Mercurial > repos > devteam > ncbi_blast_plus
view tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @ 11:4c4a0da938ff draft
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
Supports $GALAXY_SLOTS.
Includes more tests and heavy use of macros.
author | peterjc |
---|---|
date | Thu, 05 Dec 2013 06:55:59 -0500 |
parents | 70e7dcbf6573 |
children | 623f727cdff1 |
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<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.22"> <description>Search nucleotide database with nucleotide query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1"></parallelism> <macros> <token name="@BINARY@">blastn</token> <import>ncbi_macros.xml</import> </macros> <expand macro="requirements" /> <command> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces blastn -query "$query" @BLAST_DB_SUBJECT@ -task $blast_type -evalue $evalue_cutoff @BLAST_OUTPUT@ @THREADS@ #if $adv_opts.adv_opts_selector=="advanced": $adv_opts.strand @ADVANCED_OPTIONS@ #if (str($adv_opts.identity_cutoff) and float(str($adv_opts.identity_cutoff)) > 0 ): -perc_identity $adv_opts.identity_cutoff #end if $adv_opts.ungapped ## End of advanced options: #end if </command> <expand macro="stdio" /> <inputs> <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> <expand macro="input_conditional_nucleotide_db" /> <param name="blast_type" type="select" display="radio" label="Type of BLAST"> <option value="megablast">megablast</option> <option value="blastn">blastn</option> <option value="blastn-short">blastn-short</option> <option value="dc-megablast">dc-megablast</option> <!-- Using BLAST 2.2.24+ this gives an error: BLAST engine error: Program type 'vecscreen' not supported <option value="vecscreen">vecscreen</option> --> </param> <expand macro="input_evalue" /> <expand macro="input_out_format" /> <expand macro="advanced_options"> <!-- Could use a select (yes, no, other) where other allows setting 'level window linker' --> <param name="filter_query" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="-dust yes" falsevalue="-dust no" checked="true" /> <expand macro="input_strand" /> <expand macro="input_max_hits" /> <param name="identity_cutoff" type="float" min="0" max="100" value="0" label="Percent identity cutoff (-perc_identity)" help="Use zero for no cutoff" /> <!-- I'd like word_size to be optional, with minimum 4 for blastn --> <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 4."> <validator type="in_range" min="0" /> </param> <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> <expand macro="input_parse_deflines" /> </expand> </inputs> <outputs> <data name="output1" format="tabular" label="${blast_type.value_label} $query.name vs @ON_DB_SUBJECT@"> <expand macro="output_change_format" /> </data> </outputs> <tests> <test> <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> <param name="db_opts_selector" value="file" /> <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> <param name="database" value="" /> <param name="evalue_cutoff" value="1e-40" /> <param name="out_format" value="6" /> <param name="adv_opts_selector" value="basic" /> <output name="output1" file="blastn_rhodopsin_vs_three_human.tabular" ftype="tabular" /> </test> </tests> <help> @SEARCH_TIME_WARNING@ **What it does** Search a *nucleotide database* using a *nucleotide query*, using the NCBI BLAST+ blastn command line tool. Algorithms include blastn, megablast, and discontiguous megablast. @FASTA_WARNING@ ----- @OUTPUT_FORMAT@ ------- **References** If you use this Galaxy tool in work leading to a scientific publication please cite the following papers: @REFERENCES@ </help> </tool>