| Previous changeset 28:ce0b2cad3626 (2017-09-19) Next changeset 30:d724d9af93ee (2017-10-30) |
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Commit message:
planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 100608715d0e98f250057fa362b99759bd750a31-dirty |
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modified:
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 |
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| diff -r ce0b2cad3626 -r 82e833f02332 tools/ncbi_blast_plus/README.rst --- 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 |
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| @@ -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). ======= ====================================================================== |
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| diff -r ce0b2cad3626 -r 82e833f02332 tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml --- 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 |
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| @@ -131,6 +131,10 @@ ------- +@CLI_OPTIONS + +------- + **References** If you use this Galaxy tool in work leading to a scientific publication please |
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| diff -r ce0b2cad3626 -r 82e833f02332 tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml --- 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 |
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| @@ -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 |
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| diff -r ce0b2cad3626 -r 82e833f02332 tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml --- 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 |
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| @@ -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** |
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| diff -r ce0b2cad3626 -r 82e833f02332 tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml --- 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 |
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| @@ -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 |
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| diff -r ce0b2cad3626 -r 82e833f02332 tools/ncbi_blast_plus/ncbi_macros.xml --- 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 |
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| b'@@ -4,12 +4,14 @@\n <!-- If job splitting is enabled, break up the query file into parts -->\n <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1" />\n </xml>\n+\n <xml name="preamble">\n <requirements>\n <requirement type="package" version="2.5.0">blast</requirement>\n </requirements>\n <version_command>@BINARY@ -version</version_command>\n </xml>\n+\n <xml name="output_change_format">\n <change_format>\n <when input="output.out_format" value="0" format="txt"/>\n@@ -21,6 +23,7 @@\n <when input="output.out_format" value="5" format="blastxml"/>\n </change_format>\n </xml>\n+\n <xml name="input_out_format">\n <conditional name="output">\n <param name="out_format" argument="-outfmt" type="select" label="Output format">\n@@ -108,6 +111,168 @@\n <when value="4 -html"/>\n </conditional>\n </xml>\n+\n+ <xml name="input_matrix_gapcosts">\n+ <conditional name="matrix_gapcosts">\n+ <param argument="-matrix" type="select" label="Scoring matrix and gap costs">\n+ <option value="" selected="true">Use Defaults</option>\n+ <option value="BLOSUM90">BLOSUM90</option>\n+ <option value="BLOSUM80">BLOSUM80</option>\n+ <option value="BLOSUM62">BLOSUM62</option>\n+ <option value="BLOSUM50">BLOSUM50</option>\n+ <option value="BLOSUM45">BLOSUM45</option>\n+ <option value="PAM250">PAM250</option>\n+ <option value="PAM70">PAM70</option>\n+ <option value="PAM30">PAM30</option>\n+ </param>\n+ <when value="">\n+ <!-- do nothing -->\n+ </when>\n+ <when value="BLOSUM90">\n+ <param name="gap_costs" type="select" label="Gap Costs">\n+ <option value="" selected="true">Use defaults</option>\n+ <option value="-gapopen 9 -gapextend 2">Existence: 9 Extension: 2</option>\n+ <option value="-gapopen 8 -gapextend 2">Existence: 8 Extension: 2</option>\n+ <option value="-gapopen 7 -gapextend 2">Existence: 7 Extension: 2</option>\n+ <option value="-gapopen 6 -gapextend 2">Existence: 6 Extension: 2</option>\n+ <option value="-gapopen 11 -gapextend 1">Existence: 11 Extension: 1</option>\n+ <option value="-gapopen 10 -gapextend 1">Existence: 10 Extension: 1</option>\n+ <option value="-gapopen 9 -gapextend 1">Existence: 9 Extension: 1</option>\n+ </param>\n+\n+ </when>\n+ <when value="BLOSUM80">\n+ <param name="gap_costs" type="select" label="Gap Costs">\n+ <option value="" selected="true">Use defaults</option>\n+ <option value="-gapopen 8 -gapextend 2">Existence: 8 Extension: 2</option>\n+ <option value="-gapopen 7 -gapextend 2">Existence: 7 Extension: 2</option>\n+ <option value="-gapopen 6 -gapextend 2">Existence: 6 Extension: 2</option>\n+ <option value="-gapopen 11 -gapextend 1">Existence: 11 Extension: 1</option>\n+ <option value="-gapopen 10 -gapextend 1">Existence: 10 Extension: 1</option>\n+ <option value="-gapopen 9 -gapextend 1">Existence: 9 Extension: 1</option>\n+ </param>\n+ </when>\n+ <when value="BLOSUM62">\n+ <param name="gap_costs" type="select" label="Gap Costs">\n+ <option value="" selected="true">Use defaults</option>\n+ <option value="-gapopen 11 -gapextend 2">Existence: 11 Extension: 2</option>\n+ <option value="-gapopen 10 -gapextend 2">Existence: 10 Extension: 2</option>\n+ <option value="-gapopen 9 -gapextend 2"'..b'd statistics</option>\n+ <option value="1">1: Composition-based statistics as in NAR 29:2994-3005, 2001</option>\n+ <option value="2">2: Composition-based score adjustment as in Bioinformatics\n+ 21:902-911, 2005, conditioned on sequence properties</option>\n+ <option value="3">3: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally</option>\n+ </param>\n+ </xml>\n+\n <xml name="advanced_options">\n <conditional name="adv_opts">\n <param name="adv_opts_selector" type="select" label="Advanced Options">\n@@ -299,6 +506,7 @@\n </when>\n </conditional>\n </xml>\n+\n <xml name="advanced_optional_id_files">\n <conditional name="adv_optional_id_files_opts">\n <param name="adv_optional_id_files_opts_selector" type="select"\n@@ -324,11 +532,20 @@\n </when>\n </conditional>\n </xml>\n+<!--Tokens-->\n+ <token name="@ADV_MATRIX_GAPCOSTS@">\n+#if str($adv_opts.matrix_gapcosts.matrix):\n+ -matrix $adv_opts.matrix_gapcosts.matrix\n+ $adv_opts.matrix_gapcosts.gap_costs\n+#end if\n+ </token>\n+\n <token name="@ADV_QCOV_HSP_PERC@">\n #if float(str($adv_opts.qcov_hsp_perc)) > 0:\n -qcov_hsp_perc $adv_opts.qcov_hsp_perc\n #end if\n </token>\n+\n <token name="@ADV_ID_LIST_FILTER@">\n #if $adv_opts.adv_optional_id_files_opts.adv_optional_id_files_opts_selector == \'negative_gilist\':\n -negative_gilist $adv_opts.adv_optional_id_files_opts.negative_gilist\n@@ -338,7 +555,9 @@\n -seqidlist $adv_opts.adv_optional_id_files_opts.seqidlist\n #end if\n </token>\n+\n <token name="@THREADS@">-num_threads "\\${GALAXY_SLOTS:-8}"</token>\n+\n <token name="@BLAST_DB_SUBJECT@">\n #if $db_opts.db_opts_selector == "db":\n -db \'${" ".join(str($db_opts.database.fields.path).split(","))}\'\n@@ -348,6 +567,7 @@\n -subject \'$db_opts.subject\'\n #end if\n </token>\n+\n <token name="@BLAST_OUTPUT@">-out \'$output1\'\n ##Set the extended list here so when we add things, saved workflows are not affected\n #if str($output.out_format)=="ext":\n@@ -381,11 +601,47 @@\n #end if\n </token>\n <token name="@ADV_WORD_SIZE@">\n-#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):\n+#if str($adv_opts.word_size):\n -word_size $adv_opts.word_size\n #end if\n $adv_opts.parse_deflines\n </token>\n+ <token name="@ADV_WINDOW_SIZE@">\n+#if str($adv_opts.window_size):\n+-window_size $adv_opts.window_size\n+#end if\n+ </token>\n+\n+ <token name="@ADV_THRESHOLD@">\n+#if str($adv_opts.threshold):\n+-threshold $adv_opts.threshold\n+#end if\n+ </token>\n+\n+ <token name="@ADV_COMP_BASED_STATS@">\n+#if str($adv_opts.comp_based_stats):\n+-comp_based_stats $adv_opts.comp_based_stats\n+#end if\n+ </token>\n+\n+ <token name="@ADV_GAPOPEN@">\n+#if str($adv_opts.gapopen):\n+-gapopen $adv_opts.gapopen\n+#end if\n+ </token>\n+\n+ <token name="@ADV_GAPEXTEND@">\n+#if str($adv_opts.gapextend):\n+-gapextend $adv_opts.gapextend\n+#end if\n+ </token>\n+\n+ <token name="@ADV_MATRIX@">\n+#if str($adv_opts.matrix):\n+-matrix $adv_opts.matrix\n+#end if\n+ </token>\n+\n <!-- @ON_DB_SUBJECT@ is for use with @BLAST_DB_SUBJECT@ -->\n <token name="@ON_DB_SUBJECT@">#if str($db_opts.db_opts_selector)==\'db\'\n \'${db_opts.database}\'\n@@ -394,6 +650,7 @@\n #else\n \'${db_opts.subject.name}\'\n #end if</token>\n+\n <token name="@REFERENCES@">\n Peter J. A. Cock, John M. Chilton, Bj\xc3\xb6rn Gr\xc3\xbcning, James E. Johnson, Nicola Soranzo (2015).\n NCBI BLAST+ integrated into Galaxy. *GigaScience* 4:39\n@@ -495,4 +752,11 @@\n \n -----\n </token>\n+\n+ <token name="@CLI_OPTIONS@">**Advanced Options**\n+\n+For help with advanced options and their default values, visit the `NCBI BLAST\xc2\xae Command Line Applications User Manual <https://www.ncbi.nlm.nih.gov/books/NBK279675/>`_.\n+For amino acid substitution matrices, the NCBI User Manual page is `here <https://www.ncbi.nlm.nih.gov/books/NBK379667/>`_.\n+\n+ </token>\n </macros>\n' |
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| diff -r ce0b2cad3626 -r 82e833f02332 tools/ncbi_blast_plus/ncbi_makeblastdb.xml --- 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 |
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| @@ -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 |
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| diff -r ce0b2cad3626 -r 82e833f02332 tools/ncbi_blast_plus/ncbi_makeprofiledb.xml --- 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 |
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| @@ -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> |
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| diff -r ce0b2cad3626 -r 82e833f02332 tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml --- 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 |
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| @@ -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 |
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| diff -r ce0b2cad3626 -r 82e833f02332 tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml --- 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 |
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| @@ -105,6 +105,10 @@ ------- +@CLI_OPTIONS@ + +------- + **References** If you use this Galaxy tool in work leading to a scientific publication please |
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| diff -r ce0b2cad3626 -r 82e833f02332 tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml --- 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 |
| b |
| @@ -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** |
| b |
| diff -r ce0b2cad3626 -r 82e833f02332 tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml --- 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 |
| b |
| @@ -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 |