Mercurial > repos > devteam > ncbi_blast_plus
diff tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @ 23:31e517610e1f draft
v0.3.0 Updated for NCBI BLAST+ 2.7.1
author | peterjc |
---|---|
date | Sat, 30 Jun 2018 17:22:46 -0400 |
parents | 6f386c5dc4fb |
children | e25d3acf6e68 |
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--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Mon Sep 18 06:21:27 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Sat Jun 30 17:22:46 2018 -0400 @@ -7,31 +7,43 @@ <expand macro="parallelism" /> <expand macro="preamble" /> <command detect_errors="aggressive"> +<![CDATA[ ## 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' +#if $query.is_of_type('fasta.gz'): +-query <(gunzip -c '${query}') +#else: +-query '${query}' +#end if @BLAST_DB_SUBJECT@ --task $blast_type --evalue $evalue_cutoff +-task '${blast_type}' +-evalue '${evalue_cutoff}' @BLAST_OUTPUT@ @THREADS@ #if $adv_opts.adv_opts_selector=="advanced": -$adv_opts.strand +${adv_opts.strand} @ADV_FILTER_QUERY@ @ADV_MAX_HITS@ @ADV_WORD_SIZE@ #if (str($adv_opts.identity_cutoff) and float(str($adv_opts.identity_cutoff)) > 0 ): --perc_identity $adv_opts.identity_cutoff +-perc_identity '${adv_opts.identity_cutoff}' #end if -$adv_opts.ungapped +${adv_opts.ungapped} @ADV_ID_LIST_FILTER@ @ADV_QCOV_HSP_PERC@ +## only use window size if dc-megablast mode is used +#if ($blast_type == "dc-megablast"): +-window_size @ADV_WINDOW_SIZE@ +#end if +@ADV_GAPOPEN@ +@ADV_GAPEXTEND@ ## End of advanced options: #end if +]]> </command> <inputs> - <param argument="-query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> + <param argument="-query" type="data" format="fasta,fasta.gz" label="Nucleotide query sequence(s)"/> <expand macro="input_conditional_nucleotide_db" /> <param name="blast_type" argument="-task" type="select" display="radio" label="Type of BLAST"> <option value="megablast">megablast - Traditional megablast used to find very similar (e.g., intraspecies or closely related species) sequences</option> @@ -53,13 +65,18 @@ <expand macro="input_strand" /> <expand macro="input_max_hits" /> <param name="identity_cutoff" argument="-perc_identity" type="float" min="0" max="100" value="0" label="Percent identity cutoff" help="Use zero for no cutoff" /> - - <!-- I'd like word_size to be optional, with minimum 4 for blastn --> - <param argument="-word_size" type="integer" min="0" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 4" /> + <expand macro="input_word_size" /> <param argument="-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" /> + <!-- the help text here is unique to the blastx application, so macro not used --> + <param name="window_size" type="integer" optional="true" min="0" + label="Multiple hits window size: use 0 to specify 1-hit algorithm, leave blank for default" + help="Only relevant for dc-megablast, and otherwise ignored. Default window size changes with substitution matrix and BLAST type. + Entering a non-negative integer will override the default."/> + <expand macro="input_gapopen"/> + <expand macro="input_gapextend"/> </expand> </inputs> <outputs> @@ -91,6 +108,16 @@ <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.gz" ftype="fasta.gz" /> + <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> + <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" /> @@ -168,6 +195,10 @@ ------- +@CLI_OPTIONS@ + +------- + **References** If you use this Galaxy tool in work leading to a scientific publication please