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view tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml @ 34:b6893f57f8d8 draft
planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 028e3e806ba6df913403a2a083a354dfa713755f
author | peterjc |
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date | Thu, 22 Feb 2024 14:47:01 +0000 |
parents | a52d2d93e595 |
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<tool id="ncbi_rpstblastn_wrapper" name="NCBI BLAST+ rpstblastn" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Search protein domain database (PSSMs) with translated nucleotide query sequence(s)</description> <macros> <token name="@BINARY@">rpstblastn</token> <import>ncbi_macros.xml</import> </macros> <expand macro="parallelism" /> <expand macro="preamble" /> <command detect_errors="aggressive"> ## 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 @QUERY@ #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 @BLAST_OUTPUT@ ## 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_FILTER_QUERY@ @ADV_MAX_HITS@ @ADV_QCOV_HSP_PERC@ ## End of advanced options: #end if </command> <inputs> <expand macro="nucl_query" /> <expand macro="input_conditional_pssm" /> <expand macro="input_evalue" /> <expand macro="input_out_format" /> <expand macro="advanced_options"> <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> <expand macro="input_filter_query_default_false" /> <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer --> <expand macro="input_max_hits" /> <expand macro="input_parse_deflines" /> <expand macro="input_qcov_hsp_perc" /> </expand> </inputs> <outputs> <data name="output1" format="tabular" label="rpstblastn on ${on_string}"> <expand macro="output_change_format" /> </data> </outputs> <tests> <test> <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> <param name="db_opts_selector" value="db" /> <param name="database" value="cd00003_and_cd00008" /> <param name="evalue_cutoff" value="1e-8" /> <param name="out_format" value="6" /> <output name="output1" file="empty_file.dat" ftype="tabular" /> </test> </tests> <help> @SEARCH_TIME_WARNING@ **What it does** Search a *protein domain database* using a *nucleotide query*, using the NCBI BLAST+ rpstblastn command line tool. The protein domain databases use position-specific scoring matrices (PSSMs) and are available for a number of domain collections including: *CDD* - NCBI curarated meta-collection of domains, see https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#NCBI_curated_domains *Kog* - PSSMs from automatically aligned sequences and sequence fragments classified in the KOGs resource, the eukaryotic counterpart to COGs, see https://www.ncbi.nlm.nih.gov/COG/ *Cog* - PSSMs from automatically aligned sequences and sequence fragments classified in the COGs resource, which focuses primarily on prokaryotes, see https://www.ncbi.nlm.nih.gov/COG/ *Pfam* - PSSMs from Pfam-A seed alignment database, see http://xfam.org/ *Smart* - PSSMs from SMART domain alignment database, see http://smart.embl-heidelberg.de/ *Tigr* - PSSMs from TIGRFAM database of protein families, see ftp://ftp.jcvi.org/data/TIGRFAMs/ *Prk* - PSSms from automatically aligned stable clusters in the Protein Clusters database, see https://www.ncbi.nlm.nih.gov/proteinclusters?cmd=search&db=proteinclusters The exact list of domain databases offered will depend on how your local Galaxy has been configured. ----- @OUTPUT_FORMAT@ ------- @CLI_OPTIONS@ ------- **References** If you use this Galaxy tool in work leading to a scientific publication please cite the following papers: @REFERENCES@ </help> <expand macro="blast_citations" /> </tool>