 blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path}"
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
12
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
13 ##TODO: What about -ctrl_a and -target_only as advanced options?
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
14
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
15 #if $id_opts.id_type=="file":
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
16 -entry_batch "$id_opts.entries"
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
17 #else:
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
18 ##Perform some simple search/replaces to remove whitespace
12
d8f2c1f560ec Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents: 9
diff changeset
19 ##and make it comma separated. Quoted so don't escape pipes.
d8f2c1f560ec Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents: 9
diff changeset
20 -entry "$id_opts.entries.replace('\r',',').replace('\n',',').replace(' ','').replace(',,',',').replace(',,',',').strip(',')"
0
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
21 #end if
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
22
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
23 ##When building a BLAST database, to ensure unique IDs makeblastdb will
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
24 ##do things like turning a FASTA entry with ID of ERP44 into lcl|ERP44
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
25 ##(if using -parse_seqids) or simply assign it an ID using the record
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
26 ##number like gnl|BL_ORD_ID|123 (to cope with duplicate IDs in the FASTA
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
27 ##file). In -parse_seqids mode, a duplicate FASTA ID gives an error.
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
28 ##
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
29 ##The BLAST plain text and XML output will contain these BLAST IDs, but
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
30 ##the tabular output does not (at least, not in BLAST 2.2.25+).
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
31 ##Therefore in general, Galaxy users won't care about the (internal)
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
32 ##BLAST identifiers.
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
33 ##
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
34 ##The blastdbcmd FASTA output will also contain these IDs, but in the
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
35 ##context of the BLAST tabular output they are not helpful. Therefore
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
36 ##to recover the original ID as used in the FASTA file for makeblastdb
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
37 ##we need a litte post processing.
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
38 ##
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
39 ##We remove the NCBI's lcl|... or gnl|BL_ORD_ID|123 prefixes
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
40 ##using sed, however the exact syntax differs for Mac OS X's sed
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
41
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
42 #if str($outfmt)=="blastid":
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
43 -out "$seq"
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
44 #else if sys.platform == "darwin":
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
45 | sed -E 's/^>(lcl\||gnl\|BL_ORD_ID\|[0-9]* )/>/1' > "$seq"
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
46 #else:
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
47 | sed 's/>\(lcl|\|gnl|BL_ORD_ID|[0-9]* \)/>/1' > "$seq"
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
48 #end if
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
49 </command>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
50 <inputs>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
51 <expand macro="input_conditional_choose_db_type" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
52 <conditional name="id_opts">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
53 <param name="id_type" type="select" label="Type of identifier list">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
54 <option value="file">From file</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
55 <option value="prompt">User entered</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
56 </param>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
57 <when value="file">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
58 <param name="entries" type="data" format="txt,tabular" label="Sequence identifier(s)" help="Plain text file with one ID per line (i.e. single column tabular file)"/>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
59 </when>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
60 <when value="prompt">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
61 <param name="entries" type="text" label="Sequence identifier(s)" help="Comma or new line separated list." optional="False" area="True" size="10x30"/>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
62 </when>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
63 </conditional>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
64 <param name="outfmt" type="select" label="Output format">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
65 <option value="original">FASTA with original identifiers</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
66 <option value="blastid">FASTA with BLAST assigned identifiers</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
67 </param>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
68 </inputs>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
69 <outputs>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
70 <data name="seq" format="fasta" label="Sequences from ${db_opts.database.fields.name}" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
71 </outputs>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
72 <tests>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
73 <test>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
74 <param name="db_opts|db_type" value="prot" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
75 <param name="db_opts|database" value="four_human_proteins" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
76 <param name="id_opts|id_type" value="prompt" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
77 <param name="id_opts|entries" value="all" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
78 <param name="outfmt" value="original" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
79 <output name="seq" file="four_human_proteins.fasta" ftype="fasta" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
80 </test>
12
d8f2c1f560ec Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents: 9
diff changeset
81 <test>
13
4dcc9429d6d2 v0.2.00, updated to depend on BLAST+ 2.5.0
peterjc
parents: 12
diff changeset
82 <!-- This used to recover the original FASTA file, but had GI numbers -->
12
d8f2c1f560ec Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents: 9
diff changeset
83 <param name="db_opts|db_type" value="nucl" />
d8f2c1f560ec Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents: 9
diff changeset
84 <param name="db_opts|database" value="rhodopsin_nucs" />
d8f2c1f560ec Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents: 9
diff changeset
85 <param name="id_opts|id_type" value="prompt" />
d8f2c1f560ec Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents: 9
diff changeset
86 <param name="id_opts|entries" value="all" />
d8f2c1f560ec Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents: 9
diff changeset
87 <param name="outfmt" value="original" />
13
4dcc9429d6d2 v0.2.00, updated to depend on BLAST+ 2.5.0
peterjc
parents: 12
diff changeset
88 <output name="seq" file="rhodopsin_nucs.no_gi.fasta" ftype="fasta" />
12
d8f2c1f560ec Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents: 9
diff changeset
89 </test>
d8f2c1f560ec Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents: 9
diff changeset
90 <test>
d8f2c1f560ec Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents: 9
diff changeset
91 <param name="db_opts|db_type" value="nucl" />
d8f2c1f560ec Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents: 9
diff changeset
92 <param name="db_opts|database" value="rhodopsin_nucs" />
d8f2c1f560ec Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents: 9
diff changeset
93 <param name="id_opts|id_type" value="prompt" />
d8f2c1f560ec Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents: 9
diff changeset
94 <param name="id_opts|entries" value="U59921.1" />
d8f2c1f560ec Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents: 9
diff changeset
95 <param name="outfmt" value="original" />
d8f2c1f560ec Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents: 9
diff changeset
96 <output name="seq" file="rhodopsin_bufo.fasta" ftype="fasta" />
d8f2c1f560ec Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents: 9
diff changeset
97 </test>
d8f2c1f560ec Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents: 9
diff changeset
98 <test>
d8f2c1f560ec Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents: 9
diff changeset
99 <param name="db_opts|db_type" value="nucl" />
d8f2c1f560ec Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents: 9
diff changeset
100 <param name="db_opts|database" value="rhodopsin_nucs" />
d8f2c1f560ec Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents: 9
diff changeset
101 <param name="id_opts|id_type" value="prompt" />
d8f2c1f560ec Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents: 9
diff changeset
102 <param name="id_opts|entries" value="gi|2734705|gb|U59921.1|BBU59921" />
d8f2c1f560ec Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents: 9
diff changeset
103 <param name="outfmt" value="original" />
d8f2c1f560ec Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents: 9
diff changeset
104 <output name="seq" file="rhodopsin_bufo.fasta" ftype="fasta" />
d8f2c1f560ec Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents: 9
diff changeset
105 </test>
0
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
106 </tests>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
107 <help>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
108
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
109 **What it does**
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
110
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
111 Extracts FASTA formatted sequences from a BLAST database
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
112 using the NCBI BLAST+ blastdbcmd command line tool.
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
113
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
114 .. class:: warningmark
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
115
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
116 **BLAST assigned identifiers**
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
117
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
118 When a BLAST database is constructed from a FASTA file, the
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
119 original identifiers can be replaced with BLAST assigned
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
120 identifiers, partly to ensure uniqueness. e.g. Sometimes
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
121 a prefix of 'lcl|' is added (lcl is short for local),
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
122 or an arbitrary name starting 'gnl|BL_ORD_ID|' is created.
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
123
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
124 If you are using the tabular output from BLAST, it will contain
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
125 the original identifiers - not the BLAST assigned identifiers
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
126 suitable for use with the blastdbcmd tool.
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
127
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
128 If you are using the XML or plain text output, this will also
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
129 contain the BLAST assigned identifiers. However, this means
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
130 getting a list of BLAST assigned identifiers isn't straightforward.
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
131
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
132 -------
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
133
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
134 **References**
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
135
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
136 If you use this Galaxy tool in work leading to a scientific publication please
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
137 cite the following papers:
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
138
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
139 @REFERENCES@
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
140 </help>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
141 <expand macro="blast_citations" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
142 </tool>