Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastn_wrapper/2.10.1+galaxy0 (this tool) |
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastn_wrapper/0.0.11 |
ncbi_tblastn_wrapper |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
blast | 2.10.1 | 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 tblastn #if $query.is_of_type('fasta.gz') and $query.ext != "fasta": -query <(gunzip -c '${query}') #else: -query '${query}' #end if #if $db_opts.db_opts_selector == "db": -db '"${'" "'.join(str($db_opts.database.fields.path).split(","))}"' #elif $db_opts.db_opts_selector == "histdb": -db '${os.path.join($db_opts.histdb.extra_files_path, "blastdb")}' #else: #if $db_opts.subject.is_of_type('fasta.gz') and $db_opts.subject.ext != "fasta": -subject <(gunzip -c '${$db_opts.subject}') #else: -subject '${db_opts.subject}' #end if #end if -task $blast_type -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"").replace(",,", ",").replace(",", " ").strip() -outfmt '6 $cols' #else: ## Note do not quote this as can be '0 -html' which is really two arguments -outfmt ${output.out_format} #end if -num_threads "\${GALAXY_SLOTS:-8}" #if $adv_opts.adv_opts_selector=="advanced": -db_gencode $adv_opts.db_gencode $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 '${adv_opts.max_hsps}' #end if #if str($adv_opts.word_size): -word_size '${adv_opts.word_size}' #end if $adv_opts.parse_deflines #if str($adv_opts.matrix_gapcosts.matrix): -matrix '${adv_opts.matrix_gapcosts.matrix}' ${adv_opts.matrix_gapcosts.gap_costs} #end if ##Ungapped disabled for now - see comments below ##$adv_opts.ungapped #if $adv_opts.adv_optional_id_files_opts.adv_optional_id_files_opts_selector == 'negative_gilist': -negative_gilist '${adv_opts.adv_optional_id_files_opts.negative_gilist}' #elif $adv_opts.adv_optional_id_files_opts.adv_optional_id_files_opts_selector == 'gilist': -gilist '{$adv_opts.adv_optional_id_files_opts.gilist}' #elif $adv_opts.adv_optional_id_files_opts.adv_optional_id_files_opts_selector == 'seqidlist': -seqidlist '${adv_opts.adv_optional_id_files_opts.seqidlist}' #elif $adv_opts.adv_optional_id_files_opts.adv_optional_id_files_opts_selector == 'taxidlist': -taxidlist '${adv_opts.adv_optional_id_files_opts.taxidlist}' #elif $adv_opts.adv_optional_id_files_opts.adv_optional_id_files_opts_selector == 'negative_taxidlist': -negative_taxidlist '${adv_opts.adv_optional_id_files_opts.negative_taxidlist}' #end if #if float(str($adv_opts.qcov_hsp_perc)) > 0: -qcov_hsp_perc '${adv_opts.qcov_hsp_perc}' #end if #if str($adv_opts.window_size): -window_size '${adv_opts.window_size}' #end if #if str($adv_opts.threshold): -threshold '${adv_opts.threshold}' #end if #if str($adv_opts.comp_based_stats): -comp_based_stats '${adv_opts.comp_based_stats}' #end if ## End of advanced options: #end if
Parallelism |
Functional tests |
name | inputs | outputs | required files |
Test-1 |
query: four_human_proteins.fasta db_opts|database: db_opts|subject: rhodopsin_nucs.fasta db_opts|db_opts_selector: file evalue_cutoff: 1e-10 output|out_format: 5 adv_opts|filter_query: False adv_opts|matrix_gapcosts|matrix: BLOSUM80 adv_opts|max_hits: 0 adv_opts|word_size: adv_opts|parse_deflines: False adv_opts|adv_opts_selector: advanced |
name: value |
four_human_proteins.fasta rhodopsin_nucs.fasta value |
Test-2 |
query: four_human_proteins.fasta db_opts|database: db_opts|subject: rhodopsin_nucs.fasta db_opts|db_opts_selector: file evalue_cutoff: 1e-10 output|out_format: ext adv_opts|filter_query: False adv_opts|matrix_gapcosts|matrix: BLOSUM80 adv_opts|max_hits: 0 adv_opts|word_size: adv_opts|parse_deflines: False adv_opts|adv_opts_selector: advanced |
name: value |
four_human_proteins.fasta rhodopsin_nucs.fasta value |
Test-3 |
query: four_human_proteins.fasta db_opts|database: db_opts|subject: rhodopsin_nucs.fasta db_opts|db_opts_selector: file evalue_cutoff: 1e-10 output|out_format: 6 adv_opts|filter_query: False adv_opts|matrix_gapcosts|matrix: BLOSUM80 adv_opts|max_hits: 0 adv_opts|word_size: adv_opts|parse_deflines: False adv_opts|adv_opts_selector: advanced |
name: value |
four_human_proteins.fasta rhodopsin_nucs.fasta value |
Test-4 |
query: four_human_proteins.fasta db_opts|database: db_opts|subject: rhodopsin_nucs.fasta db_opts|db_opts_selector: file evalue_cutoff: 1e-10 output|out_format: 6 adv_opts|filter_query: False adv_opts|matrix_gapcosts|matrix: BLOSUM80 adv_opts|max_hits: 0 adv_opts|word_size: adv_opts|parse_deflines: True adv_opts|adv_opts_selector: advanced |
name: value |
four_human_proteins.fasta rhodopsin_nucs.fasta value |
Test-5 |
query: four_human_proteins.fasta db_opts|database: db_opts|subject: rhodopsin_nucs.fasta db_opts|db_opts_selector: file evalue_cutoff: 1e-10 output|out_format: 0 -html adv_opts|filter_query: False adv_opts|matrix_gapcosts|matrix: BLOSUM80 adv_opts|max_hits: 0 adv_opts|word_size: adv_opts|parse_deflines: False adv_opts|adv_opts_selector: advanced |
name: value |
four_human_proteins.fasta rhodopsin_nucs.fasta value |