Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml @ 16:b5f1f599d1fb draft
Uploaded v0.1.04, fix regression with BLAST database from history
author | peterjc |
---|---|
date | Wed, 22 Jul 2015 05:01:11 -0400 |
parents | c16c30e9ad5b |
children | 697f40151eaf |
rev | line source |
---|---|
16
b5f1f599d1fb
Uploaded v0.1.04, fix regression with BLAST database from history
peterjc
parents:
15
diff
changeset
|
1 <tool id="ncbi_rpsblast_wrapper" name="NCBI BLAST+ rpsblast" version="0.1.04"> |
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:
diff
changeset
|
2 <description>Search protein domain database (PSSMs) with protein query sequence(s)</description> |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
3 <!-- If job splitting is enabled, break up the query file into parts --> |
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
|
4 <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1" /> |
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
|
5 <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
|
6 <token name="@BINARY@">deltablast</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
|
7 <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
|
8 </macros> |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
9 <expand macro="preamble" /> |
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:
diff
changeset
|
10 <command> |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
11 ## The command is a Cheetah template which allows some Python based syntax. |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
12 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
13 rpsblast |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
14 -query "$query" |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
15 #if $db_opts.db_opts_selector == "db": |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
16 -db "${db_opts.database.fields.path}" |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
17 #elif $db_opts.db_opts_selector == "histdb": |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
18 -db "${os.path.join($db_opts.histdb.files_path,'blastdb')}" |
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:
diff
changeset
|
19 #end if |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
20 -evalue $evalue_cutoff |
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
|
21 @BLAST_OUTPUT@ |
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
|
22 @THREADS@ |
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:
diff
changeset
|
23 #if $adv_opts.adv_opts_selector=="advanced": |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
24 @ADV_FILTER_QUERY@ |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
25 @ADV_MAX_HITS@ |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
26 @ADV_QCOV_HSP_PERC@ |
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:
diff
changeset
|
27 ## End of advanced options: |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
28 #end if |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
29 </command> |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
30 <inputs> |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
31 <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> |
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
|
32 |
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 <expand macro="input_conditional_pssm" /> |
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
|
34 |
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
|
35 <expand macro="input_evalue" /> |
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
|
36 |
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
|
37 <expand macro="input_out_format" /> |
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
|
38 |
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
|
39 <expand macro="advanced_options"> |
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
|
40 <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> |
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
|
41 <expand macro="input_filter_query_default_false" /> |
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
|
42 <expand macro="input_max_hits" /> |
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
|
43 <expand macro="input_parse_deflines" /> |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
44 <expand macro="input_qcov_hsp_perc" /> |
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
|
45 </expand> |
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:
diff
changeset
|
46 </inputs> |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
47 <outputs> |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
48 <data name="output1" format="tabular" label="rpsblast on ${on_string}"> |
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
|
49 |
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
|
50 <expand macro="output_change_format" /> |
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
|
51 |
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:
diff
changeset
|
52 </data> |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
53 </outputs> |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
54 <tests> |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
55 <!-- Disable for ToolShed where *.loc tests not yet supported |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
56 See https://github.com/peterjc/galaxy_blast/issues/53 |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
57 <test> |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
58 <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
59 <param name="db_opts_selector" value="db" /> |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
60 <param name="database" value="cd00003_and_cd00008" /> |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
61 <param name="evalue_cutoff" value="1e-8" /> |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
62 <param name="out_format" value="6" /> |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
63 <output name="output1" file="empty_file.dat" ftype="tabular" /> |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
64 </test> |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
65 --> |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
66 </tests> |
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:
diff
changeset
|
67 <help> |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
68 |
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
|
69 @SEARCH_TIME_WARNING@ |
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:
diff
changeset
|
70 |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
71 **What it does** |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
72 |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
73 Search a *protein domain database* using a *protein query*, |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
74 using the NCBI BLAST+ rpsblast command line tool. |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
75 |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
76 The protein domain databases use position-specific scoring matrices |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
77 (PSSMs) and are available for a number of domain collections including: |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
78 |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
79 *CDD* - NCBI curarated meta-collection of domains, see |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
80 http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#NCBI_curated_domains |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
81 |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
82 *Kog* - PSSMs from automatically aligned sequences and sequence |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
83 fragments classified in the KOGs resource, the eukaryotic |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
84 counterpart to COGs, see http://www.ncbi.nlm.nih.gov/COG/new/ |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
85 |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
86 *Cog* - PSSMs from automatically aligned sequences and sequence |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
87 fragments classified in the COGs resource, which focuses primarily |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
88 on prokaryotes, see http://www.ncbi.nlm.nih.gov/COG/new/ |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
89 |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
90 *Pfam* - PSSMs from Pfam-A seed alignment database, see |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
91 http://pfam.sanger.ac.uk/ |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
92 |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
93 *Smart* - PSSMs from SMART domain alignment database, see |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
94 http://smart.embl-heidelberg.de/ |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
95 |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
96 *Tigr* - PSSMs from TIGRFAM database of protein families, see |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
97 http://www.jcvi.org/cms/research/projects/tigrfams/overview/ |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
98 |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
99 *Prk* - PSSms from automatically aligned stable clusters in the |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
100 Protein Clusters database, see |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
101 http://www.ncbi.nlm.nih.gov/proteinclusters?cmd=search&db=proteinclusters |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
102 |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
103 The exact list of domain databases offered will depend on how your |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
104 local Galaxy has been configured. |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
105 |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
106 ----- |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
107 |
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
|
108 @OUTPUT_FORMAT@ |
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:
diff
changeset
|
109 |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
110 ------- |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
111 |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
112 **References** |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff
changeset
|
113 |
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
|
114 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
|
115 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
|
116 |
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
|
117 @REFERENCES@ |
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:
diff
changeset
|
118 </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
|
119 <expand macro="blast_citations" /> |
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:
diff
changeset
|
120 </tool> |