Mercurial > repos > devteam > ncbi_blast_plus
view tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @ 14:2fe07f50a41e draft
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
author | peterjc |
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date | Mon, 01 Dec 2014 05:59:16 -0500 |
parents | 623f727cdff1 |
children | c16c30e9ad5b |
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<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.1.01"> <description>Search protein database 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@">blastp</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 blastp -query "$query" @BLAST_DB_SUBJECT@ -task $blast_type -evalue $evalue_cutoff @BLAST_OUTPUT@ @THREADS@ #if $adv_opts.adv_opts_selector=="advanced": -matrix $adv_opts.matrix @ADVANCED_OPTIONS@ ##Ungapped disabled for now - see comments below ##$adv_opts.ungapped @ADV_ID_LIST_FILTER@ ## 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_protein_db" /> <param name="blast_type" type="select" display="radio" label="Type of BLAST"> <option value="blastp">blastp - Traditional BLASTP to compare a protein query to a protein database</option> <option value="blastp-short">blastp-short - BLASTP optimized for queries shorter than 30 residues</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 'window locut hicut' --> <expand macro="input_filter_query_default_false" /> <expand macro="input_scoring_matrix" /> <expand macro="input_max_hits" /> <expand macro="input_word_size" /> <!-- Can't use '-ungapped' on its own, error back is: Composition-adjusted searched are not supported with an ungapped search, please add -comp_based_stats F or do a gapped search Tried using '-ungapped -comp_based_stats F' and blastp crashed with 'Attempt to access NULL pointer.' <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" /> --> <expand macro="input_parse_deflines" /> <expand macro="advanced_optional_id_files" /> </expand> </inputs> <outputs> <data name="output1" format="tabular" label="${blast_type.value} $query.name vs @ON_DB_SUBJECT@"> <expand macro="output_change_format" /> </data> </outputs> <tests> <test> <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> <param name="db_opts_selector" value="file" /> <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" /> <param name="database" value="" /> <param name="evalue_cutoff" value="1e-8" /> <param name="blast_type" value="blastp" /> <param name="out_format" value="5" /> <param name="adv_opts_selector" value="advanced" /> <param name="filter_query" value="False" /> <param name="matrix" value="BLOSUM62" /> <param name="max_hits" value="0" /> <param name="word_size" value="0" /> <param name="parse_deflines" value="True" /> <output name="output1" file="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" /> </test> <test> <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> <param name="db_opts_selector" value="file" /> <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" /> <param name="database" value="" /> <param name="evalue_cutoff" value="1e-8" /> <param name="blast_type" value="blastp" /> <param name="out_format" value="6" /> <param name="adv_opts_selector" value="advanced" /> <param name="filter_query" value="False" /> <param name="matrix" value="BLOSUM62" /> <param name="max_hits" value="0" /> <param name="word_size" value="0" /> <param name="parse_deflines" value="True" /> <output name="output1" file="blastp_four_human_vs_rhodopsin.tabular" ftype="tabular" /> </test> <test> <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> <param name="db_opts_selector" value="file" /> <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" /> <param name="database" value="" /> <param name="evalue_cutoff" value="1e-8" /> <param name="blast_type" value="blastp" /> <param name="out_format" value="ext" /> <param name="adv_opts_selector" value="advanced" /> <param name="filter_query" value="False" /> <param name="matrix" value="BLOSUM62" /> <param name="max_hits" value="0" /> <param name="word_size" value="0" /> <param name="parse_deflines" value="True" /> <output name="output1" file="blastp_four_human_vs_rhodopsin_ext.tabular" ftype="tabular" /> </test> <test> <param name="query" value="rhodopsin_proteins.fasta" ftype="fasta" /> <param name="db_opts_selector" value="file" /> <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> <param name="database" value="" /> <param name="evalue_cutoff" value="1e-8" /> <param name="blast_type" value="blastp" /> <param name="out_format" value="6" /> <param name="adv_opts_selector" value="basic" /> <output name="output1" file="blastp_rhodopsin_vs_four_human.tabular" ftype="tabular" /> </test> </tests> <help> @SEARCH_TIME_WARNING@ **What it does** Search a *protein database* using a *protein query*, using the NCBI BLAST+ blastp command line tool. @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> <expand macro="blast_citations" /> </tool>