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view tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @ 27:6f8ea4b9a2c4 draft
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
author | peterjc |
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date | Wed, 09 Sep 2020 15:32:17 +0000 |
parents | e25d3acf6e68 |
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<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Search translated nucleotide database with translated nucleotide query sequence(s)</description> <macros> <token name="@BINARY@">tblastx</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 tblastx @QUERY@ @BLAST_DB_SUBJECT@ -query_gencode $query_gencode -evalue $evalue_cutoff @BLAST_OUTPUT@ @THREADS@ #if $adv_opts.adv_opts_selector=="advanced": -db_gencode $adv_opts.db_gencode $adv_opts.strand @ADV_MATRIX@ @ADV_FILTER_QUERY@ @ADV_MAX_HITS@ @ADV_WORD_SIZE@ @ADV_ID_LIST_FILTER@ @ADV_QCOV_HSP_PERC@ @ADV_THRESHOLD@ ## End of advanced options: #end if </command> <inputs> <expand macro="nucl_query" /> <expand macro="input_conditional_nucleotide_db" /> <expand macro="input_query_gencode" /> <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_strand" /> <expand macro="input_scoring_matrix" /> <expand macro="input_max_hits" /> <!-- I'd like word_size to be optional, with minimum 2 for tblastx --> <expand macro="input_word_size" /> <expand macro="input_parse_deflines" /> <expand macro="advanced_optional_id_files" /> <expand macro="input_qcov_hsp_perc" /> <expand macro="input_threshold" /> </expand> </inputs> <outputs> <data name="output1" format="tabular" label="tblastx $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="tblastx_rhodopsin_vs_three_human.tabular" ftype="tabular" /> </test> </tests> <help> @SEARCH_TIME_WARNING@ **What it does** Search a *translated nucleotide database* using a *translated nucleotide query*, using the NCBI BLAST+ tblastx 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>