Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_wrapper/2.14.1+galaxy2 (this tool) |
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_wrapper/2.14.1+galaxy1 |
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_wrapper/2.14.1+galaxy0 |
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_wrapper/2.10.1+galaxy2 |
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_wrapper/2.10.1+galaxy1 |
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_wrapper/2.10.1+galaxy0 |
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_wrapper/0.0.3 |
ncbi_blastdbcmd_wrapper |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
blast | 2.14.1 | package |
Additional information about this tool |
## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces blastdbcmd -dbtype "$db_opts.db_type" #if $db_opts.db_origin.db_origin_selector=="db": -db "${db_opts.db_origin.database.fields.path.replace(',',' ')}" #else if $db_opts.db_origin.db_origin_selector=="histdb": -db '${os.path.join($db_opts.db_origin.histdb.extra_files_path, "blastdb")}' #end if #if $id_opts.id_type=="file": -entry_batch '$id_opts.entries' #else: ##Perform some simple search/replaces to remove whitespace ##and make it comma separated. Quoted so don't escape pipes. -entry "$id_opts.entries.replace('\r',',').replace('\n',',').replace(' ','').replace(',,',',').replace(',,',',').strip(',')" #end if ##When building a BLAST database, to ensure unique IDs makeblastdb will ##do things like turning a FASTA entry with ID of ERP44 into lcl|ERP44 ##(if using -parse_seqids) or simply assign it an ID using the record ##number like gnl|BL_ORD_ID|123 (to cope with duplicate IDs in the FASTA ##file). In -parse_seqids mode, a duplicate FASTA ID gives an error. ## ##The BLAST plain text and XML output will contain these BLAST IDs, but ##the tabular output does not (at least, not in BLAST 2.2.25+). ##Therefore in general, Galaxy users won't care about the (internal) ##BLAST identifiers. ## ##The blastdbcmd FASTA output will also contain these IDs, but in the ##context of the BLAST tabular output they are not helpful. Therefore ##to recover the original ID as used in the FASTA file for makeblastdb ##we need a litte post processing. ## ##We remove the NCBI's lcl|... or gnl|BL_ORD_ID|123 prefixes ##using sed, however the exact syntax differs for Mac OS X's sed #if str($outfmt)=="blastid": -out '$seq' #else if sys.platform == "darwin": | sed -E 's/^>(lcl\||gnl\|BL_ORD_ID\|[0-9]* )/>/1' > "$seq" #else: | sed 's/>\(lcl|\|gnl|BL_ORD_ID|[0-9]* \)/>/1' > "$seq" #end if
Functional tests |
name | inputs | outputs | required files |
Test-1 |
db_opts|db_origin|database: four_human_proteins db_opts|db_origin|db_origin_selector: db db_opts|db_type: prot id_opts|entries: all id_opts|id_type: prompt outfmt: original |
name: value |
value |
Test-2 |
db_opts|db_origin|database: rhodopsin_nucs db_opts|db_type: nucl id_opts|entries: all id_opts|id_type: prompt outfmt: original |
name: value |
value |
Test-3 |
db_opts|db_origin|database: rhodopsin_nucs db_opts|db_type: nucl id_opts|entries: rhodopsin_nucs.blastdbcmd.txt id_opts|id_type: file outfmt: original |
name: value |
rhodopsin_nucs.blastdbcmd.txt value |
Test-4 |
db_opts|db_origin|database: rhodopsin_nucs db_opts|db_type: nucl id_opts|entries: U59921.1 id_opts|id_type: prompt outfmt: original |
name: value |
value |
Test-5 |
db_opts|db_origin|database: ['rhodopsin_nucs', 'three_human_mRNA'] db_opts|db_type: nucl id_opts|entries: gi|2734705|gb|U59921.1|BBU59921 id_opts|id_type: prompt outfmt: original |
name: value |
value |