Mercurial > repos > peterjc > ncbi_blast_plus
view tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml @ 38:2f7fac29bb3c draft
Uploaded v0.1.00 preview 1, updated to wrap BLAST+ 2.2.29
author | peterjc |
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date | Wed, 15 Jan 2014 05:38:14 -0500 |
parents | b2795652d2b4 |
children | 148eceb80cbb |
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<tool id="ncbi_rpsblast_wrapper" name="NCBI BLAST+ rpsblast" version="0.1.00"> <description>Search protein domain database (PSSMs) with protein query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1" /> <macros> <token name="@BINARY@">deltablast</token> <import>ncbi_macros.xml</import> </macros> <expand macro="requirements" /> <command> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces rpsblast -query "$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.extra_files_path,'blastdb')}" #end if -evalue $evalue_cutoff @BLAST_OUTPUT@ @THREADS@ #if $adv_opts.adv_opts_selector=="advanced": @ADVANCED_OPTIONS@ ## End of advanced options: #end if </command> <expand macro="stdio" /> <inputs> <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> <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" /> <expand macro="input_max_hits" /> <expand macro="input_word_size" /> <expand macro="input_parse_deflines" /> </expand> </inputs> <outputs> <data name="output1" format="tabular" label="rpsblast on ${on_string}"> <expand macro="output_change_format" /> </data> </outputs> <help> @SEARCH_TIME_WARNING@ **What it does** Search a *protein domain database* using a *protein query*, using the NCBI BLAST+ rpsblast 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 http://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 http://www.ncbi.nlm.nih.gov/COG/new/ *Cog* - PSSMs from automatically aligned sequences and sequence fragments classified in the COGs resource, which focuses primarily on prokaryotes, see http://www.ncbi.nlm.nih.gov/COG/new/ *Pfam* - PSSMs from Pfam-A seed alignment database, see http://pfam.sanger.ac.uk/ *Smart* - PSSMs from SMART domain alignment database, see http://smart.embl-heidelberg.de/ *Tigr* - PSSMs from TIGRFAM database of protein families, see http://www.jcvi.org/cms/research/projects/tigrfams/overview/ *Prk* - PSSms from automatically aligned stable clusters in the Protein Clusters database, see http://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@ ------- **References** If you use this Galaxy tool in work leading to a scientific publication please cite the following papers: @REFERENCES@ </help> </tool>