Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpstblastn_wrapper/2.14.1+galaxy2 (this tool) |
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpstblastn_wrapper/0.0.3 |
ncbi_rpstblastn_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 rpstblastn #if $query.is_of_type('fasta.gz') and $query.ext != "fasta": -query <(gunzip -c '${query}') #else: -query '${query}' #end if #if $db_opts.db_opts_selector == "db": -db '${db_opts.database.fields.path}' #elif $db_opts.db_opts_selector == "histdb": -db '${os.path.join($db_opts.histdb.files_path, "blastdb")}' #end if -evalue $evalue_cutoff -out '$output1' ##Set the extended list here so when we add things, saved workflows are not affected #if str($output.out_format)=="ext": -outfmt '6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen salltitles' #elif str($output.out_format)=="cols" ##Pick your own columns. Galaxy gives us it comma separated, BLAST+ wants space separated: ##Can we catch the user picking no columns and raise an error here? #set cols = (str($output.std_cols)+","+str($output.ext_cols)+","+str($output.ids_cols)+","+str($output.misc_cols)+","+str($output.tax_cols)).replace("None", "").replace(",,", ",").replace(",", " ").strip() -outfmt '6 $cols' #else: ## Note do not quote this as can be '0 -html' which is really two arguments -outfmt ${output.out_format} #end if ## rpstblastn does not support multiple threads up to release 2.2.27+. Added in BLAST 2.2.28+. ##-num_threads 8 #if $adv_opts.adv_opts_selector=="advanced": $adv_opts.filter_query ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string ## ## Quoting BLAST 2.7.1+ output from "blastp --help" or "blastn --help": ## ## *** Formatting options ## -num_descriptions <Integer, >=0> ## Number of database sequences to show one-line descriptions for ## Not applicable for outfmt > 4 ## Default = `500' ## * Incompatible with: max_target_seqs ## -num_alignments <Integer, >=0> ## Number of database sequences to show alignments for ## Default = `250' ## * Incompatible with: max_target_seqs ## ## *** Restrict search or results ## ## -max_target_seqs <Integer, >=1> ## Maximum number of aligned sequences to keep ## Not applicable for outfmt <= 4 ## Default = `500' ## * Incompatible with: num_descriptions, num_alignments ## ## So, taken at face value we do still need to treat the Text and HTML output ## differently from the Tabular and XML, yet the treatment of these limits is ## different (during search or after the search when writing the output): ## https://blastedbio.blogspot.com/2015/12/blast-max-target-sequences-bug.html ## ## See also our user-facing help text. #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): #if str($output.out_format) in ["6", "ext", "cols", "5"]: ## Most output formats use this, including tabular and XML: -max_target_seqs '${adv_opts.max_hits}' #else ## Text and HTML output formats 0-4 currently need this instead: -num_descriptions '${adv_opts.max_hits}' -num_alignments '${adv_opts.max_hits}' #end if #end if #if str($adv_opts.max_hsps) -max_hsps '${adv_opts.max_hsps}' #end if #if float(str($adv_opts.qcov_hsp_perc)) > 0: -qcov_hsp_perc '${adv_opts.qcov_hsp_perc}' #end if ## End of advanced options: #end if
Parallelism |
Functional tests |
name | inputs | outputs | required files |
Test-1 |
query: rhodopsin_nucs.fasta db_opts|database: cd00003_and_cd00008 db_opts|db_opts_selector: db evalue_cutoff: 1e-8 output|out_format: 6 |
name: value |
rhodopsin_nucs.fasta value |