Mercurial > repos > devteam > ncbi_blast_plus
changeset 29:82e833f02332 draft
planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 100608715d0e98f250057fa362b99759bd750a31-dirty
| author | peterjc |
|---|---|
| date | Wed, 11 Oct 2017 07:43:09 -0400 |
| parents | ce0b2cad3626 |
| children | d724d9af93ee |
| files | tools/ncbi_blast_plus/README.rst tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml tools/ncbi_blast_plus/ncbi_macros.xml tools/ncbi_blast_plus/ncbi_makeblastdb.xml tools/ncbi_blast_plus/ncbi_makeprofiledb.xml tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml |
| diffstat | 12 files changed, 419 insertions(+), 38 deletions(-) [+] |
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--- a/tools/ncbi_blast_plus/README.rst Tue Sep 19 07:41:16 2017 -0400 +++ b/tools/ncbi_blast_plus/README.rst Wed Oct 11 07:43:09 2017 -0400 @@ -3,7 +3,7 @@ These wrappers are copyright 2010-2017 by Peter Cock (The James Hutton Institute, UK) and additional contributors including Edward Kirton, John Chilton, -Nicola Soranzo, Jim Johnson, and Bjoern Gruening. +Nicola Soranzo, Jim Johnson, Bjoern Gruening, and Caleb Easterly. See the licence text below. @@ -250,6 +250,11 @@ - Add ``-use_sw_tback`` option for BLASTP (Nicola Soranzo). v0.2.02 - Document the BLAST+ 2.5.0 change in the standard 12 column output from ``qseqid,sseqid,...`` to ``qacc,sacc,...`` instead. + - Support for per-matrix recommended gaps settings (``-gapopen`` and + ``-gapextend``, contribution from Caleb Easterly and Jim Johnson). + - Support for ``-window_size``, ``-threshold``, ``-comp_based_stats`` + and revising ``-word_size`` to avoid using zero to mean default + (contribution from Caleb Easterly). ======= ======================================================================
--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Tue Sep 19 07:41:16 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Wed Oct 11 07:43:09 2017 -0400 @@ -131,6 +131,10 @@ ------- +@CLI_OPTIONS + +------- + **References** If you use this Galaxy tool in work leading to a scientific publication please
--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Tue Sep 19 07:41:16 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Wed Oct 11 07:43:09 2017 -0400 @@ -27,6 +27,12 @@ $adv_opts.ungapped @ADV_ID_LIST_FILTER@ @ADV_QCOV_HSP_PERC@ +## only use window size if dc-megablast mode is used +#if ($blast_type == "dc-megablast"): +-window_size @ADV_WINDOW_SIZE@ +#end if +@ADV_GAPOPEN@ +@ADV_GAPEXTEND@ ## End of advanced options: #end if </command> @@ -53,13 +59,18 @@ <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> @@ -168,6 +179,10 @@ ------- +@CLI_OPTIONS@ + +------- + **References** If you use this Galaxy tool in work leading to a scientific publication please
--- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Tue Sep 19 07:41:16 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Wed Oct 11 07:43:09 2017 -0400 @@ -17,7 +17,7 @@ @BLAST_OUTPUT@ @THREADS@ #if $adv_opts.adv_opts_selector=="advanced": - -matrix $adv_opts.matrix + @ADV_MATRIX_GAPCOSTS@ @ADV_FILTER_QUERY@ @ADV_MAX_HITS@ @ADV_WORD_SIZE@ @@ -26,6 +26,10 @@ @ADV_ID_LIST_FILTER@ @ADV_QCOV_HSP_PERC@ $adv_opts.use_sw_tback + @ADV_WINDOW_SIZE@ + @ADV_THRESHOLD@ + @ADV_COMP_BASED_STATS@ +## End of advanced options: #end if </command> <inputs> @@ -33,19 +37,24 @@ <expand macro="input_conditional_protein_db" /> - <param name="blast_type" argument="-task" type="select" display="radio" label="Type of BLAST"> + <param name="blast_type" argument="-task" type="select" display="radio" + label="Type of BLAST" + help="See help text for default parameter values for each BLAST type."> <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> <option value="blastp-fast">blastp-fast - Use longer words for seeding, faster but less accurate</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_matrix_gapcosts" /> <expand macro="input_max_hits" /> <expand macro="input_word_size" /> + <expand macro="input_window_size" /> + <expand macro="input_threshold" /> + <expand macro="input_comp_based_stats" /> <!-- 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 @@ -76,7 +85,8 @@ <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="word_size" value="" /> + <param name="window_size" value="40" /> <param name="parse_deflines" value="true" /> <param name="qcov_hsp_perc" value="25" /> <output name="output1" file="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" /> @@ -93,7 +103,8 @@ <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="word_size" value="" /> + <param name="window_size" value="40" /> <param name="parse_deflines" value="true" /> <param name="qcov_hsp_perc" value="25" /> <output name="output1" file="blastp_four_human_vs_rhodopsin.tabular" ftype="tabular" /> @@ -110,7 +121,7 @@ <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="word_size" value="" /> <param name="parse_deflines" value="true" /> <param name="qcov_hsp_perc" value="25" /> <output name="output1" file="blastp_four_human_vs_rhodopsin_ext.tabular" ftype="tabular" /> @@ -126,6 +137,32 @@ <param name="adv_opts_selector" value="basic" /> <output name="output1" file="blastp_rhodopsin_vs_four_human.tabular" ftype="tabular" /> </test> + <test> + <param name="query" value="rhodopsin_peptides.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="200000" /> + <param name="blast_type" value="blastp-short" /> + <param name="out_format" value="6" /> + <param name="adv_opts_selector" value="basic" /> + <output name="output1" file="blastp_rhodopsin_peptides_vs_four_human.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="advanced"/> + <param name="window_size" value="35" /> + <param name="matrix" value="BLOSUM62" /> + <param name="gap_costs" value="-gapopen 11 -gapextend 1"/> + <param name="comp_based_stats" value="3" /> + <output name="output1" file="blastp_rhodopsin_adv_vs_four_human.tabular" ftype="tabular" /> + </test> </tests> <help> @@ -138,10 +175,14 @@ @FASTA_WARNING@ ------ +------- @OUTPUT_FORMAT@ +------ + +@CLI_OPTIONS@ + ------- **References**
--- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Tue Sep 19 07:41:16 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Wed Oct 11 07:43:09 2017 -0400 @@ -19,13 +19,16 @@ @THREADS@ #if $adv_opts.adv_opts_selector=="advanced": $adv_opts.strand --matrix $adv_opts.matrix +@ADV_MATRIX_GAPCOSTS@ @ADV_FILTER_QUERY@ @ADV_MAX_HITS@ @ADV_WORD_SIZE@ $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> @@ -45,13 +48,16 @@ <!-- 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_matrix_gapcosts" /> <expand macro="input_max_hits" /> <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" /> + <expand macro="input_window_size" /> + <expand macro="input_threshold" /> + <expand macro="input_comp_based_stats" /> </expand> </inputs> <outputs> @@ -105,6 +111,17 @@ <param name="adv_opts_selector" value="basic" /> <output name="output1" file="blastx_rhodopsin_vs_four_human_all.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="6" /> + <param name="adv_opts_selector" value="advanced" /> + <param name="matrix" value="BLOSUM62" /> + <output name="output1" file="blastx_rhodopsin_adv_vs_four_human.tabular" ftype="tabular" /> + </test> </tests> <help> @@ -117,12 +134,16 @@ @FASTA_WARNING@ ------ +------- @OUTPUT_FORMAT@ ------- +@CLI_OPTIONS@ + +------- + **References** If you use this Galaxy tool in work leading to a scientific publication please
--- a/tools/ncbi_blast_plus/ncbi_macros.xml Tue Sep 19 07:41:16 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_macros.xml Wed Oct 11 07:43:09 2017 -0400 @@ -4,12 +4,14 @@ <!-- 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" /> </xml> + <xml name="preamble"> <requirements> <requirement type="package" version="2.5.0">blast</requirement> </requirements> <version_command>@BINARY@ -version</version_command> </xml> + <xml name="output_change_format"> <change_format> <when input="output.out_format" value="0" format="txt"/> @@ -21,6 +23,7 @@ <when input="output.out_format" value="5" format="blastxml"/> </change_format> </xml> + <xml name="input_out_format"> <conditional name="output"> <param name="out_format" argument="-outfmt" type="select" label="Output format"> @@ -108,6 +111,168 @@ <when value="4 -html"/> </conditional> </xml> + + <xml name="input_matrix_gapcosts"> + <conditional name="matrix_gapcosts"> + <param argument="-matrix" type="select" label="Scoring matrix and gap costs"> + <option value="" selected="true">Use Defaults</option> + <option value="BLOSUM90">BLOSUM90</option> + <option value="BLOSUM80">BLOSUM80</option> + <option value="BLOSUM62">BLOSUM62</option> + <option value="BLOSUM50">BLOSUM50</option> + <option value="BLOSUM45">BLOSUM45</option> + <option value="PAM250">PAM250</option> + <option value="PAM70">PAM70</option> + <option value="PAM30">PAM30</option> + </param> + <when value=""> + <!-- do nothing --> + </when> + <when value="BLOSUM90"> + <param name="gap_costs" type="select" label="Gap Costs"> + <option value="" selected="true">Use defaults</option> + <option value="-gapopen 9 -gapextend 2">Existence: 9 Extension: 2</option> + <option value="-gapopen 8 -gapextend 2">Existence: 8 Extension: 2</option> + <option value="-gapopen 7 -gapextend 2">Existence: 7 Extension: 2</option> + <option value="-gapopen 6 -gapextend 2">Existence: 6 Extension: 2</option> + <option value="-gapopen 11 -gapextend 1">Existence: 11 Extension: 1</option> + <option value="-gapopen 10 -gapextend 1">Existence: 10 Extension: 1</option> + <option value="-gapopen 9 -gapextend 1">Existence: 9 Extension: 1</option> + </param> + + </when> + <when value="BLOSUM80"> + <param name="gap_costs" type="select" label="Gap Costs"> + <option value="" selected="true">Use defaults</option> + <option value="-gapopen 8 -gapextend 2">Existence: 8 Extension: 2</option> + <option value="-gapopen 7 -gapextend 2">Existence: 7 Extension: 2</option> + <option value="-gapopen 6 -gapextend 2">Existence: 6 Extension: 2</option> + <option value="-gapopen 11 -gapextend 1">Existence: 11 Extension: 1</option> + <option value="-gapopen 10 -gapextend 1">Existence: 10 Extension: 1</option> + <option value="-gapopen 9 -gapextend 1">Existence: 9 Extension: 1</option> + </param> + </when> + <when value="BLOSUM62"> + <param name="gap_costs" type="select" label="Gap Costs"> + <option value="" selected="true">Use defaults</option> + <option value="-gapopen 11 -gapextend 2">Existence: 11 Extension: 2</option> + <option value="-gapopen 10 -gapextend 2">Existence: 10 Extension: 2</option> + <option value="-gapopen 9 -gapextend 2">Existence: 9 Extension: 2</option> + <option value="-gapopen 8 -gapextend 2">Existence: 8 Extension: 2</option> + <option value="-gapopen 7 -gapextend 2">Existence: 7 Extension: 2</option> + <option value="-gapopen 6 -gapextend 2">Existence: 6 Extension: 2</option> + <option value="-gapopen 13 -gapextend 1">Existence: 13 Extension: 1</option> + <option value="-gapopen 12 -gapextend 1">Existence: 12 Extension: 1</option> + <option value="-gapopen 11 -gapextend 1">Existence: 11 Extension: 1</option> + <option value="-gapopen 10 -gapextend 1">Existence: 10 Extension: 1</option> + <option value="-gapopen 9 -gapextend 1">Existence: 9 Extension: 1</option> + </param> + + </when> + <when value="BLOSUM50"> + <param name="gap_costs" type="select" label="Gap Costs"> + <option value="" selected="true">Use defaults</option> + <option value="-gapopen 13 -gapextend 3">Existence: 13 Extension: 3</option> + <option value="-gapopen 12 -gapextend 3">Existence: 12 Extension: 3</option> + <option value="-gapopen 11 -gapextend 3">Existence: 11 Extension: 3</option> + <option value="-gapopen 10 -gapextend 3">Existence: 10 Extension: 3</option> + <option value="-gapopen 9 -gapextend 3">Existence: 9 Extension: 3</option> + <option value="-gapopen 16 -gapextend 2">Existence: 16 Extension: 2</option> + <option value="-gapopen 15 -gapextend 2">Existence: 15 Extension: 2</option> + <option value="-gapopen 14 -gapextend 2">Existence: 14 Extension: 2</option> + <option value="-gapopen 13 -gapextend 2">Existence: 13 Extension: 2</option> + <option value="-gapopen 12 -gapextend 2">Existence: 12 Extension: 2</option> + <option value="-gapopen 19 -gapextend 1">Existence: 19 Extension: 1</option> + <option value="-gapopen 18 -gapextend 1">Existence: 18 Extension: 1</option> + <option value="-gapopen 17 -gapextend 1">Existence: 17 Extension: 1</option> + <option value="-gapopen 16 -gapextend 1">Existence: 16 Extension: 1</option> + <option value="-gapopen 15 -gapextend 1">Existence: 15 Extension: 1</option> + </param> + + </when> + <when value="BLOSUM45"> + <param name="gap_costs" type="select" label="Gap Costs"> + <option value="" selected="true">Use defaults</option> + <option value="-gapopen 13 -gapextend 3">Existence: 13 Extension: 3</option> + <option value="-gapopen 12 -gapextend 3">Existence: 12 Extension: 3</option> + <option value="-gapopen 11 -gapextend 3">Existence: 11 Extension: 3</option> + <option value="-gapopen 10 -gapextend 3">Existence: 10 Extension: 3</option> + <option value="-gapopen 15 -gapextend 2">Existence: 15 Extension: 2</option> + <option value="-gapopen 14 -gapextend 2">Existence: 14 Extension: 2</option> + <option value="-gapopen 13 -gapextend 2">Existence: 13 Extension: 2</option> + <option value="-gapopen 12 -gapextend 2">Existence: 12 Extension: 2</option> + <option value="-gapopen 19 -gapextend 1">Existence: 19 Extension: 1</option> + <option value="-gapopen 18 -gapextend 1">Existence: 18 Extension: 1</option> + <option value="-gapopen 17 -gapextend 1">Existence: 17 Extension: 1</option> + <option value="-gapopen 16 -gapextend 1">Existence: 16 Extension: 1</option> + </param> + </when> + <when value="PAM250"> + <param name="gap_costs" type="select" label="Gap Costs"> + <option value="" selected="true">Use defaults</option> + <option value="-gapopen 15 -gapextend 3">Existence: 15 Extension: 3</option> + <option value="-gapopen 14 -gapextend 3">Existence: 14 Extension: 3</option> + <option value="-gapopen 13 -gapextend 3">Existence: 13 Extension: 3</option> + <option value="-gapopen 12 -gapextend 3">Existence: 12 Extension: 3</option> + <option value="-gapopen 17 -gapextend 2">Existence: 17 Extension: 2</option> + <option value="-gapopen 16 -gapextend 2">Existence: 16 Extension: 2</option> + <option value="-gapopen 15 -gapextend 2">Existence: 15 Extension: 2</option> + <option value="-gapopen 14 -gapextend 2">Existence: 14 Extension: 2</option> + <option value="-gapopen 13 -gapextend 2">Existence: 13 Extension: 2</option> + <option value="-gapopen 21 -gapextend 1">Existence: 21 Extension: 1</option> + <option value="-gapopen 20 -gapextend 1">Existence: 20 Extension: 1</option> + <option value="-gapopen 19 -gapextend 1">Existence: 19 Extension: 1</option> + <option value="-gapopen 18 -gapextend 1">Existence: 18 Extension: 1</option> + <option value="-gapopen 17 -gapextend 1">Existence: 17 Extension: 1</option> + </param> + + </when> + <when value="PAM70"> + <param name="gap_costs" type="select" label="Gap Costs"> + <option value="" selected="true">Use defaults</option> + <option value="-gapopen 12 -gapextend 3">Existence: 12 Extension: 3</option> + <option value="-gapopen 11 -gapextend 2">Existence: 11 Extension: 2</option> + <option value="-gapopen 8 -gapextend 2">Existence: 8 Extension: 2</option> + <option value="-gapopen 7 -gapextend 2">Existence: 7 Extension: 2</option> + <option value="-gapopen 6 -gapextend 2">Existence: 6 Extension: 2</option> + <option value="-gapopen 11 -gapextend 1">Existence: 11 Extension: 1</option> + <option value="-gapopen 10 -gapextend 1">Existence: 10 Extension: 1</option> + <option value="-gapopen 9 -gapextend 1">Existence: 9 Extension: 1</option> + </param> + + </when> + <when value="PAM30"> + <param name="gap_costs" type="select" label="Gap Costs"> + <option value="" selected="true">Use defaults</option> + <option value="-gapopen 15 -gapextend 3">Existence: 15 Extension: 3</option> + <option value="-gapopen 13 -gapextend 3">Existence: 13 Extension: 3</option> + <option value="-gapopen 14 -gapextend 2">Existence: 14 Extension: 2</option> + <option value="-gapopen 7 -gapextend 2">Existence: 7 Extension: 2</option> + <option value="-gapopen 6 -gapextend 2">Existence: 6 Extension: 2</option> + <option value="-gapopen 5 -gapextend 2">Existence: 5 Extension: 2</option> + <option value="-gapopen 14 -gapextend 1">Existence: 14 Extension: 1</option> + <option value="-gapopen 10 -gapextend 1">Existence: 10 Extension: 1</option> + <option value="-gapopen 9 -gapextend 1">Existence: 9 Extension: 1</option> + <option value="-gapopen 8 -gapextend 1">Existence: 8 Extension: 1</option> + </param> + </when> + </conditional> + </xml> + <!-- these gapopen and gapextend macros are only used in blastn. + otherwise, the combined matrix/gapcosts macro is used --> + <xml name="input_gapopen"> + <param argument="-gapopen" type="integer" optional="true" min="0" + label="Cost to open a gap" + help="Leave blank for default. See tool help for defaults."/> + </xml> + + <xml name="input_gapextend"> + <param argument="-gapextend" type="integer" optional="true" min="1" + label="Cost to extend a gap" + help="Leave blank for default. See tool help for defaults."/> + </xml> + + <!-- this matrix macro is used in deltablast, makeprofiledb, psiblast, and tblastx --> <xml name="input_scoring_matrix"> <param argument="-matrix" type="select" label="Scoring matrix"> <option value="BLOSUM90">BLOSUM90</option> @@ -120,6 +285,7 @@ <option value="PAM30">PAM30</option> </param> </xml> + <xml name="input_query_gencode"> <param argument="-query_gencode" type="select" label="Query genetic code"> <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details --> @@ -143,6 +309,7 @@ <option value="24">24. Pterobranchia mitochondrial code</option> </param> </xml> + <xml name="input_db_gencode"> <param argument="-db_gencode" type="select" label="Database/subject genetic code"> <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details --> @@ -166,6 +333,7 @@ <option value="24">24. Pterobranchia mitochondrial code</option> </param> </xml> + <xml name="input_conditional_nucleotide_db"> <!-- Usually database argument mapped to -db, but -in in dustmasker --> <conditional name="db_opts"> @@ -193,6 +361,7 @@ </when> </conditional> </xml> + <xml name="input_conditional_protein_db"> <!-- Usually database argument mapped to -db, but -in in segmasker --> <conditional name="db_opts"> @@ -220,6 +389,7 @@ </when> </conditional> </xml> + <xml name="input_conditional_pssm"> <conditional name="db_opts"> <param name="db_opts_selector" type="select" label="Protein domain database (PSSM)"> @@ -240,6 +410,7 @@ </when> </conditional> </xml> + <xml name="input_conditional_choose_db_type"> <conditional name="db_opts"> <param argument="-db_type" type="select" label="Type of BLAST database"> @@ -258,25 +429,34 @@ </when> </conditional> </xml> + <xml name="input_parse_deflines"> <param argument="-parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/> </xml> + <xml name="input_filter_query_default_false"> <param name="filter_query" argument="-seg" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="false" /> </xml> + <xml name="input_filter_query_default_true"> <param name="filter_query" argument="-seg" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /> </xml> + <xml name="input_max_hits"> <param name="max_hits" type="integer" min="0" value="0" label="Maximum hits to show" help="Use zero for default limits" /> <param argument="-max_hsps" type="integer" min="1" optional="true" value="" label="Maximum number of HSPs (alignments) to keep for any single query-subject pair" help="The HSPs shown will be the best as judged by expect value. If this option is not set, BLAST shows all HSPs meeting the expect value criteria" /> </xml> + <xml name="input_evalue"> <param name="evalue_cutoff" argument="-evalue" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> </xml> + <xml name="input_word_size"> - <param argument="-word_size" type="integer" min="0" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2" /> + <param argument="-word_size" type="integer" min="2" optional="true" + label="Word size for wordfinder algorithm" + help="Leave blank for default, otherwise minimum 2" /> </xml> + <xml name="input_strand"> <param argument="-strand" type="select" label="Query strand(s) to search against database/subject"> <option value="-strand both">Both</option> @@ -284,9 +464,36 @@ <option value="-strand minus">Minus (reverse complement)</option> </param> </xml> + <xml name="input_qcov_hsp_perc"> <param argument="-qcov_hsp_perc" type="float" value="0" min="0" max="100" label="Minimum query coverage per hsp (percentage, 0 to 100)" help="See also the output column qcovhsp"/> </xml> + + <xml name="input_window_size"> + <param argument="-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="Default window size varies with substitution matrix and BLAST type. Enter an integer to override the default."/> + </xml> + + <xml name="input_threshold"> + <param argument="-threshold" type="integer" optional="true" min="0" + label="Minimum score to add a word to the BLAST lookup table." + help="Leave blank for default, which varies based on application."/> + </xml> + + <xml name="input_comp_based_stats"> + <param argument="-comp_based_stats" type="select" + label="Composition-based statistics" + help="The default value varies based on application and task. Most common default is 2."> + <option value="">Use default</option> + <option value="0">0: No composition-based statistics</option> + <option value="1">1: Composition-based statistics as in NAR 29:2994-3005, 2001</option> + <option value="2">2: Composition-based score adjustment as in Bioinformatics + 21:902-911, 2005, conditioned on sequence properties</option> + <option value="3">3: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally</option> + </param> + </xml> + <xml name="advanced_options"> <conditional name="adv_opts"> <param name="adv_opts_selector" type="select" label="Advanced Options"> @@ -299,6 +506,7 @@ </when> </conditional> </xml> + <xml name="advanced_optional_id_files"> <conditional name="adv_optional_id_files_opts"> <param name="adv_optional_id_files_opts_selector" type="select" @@ -324,11 +532,20 @@ </when> </conditional> </xml> +<!--Tokens--> + <token name="@ADV_MATRIX_GAPCOSTS@"> +#if str($adv_opts.matrix_gapcosts.matrix): + -matrix $adv_opts.matrix_gapcosts.matrix + $adv_opts.matrix_gapcosts.gap_costs +#end if + </token> + <token name="@ADV_QCOV_HSP_PERC@"> #if float(str($adv_opts.qcov_hsp_perc)) > 0: -qcov_hsp_perc $adv_opts.qcov_hsp_perc #end if </token> + <token name="@ADV_ID_LIST_FILTER@"> #if $adv_opts.adv_optional_id_files_opts.adv_optional_id_files_opts_selector == 'negative_gilist': -negative_gilist $adv_opts.adv_optional_id_files_opts.negative_gilist @@ -338,7 +555,9 @@ -seqidlist $adv_opts.adv_optional_id_files_opts.seqidlist #end if </token> + <token name="@THREADS@">-num_threads "\${GALAXY_SLOTS:-8}"</token> + <token name="@BLAST_DB_SUBJECT@"> #if $db_opts.db_opts_selector == "db": -db '${" ".join(str($db_opts.database.fields.path).split(","))}' @@ -348,6 +567,7 @@ -subject '$db_opts.subject' #end if </token> + <token name="@BLAST_OUTPUT@">-out '$output1' ##Set the extended list here so when we add things, saved workflows are not affected #if str($output.out_format)=="ext": @@ -381,11 +601,47 @@ #end if </token> <token name="@ADV_WORD_SIZE@"> -#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): +#if str($adv_opts.word_size): -word_size $adv_opts.word_size #end if $adv_opts.parse_deflines </token> + <token name="@ADV_WINDOW_SIZE@"> +#if str($adv_opts.window_size): +-window_size $adv_opts.window_size +#end if + </token> + + <token name="@ADV_THRESHOLD@"> +#if str($adv_opts.threshold): +-threshold $adv_opts.threshold +#end if + </token> + + <token name="@ADV_COMP_BASED_STATS@"> +#if str($adv_opts.comp_based_stats): +-comp_based_stats $adv_opts.comp_based_stats +#end if + </token> + + <token name="@ADV_GAPOPEN@"> +#if str($adv_opts.gapopen): +-gapopen $adv_opts.gapopen +#end if + </token> + + <token name="@ADV_GAPEXTEND@"> +#if str($adv_opts.gapextend): +-gapextend $adv_opts.gapextend +#end if + </token> + + <token name="@ADV_MATRIX@"> +#if str($adv_opts.matrix): +-matrix $adv_opts.matrix +#end if + </token> + <!-- @ON_DB_SUBJECT@ is for use with @BLAST_DB_SUBJECT@ --> <token name="@ON_DB_SUBJECT@">#if str($db_opts.db_opts_selector)=='db' '${db_opts.database}' @@ -394,6 +650,7 @@ #else '${db_opts.subject.name}' #end if</token> + <token name="@REFERENCES@"> Peter J. A. Cock, John M. Chilton, Björn Grüning, James E. Johnson, Nicola Soranzo (2015). NCBI BLAST+ integrated into Galaxy. *GigaScience* 4:39 @@ -495,4 +752,11 @@ ----- </token> + + <token name="@CLI_OPTIONS@">**Advanced Options** + +For help with advanced options and their default values, visit the `NCBI BLAST® Command Line Applications User Manual <https://www.ncbi.nlm.nih.gov/books/NBK279675/>`_. +For amino acid substitution matrices, the NCBI User Manual page is `here <https://www.ncbi.nlm.nih.gov/books/NBK379667/>`_. + + </token> </macros>
--- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Tue Sep 19 07:41:16 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Wed Oct 11 07:43:09 2017 -0400 @@ -184,15 +184,16 @@ This is a wrapper for the NCBI BLAST+ tool 'makeblastdb', which is the replacement for the 'formatdb' tool in the NCBI 'legacy' BLAST suite. +More information about makeblastdb can be found in the `BLAST Command Line Applications User Manual`_. + +.. _BLAST Command Line Applications User Manual: https://www.ncbi.nlm.nih.gov/books/NBK279690/ + + <!-- Applying masks to an existing BLAST database will not change the original database; a new database will be created. For this reason, it's best to apply all masks at once to minimize the number of unnecessary intermediate databases. --> -**Documentation** - -https://www.ncbi.nlm.nih.gov/books/NBK279690/ - **References** If you use this Galaxy tool in work leading to a scientific publication please
--- a/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml Tue Sep 19 07:41:16 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml Wed Oct 11 07:43:09 2017 -0400 @@ -69,6 +69,10 @@ <param argument="-gapextend" type="integer" size="5" value="" label="Cost to extend a gap" /> <param argument="-scale" type="float" size="5" value="" label="PSSM scale factor" /> <expand macro="input_scoring_matrix" /> + <param argument="-gapopen" type="integer" min="0" + label="Cost to open a gap" /> + <param argument="-gapextend" type="integer" min="0" + label="Cost to extend a gap" /> </when> </conditional>
--- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Tue Sep 19 07:41:16 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Wed Oct 11 07:43:09 2017 -0400 @@ -23,6 +23,7 @@ @ADV_FILTER_QUERY@ @ADV_MAX_HITS@ @ADV_QCOV_HSP_PERC@ +@ADV_WINDOW_SIZE@ ## End of advanced options: #end if </command> @@ -41,6 +42,7 @@ <expand macro="input_max_hits" /> <expand macro="input_parse_deflines" /> <expand macro="input_qcov_hsp_perc" /> + <expand macro="input_window_size" /> </expand> </inputs> <outputs> @@ -105,6 +107,10 @@ ------- +@CLI_OPTIONS@ + +------- + **References** If you use this Galaxy tool in work leading to a scientific publication please
--- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Tue Sep 19 07:41:16 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Wed Oct 11 07:43:09 2017 -0400 @@ -105,6 +105,10 @@ ------- +@CLI_OPTIONS@ + +------- + **References** If you use this Galaxy tool in work leading to a scientific publication please
--- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Tue Sep 19 07:41:16 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Wed Oct 11 07:43:09 2017 -0400 @@ -18,14 +18,17 @@ @THREADS@ #if $adv_opts.adv_opts_selector=="advanced": -db_gencode $adv_opts.db_gencode --matrix $adv_opts.matrix @ADV_FILTER_QUERY@ @ADV_MAX_HITS@ @ADV_WORD_SIZE@ +@ADV_MATRIX_GAPCOSTS@ ##Ungapped disabled for now - see comments below ##$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> @@ -44,7 +47,7 @@ <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> <expand macro="input_filter_query_default_true" /> - <expand macro="input_scoring_matrix" /> + <expand macro="input_matrix_gapcosts" /> <expand macro="input_max_hits" /> <expand macro="input_word_size" /> <!-- @@ -56,6 +59,9 @@ <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> @@ -75,7 +81,7 @@ <param name="filter_query" value="false" /> <param name="matrix" value="BLOSUM80" /> <param name="max_hits" value="0" /> - <param name="word_size" 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> @@ -90,7 +96,7 @@ <param name="filter_query" value="false" /> <param name="matrix" value="BLOSUM80" /> <param name="max_hits" value="0" /> - <param name="word_size" 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> @@ -105,7 +111,7 @@ <param name="filter_query" value="false" /> <param name="matrix" value="BLOSUM80" /> <param name="max_hits" value="0" /> - <param name="word_size" 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> @@ -122,7 +128,7 @@ <param name="filter_query" value="false" /> <param name="matrix" value="BLOSUM80" /> <param name="max_hits" value="0" /> - <param name="word_size" 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> @@ -138,7 +144,7 @@ <param name="filter_query" value="false" /> <param name="matrix" value="BLOSUM80" /> <param name="max_hits" value="0" /> - <param name="word_size" 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="8" /> </test> @@ -154,11 +160,15 @@ @FASTA_WARNING@ ------ +------ @OUTPUT_FORMAT@ -------- +------ + +@CLI_OPTIONS + +------ **References**
--- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Tue Sep 19 07:41:16 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Wed Oct 11 07:43:09 2017 -0400 @@ -17,14 +17,15 @@ @BLAST_OUTPUT@ @THREADS@ #if $adv_opts.adv_opts_selector=="advanced": --db_gencode $adv_opts.db_gencode -$adv_opts.strand --matrix $adv_opts.matrix -@ADV_FILTER_QUERY@ -@ADV_MAX_HITS@ -@ADV_WORD_SIZE@ -@ADV_ID_LIST_FILTER@ -@ADV_QCOV_HSP_PERC@ + -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> @@ -49,6 +50,7 @@ <expand macro="input_parse_deflines" /> <expand macro="advanced_optional_id_files" /> <expand macro="input_qcov_hsp_perc" /> + <expand macro="input_threshold" /> </expand> </inputs> <outputs> @@ -85,6 +87,10 @@ ------- +@CLI_OPTIONS@ + +------- + **References** If you use this Galaxy tool in work leading to a scientific publication please