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view tools/ncbi_blast_plus/ncbi_tblastn_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 | 6f8ea4b9a2c4 |
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<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Search translated nucleotide database with protein query sequence(s)</description> <macros> <token name="@BINARY@">tblastn</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 tblastn @QUERY@ @BLAST_DB_SUBJECT@ -task $blast_type -evalue $evalue_cutoff @BLAST_OUTPUT@ @THREADS@ #if $adv_opts.adv_opts_selector=="advanced": -db_gencode $adv_opts.db_gencode @ADV_FILTER_QUERY@ @ADV_MAX_HITS@ @ADV_WORD_SIZE@ @ADV_MATRIX_GAPCOSTS@ ##Ungapped disabled for now - see comments below ##$adv_opts.ungapped @ADV_ID_LIST_FILTER@ @ADV_QCOV_HSP_PERC@ @ADV_WINDOW_SIZE@ @ADV_THRESHOLD@ @ADV_COMP_BASED_STATS@ ## End of advanced options: #end if </command> <inputs> <expand macro="prot_query" /> <expand macro="input_conditional_nucleotide_db" /> <param name="blast_type" argument="-task" type="select" display="radio" label="Type of BLAST"> <option value="tblastn">tblastn - Traditional TBLASTN to compare protein query to translated nucleotide database</option> <option value="tblastn-fast">tblastn-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"> <expand macro="input_db_gencode" /> <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> <expand macro="input_filter_query_default_true" /> <expand macro="input_matrix_gapcosts" /> <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 tblastn crashed with 'Attempt to access NULL pointer.' <param argument="-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 macro="input_qcov_hsp_perc" /> <expand macro="input_window_size" /> <expand macro="input_threshold" /> <expand macro="input_comp_based_stats" /> </expand> </inputs> <outputs> <data name="output1" format="tabular" label="tblastn $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_nucs.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="advanced" /> <param name="filter_query" value="false" /> <param name="matrix" value="BLOSUM80" /> <param name="max_hits" value="0" /> <param name="word_size" value="" /> <param name="parse_deflines" value="false" /> <output name="output1" file="tblastn_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_nucs.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="advanced" /> <param name="filter_query" value="false" /> <param name="matrix" value="BLOSUM80" /> <param name="max_hits" value="0" /> <param name="word_size" value="" /> <param name="parse_deflines" value="false" /> <output name="output1" file="tblastn_four_human_vs_rhodopsin_ext.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_nucs.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="advanced" /> <param name="filter_query" value="false" /> <param name="matrix" value="BLOSUM80" /> <param name="max_hits" value="0" /> <param name="word_size" value="" /> <param name="parse_deflines" value="false" /> <output name="output1" file="tblastn_four_human_vs_rhodopsin.tabular" ftype="tabular" /> </test> <test> <!-- Same as above, but parse deflines --> <!-- Note back on BLAST 2.2.25+ - 2.2.27+ made no difference --> <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> <param name="db_opts_selector" value="file" /> <param name="subject" value="rhodopsin_nucs.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="advanced" /> <param name="filter_query" value="false" /> <param name="matrix" value="BLOSUM80" /> <param name="max_hits" value="0" /> <param name="word_size" value="" /> <param name="parse_deflines" value="true" /> <output name="output1" file="tblastn_four_human_vs_rhodopsin_deflines.tabular" ftype="tabular" /> </test> <test> <!-- As of BLAST 2.5.0+ the full path appears twice, so get small diff --> <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> <param name="db_opts_selector" value="file" /> <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> <param name="database" value="" /> <param name="evalue_cutoff" value="1e-10" /> <param name="out_format" value="0 -html" /> <param name="adv_opts_selector" value="advanced" /> <param name="filter_query" value="false" /> <param name="matrix" value="BLOSUM80" /> <param name="max_hits" value="0" /> <param name="word_size" value="" /> <param name="parse_deflines" value="false" /> <output name="output1" file="tblastn_four_human_vs_rhodopsin.html" ftype="html" lines_diff="10" /> </test> </tests> <help> @SEARCH_TIME_WARNING@ **What it does** Search a *translated nucleotide database* using a *protein query*, using the NCBI BLAST+ tblastn command line tool. @FASTA_WARNING@ ------ @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>