Mercurial > repos > devteam > ncbi_blast_plus
view tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @ 15:c16c30e9ad5b draft
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
author | peterjc |
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date | Sun, 05 Jul 2015 10:37:27 -0400 |
parents | 2fe07f50a41e |
children | b5f1f599d1fb |
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<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.1.03"> <description>Search protein database with translated 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@">blastx</token> <import>ncbi_macros.xml</import> </macros> <expand macro="preamble" /> <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 blastx -query "$query" @BLAST_DB_SUBJECT@ -query_gencode $query_gencode -task $blast_type -evalue $evalue_cutoff @BLAST_OUTPUT@ @THREADS@ #if $adv_opts.adv_opts_selector=="advanced": $adv_opts.strand -matrix $adv_opts.matrix @ADV_FILTER_QUERY@ @ADV_MAX_HITS@ @ADV_WORD_SIZE@ $adv_opts.ungapped @ADV_ID_LIST_FILTER@ @ADV_QCOV_HSP_PERC@ ## End of advanced options: #end if </command> <inputs> <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> <expand macro="input_conditional_protein_db" /> <expand macro="input_query_gencode" /> <param name="blast_type" type="select" display="radio" label="Type of BLAST"> <option value="blastx">blastx - Traditional BLASTX to compare translated nucleotide query to protein database</option> <option value="blastx-fast">blastx-fast - Use longer words for seeding, faster but less accurate</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_true" /> <expand macro="input_strand" /> <expand macro="input_scoring_matrix" /> <expand macro="input_max_hits" /> <expand macro="input_word_size" /> <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> <expand macro="input_parse_deflines" /> <expand macro="advanced_optional_id_files" /> <expand macro="input_qcov_hsp_perc" /> </expand> </inputs> <outputs> <data name="output1" format="tabular" label="blastx $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="four_human_proteins.fasta" ftype="fasta" /> <param name="database" value="" /> <param name="evalue_cutoff" value="1e-10" /> <param name="out_format" value="5" /> <param name="adv_opts_selector" value="basic" /> <output name="output1" file="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" /> </test> <test> <param name="query" value="rhodopsin_nucs.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-10" /> <param name="out_format" value="6" /> <param name="adv_opts_selector" value="basic" /> <output name="output1" file="blastx_rhodopsin_vs_four_human.tabular" ftype="tabular" /> </test> <test> <param name="query" value="rhodopsin_nucs.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-10" /> <param name="out_format" value="ext" /> <param name="adv_opts_selector" value="basic" /> <output name="output1" file="blastx_rhodopsin_vs_four_human_ext.tabular" ftype="tabular" /> </test> <test> <param name="query" value="rhodopsin_nucs.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-10" /> <param name="out_format" value="cols" /> <param name="std_cols" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore" /> <param name="ext_cols" value="sallseqid,score,nident,positive,gaps,ppos,qframe,sframe,qseq,sseq,qlen,slen,salltitles" /> <param name="ids_cols" value="qgi,qacc,qaccver,sallseqid,sgi,sallgi,sacc,saccver,sallacc,stitle" /> <param name="misc_cols" value="sstrand,frames,btop,qcovs,qcovhsp" /> <param name="tax_cols" value="staxids,sscinames,scomnames,sblastnames,sskingdoms" /> <param name="adv_opts_selector" value="basic" /> <output name="output1" file="blastx_rhodopsin_vs_four_human_all.tabular" ftype="tabular" /> </test> </tests> <help> @SEARCH_TIME_WARNING@ **What it does** Search a *protein database* using a *translated nucleotide query*, using the NCBI BLAST+ blastx 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>