| Previous changeset 21:7538e2bfcd41 (2017-04-19) Next changeset 23:31e517610e1f (2018-06-30) |
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Commit message:
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates |
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modified:
tools/ncbi_blast_plus/README.rst tools/ncbi_blast_plus/blastxml_to_tabular.py tools/ncbi_blast_plus/blastxml_to_tabular.xml tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml 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_convert2blastmask_wrapper.xml tools/ncbi_blast_plus/ncbi_dustmasker_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_segmasker_wrapper.xml tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml |
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| diff -r 7538e2bfcd41 -r 6f386c5dc4fb tools/ncbi_blast_plus/README.rst --- a/tools/ncbi_blast_plus/README.rst Wed Apr 19 05:27:19 2017 -0400 +++ b/tools/ncbi_blast_plus/README.rst Mon Sep 18 06:21:27 2017 -0400 |
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| @@ -1,7 +1,7 @@ Galaxy wrappers for NCBI BLAST+ suite ===================================== -These wrappers are copyright 2010-2016 by Peter Cock (The James Hutton Institute, +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. @@ -213,7 +213,7 @@ table definitions in Galaxy's ``tool_data_table_conf.xml`` file, setup via ``tool-data/tool_data_table_conf.xml.sample`` - Replace ``.extra_files_path`` with ``.files_path`` (internal change, - thanks to Bjoern Gruening and John Chilton). + thanks to Bjoern Gruening and John Chilton). - Added "NCBI BLAST+ integrated into Galaxy" preprint citation. v0.1.03 - Reorder XML elements (internal change only). - Planemo for Tool Shed upload (``.shed.yml``, internal change only). @@ -233,15 +233,21 @@ (contribution from Gildas Le Corguillé and Emma Prudent). - Minor XML and Python style changes (internal change only). - Set ``allow_duplicate_entries="False"`` in sample configuration file - ``tool_data_table_conf.xml``. + ``tool_data_table_conf.xml``. - Fix identifers with pipes in ``blastdbcmd`` wrapper (Devon Ryan). v0.2.00 - Updated for NCBI BLAST+ 2.5.0, where GI numbers are less visible, tabular output changes with `-parse_deflines`, and percentage - identifies are now given to 3dp rather than 2dp. + identifies are now given to 3dp rather than 2dp. - Depends on ``package_blast_plus_2_5_0`` in ToolShed, or BioConda. - ``blastxml_to_tabular`` now also gives percentage idenity to 3dp. - Removed never-used binary and Python module dependency declarations (internal change only). +v0.2.01 - Use ``<command detect_errors="aggressive">`` (internal change only). + - Single quote command line arguments (internal change only). + - Show BLAST command line argument corresponding to each tool + parameter (contribution from Nicola Soranzo). + - Add ``-max_hsps`` option (contribution from Nicola Soranzo). + - Add ``-use_sw_tback`` option for BLASTP (Nicola Soranzo). ======= ====================================================================== @@ -278,7 +284,7 @@ $ planemo shed_upload --tar_only tools/ncbi_blast_plus/ ... - $ tar -tzf shed_upload.tar.gz + $ tar -tzf shed_upload.tar.gz test-data/blastdb.loc ... tools/ncbi_blast_plus/tool_dependencies.xml |
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| diff -r 7538e2bfcd41 -r 6f386c5dc4fb tools/ncbi_blast_plus/blastxml_to_tabular.py --- a/tools/ncbi_blast_plus/blastxml_to_tabular.py Wed Apr 19 05:27:19 2017 -0400 +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.py Mon Sep 18 06:21:27 2017 -0400 |
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| @@ -61,6 +61,7 @@ space character (probably a bug). """ +from __future__ import print_function import os import re @@ -69,7 +70,7 @@ from optparse import OptionParser if "-v" in sys.argv or "--version" in sys.argv: - print "v0.2.00" + print("v0.2.01") sys.exit(0) if sys.version_info[:2] >= (2, 5): @@ -295,7 +296,7 @@ salltitles = "<>".join(name.split(None, 1)[1] for name in hit_def.split(" >")) except IndexError as e: sys.exit("Problem splitting multuple hits?\n%r\n--> %s" % (hit_def, e)) - # print hit_def, "-->", sallseqid + # print(hit_def, "-->", sallseqid) positive = hsp.findtext("Hsp_positive") ppos = "%0.2f" % (100 * float(positive) / float(length)) qframe = hsp.findtext("Hsp_query-frame") @@ -325,7 +326,7 @@ if cols: # Only a subset of the columns are needed values = [values[colnames.index(c)] for c in cols] - # print "\t".join(values) + # print("\t".join(values)) output_handle.write("\t".join(values) + "\n") # prevents ElementTree from growing large datastructure root.clear() |
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| diff -r 7538e2bfcd41 -r 6f386c5dc4fb tools/ncbi_blast_plus/blastxml_to_tabular.xml --- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml Wed Apr 19 05:27:19 2017 -0400 +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.xml Mon Sep 18 06:21:27 2017 -0400 |
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| @@ -3,27 +3,22 @@ <macros> <import>ncbi_macros.xml</import> </macros> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> - <version_command interpreter="python">blastxml_to_tabular.py --version</version_command> - <command interpreter="python"> -blastxml_to_tabular.py -o "$tabular_file" + <version_command>python $__tool_directory__/blastxml_to_tabular.py --version</version_command> + <command detect_errors="aggressive"> +python $__tool_directory__/blastxml_to_tabular.py -o '$tabular_file' #if $output.out_format == "cols": #set cols = (str($output.std_cols)+","+str($output.ext_cols)).replace("None", " ").replace(",,", ",").replace(",", " ") --c "$cols" +-c '$cols' #else --c "$output.out_format" +-c '$output.out_format' #end if -#for i in $blastxml_file#"${i}" #end for# +#for i in $blastxml_file#'${i}' #end for# </command> <inputs> <param name="blastxml_file" type="data" format="blastxml" multiple="true" label="BLAST results as XML"/> <conditional name="output"> <param name="out_format" type="select" label="Output format"> - <option value="std" selected="True">Tabular (standard 12 columns)</option> + <option value="std" selected="true">Tabular (standard 12 columns)</option> <option value="ext">Tabular (extended 25 columns)</option> <option value="cols">Tabular (select columns to output)</option> </param> @@ -139,7 +134,7 @@ </test> </tests> <help> - + **What it does** NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of |
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| diff -r 7538e2bfcd41 -r 6f386c5dc4fb tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml --- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Wed Apr 19 05:27:19 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Mon Sep 18 06:21:27 2017 -0400 |
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| @@ -5,7 +5,7 @@ <import>ncbi_macros.xml</import> </macros> <expand macro="preamble" /> - <command> + <command detect_errors="aggressive"> blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path}" -info -out "$info" </command> <inputs> @@ -32,7 +32,7 @@ </test> </tests> <help> - + **What it does** Calls the NCBI BLAST+ blastdbcmd command line tool with the -info |
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| diff -r 7538e2bfcd41 -r 6f386c5dc4fb tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Wed Apr 19 05:27:19 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Mon Sep 18 06:21:27 2017 -0400 |
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| @@ -5,7 +5,7 @@ <import>ncbi_macros.xml</import> </macros> <expand macro="preamble" /> - <command> + <command detect_errors="aggressive" strict="true"> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path}" @@ -13,7 +13,7 @@ ##TODO: What about -ctrl_a and -target_only as advanced options? #if $id_opts.id_type=="file": --entry_batch "$id_opts.entries" +-entry_batch '$id_opts.entries' #else: ##Perform some simple search/replaces to remove whitespace ##and make it comma separated. Quoted so don't escape pipes. @@ -40,11 +40,11 @@ ##using sed, however the exact syntax differs for Mac OS X's sed #if str($outfmt)=="blastid": --out "$seq" +-out '$seq' #else if sys.platform == "darwin": -| sed -E 's/^>(lcl\||gnl\|BL_ORD_ID\|[0-9]* )/>/1' > "$seq" +| sed -E 's/^>(lcl\||gnl\|BL_ORD_ID\|[0-9]* )/>/1' > "$seq" #else: -| sed 's/>\(lcl|\|gnl|BL_ORD_ID|[0-9]* \)/>/1' > "$seq" +| sed 's/>\(lcl|\|gnl|BL_ORD_ID|[0-9]* \)/>/1' > "$seq" #end if </command> <inputs> @@ -55,10 +55,10 @@ <option value="prompt">User entered</option> </param> <when value="file"> - <param name="entries" type="data" format="txt,tabular" label="Sequence identifier(s)" help="Plain text file with one ID per line (i.e. single column tabular file)"/> + <param name="entries" argument="-entry_batch" type="data" format="txt,tabular" label="Sequence identifier(s)" help="Plain text file with one ID per line (i.e. single column tabular file)"/> </when> <when value="prompt"> - <param name="entries" type="text" label="Sequence identifier(s)" help="Comma or new line separated list." optional="False" area="True" size="10x30"/> + <param name="entries" argument="-entry" type="text" optional="false" area="true" size="10x30" label="Sequence identifier(s)" help="Comma or new line separated list"/> </when> </conditional> <param name="outfmt" type="select" label="Output format"> @@ -105,7 +105,7 @@ </test> </tests> <help> - + **What it does** Extracts FASTA formatted sequences from a BLAST database @@ -138,5 +138,5 @@ @REFERENCES@ </help> - <expand macro="blast_citations" /> + <expand macro="blast_citations" /> </tool> |
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| diff -r 7538e2bfcd41 -r 6f386c5dc4fb tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Wed Apr 19 05:27:19 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Mon Sep 18 06:21:27 2017 -0400 |
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| @@ -6,11 +6,11 @@ </macros> <expand macro="parallelism" /> <expand macro="preamble" /> - <command> + <command detect_errors="aggressive"> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces blastn --query "$query" +-query '$query' @BLAST_DB_SUBJECT@ -task $blast_type -evalue $evalue_cutoff @@ -31,9 +31,9 @@ #end if </command> <inputs> - <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> + <param argument="-query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> <expand macro="input_conditional_nucleotide_db" /> - <param name="blast_type" type="select" display="radio" label="Type of BLAST"> + <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> <option value="blastn">blastn - Traditional BLASTN requiring an exact match of 11, for somewhat similar sequences</option> <option value="blastn-short">blastn-short - BLASTN program optimized for sequences shorter than 50 bases</option> @@ -49,16 +49,14 @@ <expand macro="input_out_format" /> <expand macro="advanced_options"> <!-- Could use a select (yes, no, other) where other allows setting 'level window linker' --> - <param name="filter_query" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="-dust yes" falsevalue="-dust no" checked="true" /> + <param name="filter_query" argument="-dust" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="-dust yes" falsevalue="-dust no" checked="true" /> <expand macro="input_strand" /> <expand macro="input_max_hits" /> - <param name="identity_cutoff" type="float" min="0" max="100" value="0" label="Percent identity cutoff (-perc_identity)" help="Use zero for no cutoff" /> - + <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 name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 4."> - <validator type="in_range" min="0" /> - </param> - <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> + <param argument="-word_size" type="integer" min="0" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 4" /> + <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" /> @@ -134,6 +132,15 @@ <param name="out_format" value="6" /> <output name="output1" file="blastn_chimera_vs_rhodopsin_db.tabular" ftype="tabular" /> </test> + <test> + <param name="query" value="chimera.fasta" ftype="fasta" /> + <param name="db_opts_selector" value="db" /> + <param name="database" value="rhodopsin_nucs" /> + <param name="out_format" value="6" /> + <param name="adv_opts_selector" value="advanced" /> + <param name="max_hsps" value="1" /> + <output name="output1" file="blastn_chimera_vs_rhodopsin_db_max_hsps1.tabular" ftype="tabular" /> + </test> <!-- next test is passing in two blast databases --> <test> <param name="query" value="chimera.fasta" ftype="fasta" /> @@ -144,7 +151,7 @@ </test> </tests> <help> - + @SEARCH_TIME_WARNING@ **What it does** |
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| diff -r 7538e2bfcd41 -r 6f386c5dc4fb tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Wed Apr 19 05:27:19 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Mon Sep 18 06:21:27 2017 -0400 |
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| @@ -6,34 +6,34 @@ </macros> <expand macro="parallelism" /> <expand macro="preamble" /> - <command> + <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 blastp --query "$query" +-query '$query' @BLAST_DB_SUBJECT@ -task $blast_type -evalue $evalue_cutoff @BLAST_OUTPUT@ @THREADS@ #if $adv_opts.adv_opts_selector=="advanced": --matrix $adv_opts.matrix -@ADV_FILTER_QUERY@ -@ADV_MAX_HITS@ -@ADV_WORD_SIZE@ -##Ungapped disabled for now - see comments below -##$adv_opts.ungapped -@ADV_ID_LIST_FILTER@ -@ADV_QCOV_HSP_PERC@ -## End of advanced options: + -matrix $adv_opts.matrix + @ADV_FILTER_QUERY@ + @ADV_MAX_HITS@ + @ADV_WORD_SIZE@ + ##Ungapped disabled for now - see comments below + ##$adv_opts.ungapped + @ADV_ID_LIST_FILTER@ + @ADV_QCOV_HSP_PERC@ + $adv_opts.use_sw_tback #end if </command> <inputs> - <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> + <param argument="-query" type="data" format="fasta" label="Protein query sequence(s)"/> <expand macro="input_conditional_protein_db" /> - <param name="blast_type" type="select" display="radio" label="Type of BLAST"> + <param name="blast_type" argument="-task" type="select" display="radio" label="Type of BLAST"> <option value="blastp">blastp - Traditional BLASTP to compare a protein query to a protein database</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> @@ -50,11 +50,12 @@ 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 blastp crashed with 'Attempt to access NULL pointer.' - <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" /> + <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" /> + <param argument="-use_sw_tback" type="boolean" truevalue="-use_sw_tback" falsevalue="" label="Compute locally optimal Smith-Waterman alignments" /> </expand> </inputs> <outputs> @@ -72,11 +73,11 @@ <param name="blast_type" value="blastp" /> <param name="out_format" value="5" /> <param name="adv_opts_selector" value="advanced" /> - <param name="filter_query" value="False" /> + <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="parse_deflines" value="True" /> + <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" /> </test> @@ -89,11 +90,11 @@ <param name="blast_type" value="blastp" /> <param name="out_format" value="6" /> <param name="adv_opts_selector" value="advanced" /> - <param name="filter_query" value="False" /> + <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="parse_deflines" value="True" /> + <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" /> </test> @@ -106,11 +107,11 @@ <param name="blast_type" value="blastp" /> <param name="out_format" value="ext" /> <param name="adv_opts_selector" value="advanced" /> - <param name="filter_query" value="False" /> + <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="parse_deflines" value="True" /> + <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" /> </test> @@ -127,7 +128,7 @@ </test> </tests> <help> - + @SEARCH_TIME_WARNING@ **What it does** @@ -150,5 +151,5 @@ @REFERENCES@ </help> - <expand macro="blast_citations" /> + <expand macro="blast_citations" /> </tool> |
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| diff -r 7538e2bfcd41 -r 6f386c5dc4fb tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Wed Apr 19 05:27:19 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Mon Sep 18 06:21:27 2017 -0400 |
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| @@ -6,11 +6,11 @@ </macros> <expand macro="parallelism" /> <expand macro="preamble" /> - <command> + <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 blastx --query "$query" +-query '$query' @BLAST_DB_SUBJECT@ -query_gencode $query_gencode -task $blast_type @@ -30,11 +30,11 @@ #end if </command> <inputs> - <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> + <param argument="-query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> <expand macro="input_conditional_protein_db" /> <expand macro="input_query_gencode" /> - <param name="blast_type" type="select" display="radio" label="Type of BLAST"> + <param name="blast_type" argument="-task" type="select" display="radio" label="Type of BLAST"> <option value="blastx">blastx - Traditional BLASTX to compare translated nucleotide query to protein database</option> <option value="blastx-fast">blastx-fast - Use longer words for seeding, faster but less accurate</option> </param> @@ -48,7 +48,7 @@ <expand macro="input_scoring_matrix" /> <expand macro="input_max_hits" /> <expand macro="input_word_size" /> - <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> + <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" /> @@ -107,7 +107,7 @@ </test> </tests> <help> - + @SEARCH_TIME_WARNING@ **What it does** |
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| diff -r 7538e2bfcd41 -r 6f386c5dc4fb tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml Wed Apr 19 05:27:19 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml Mon Sep 18 06:21:27 2017 -0400 |
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| @@ -5,36 +5,36 @@ <import>ncbi_macros.xml</import> </macros> <expand macro="preamble" /> - <command> + <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 convert2blastmask --in $infile --masking_algorithm "$masking_algorithm" --masking_options "$masking_options" +-in '$infile' +-masking_algorithm '$masking_algorithm' +-masking_options '$masking_options' $parse_seqids --out "$outfile" +-out '$outfile' -outfmt $outformat </command> <inputs> - <param name="infile" type="data" format="fasta" label="masked FASTA file"/> - <param name="masking_algorithm" type="select" label="Used masking algorithm"> + <param name="infile" argument="-in" type="data" format="fasta" label="Masked FASTA file"/> + <param argument="-masking_algorithm" type="select" label="Used masking algorithm"> <option value="dust">DUST</option> <option value="seg" selected="true">SEG</option> <option value="windowmasker">windowmasker</option> <option value="repeat">repeat</option> <option value="other">other</option> </param> - <param name="masking_options" type="text" value="" size="20" label="Masking algorithm options to create the masked input" - help ="free text to describe the options used to create the masking files. (-masking_options)"> + <param argument="-masking_options" type="text" value="" size="20" label="Masking algorithm options to create the masked input" + help ="Free text to describe the options used to create the masking files"> <sanitizer invalid_char=""> <valid initial="string.printable" /> </sanitizer> </param> - <param name="parse_seqids" type="boolean" truevalue="-parse_seqids" falsevalue="" checked="true" label="Parse Seq-ids in FASTA input" help="(-parse_seqids)" /> - <param name="outformat" type="select" label="Output format"> + <param argument="-parse_seqids" type="boolean" truevalue="-parse_seqids" falsevalue="" checked="true" label="Parse Seq-ids in FASTA input" help="(-parse_seqids)" /> + <param name="outformat" argument="-outfmt" type="select" label="Output format"> <option value="maskinfo_asn1_bin">maskinfo ASN.1 binary</option> - <option value="maskinfo_asn1_text" selected="True">maskinfo ASN.1 text</option> + <option value="maskinfo_asn1_text" selected="true">maskinfo ASN.1 text</option> <option value="maskinfo_xml">maskinfo_xml</option> </param> </inputs> @@ -42,9 +42,9 @@ <data name="outfile" format="maskinfo-asn1" label="SEG Masked File"> <change_format> <when input="outformat" value="maskinfo_asn1_bin" format="maskinfo-asn1-binary" /> - <!-- + <!-- <when input="outformat" value="maskinfo_asn1_text" format="maskinfo-asn1" /> - --> + --> <when input="outformat" value="maskinfo_xml" format="xml" /> </change_format> </data> @@ -54,7 +54,7 @@ <param name="infile" value="four_human_proteins_masked.fasta" ftype="fasta" /> <param name="masking_algorithm" value="seg" /> <param name="masking_options" value="window=12; locut=2.2; hicut=2.5" /> - <param name="parse_seqids" value="True" /> + <param name="parse_seqids" value="true" /> <param name="outformat" value="maskinfo_asn1_bin" /> <output name="outfile" file="convert2blastmask_four_human_masked.maskinfo-asn1-binary" /> </test> @@ -62,7 +62,7 @@ <param name="infile" value="four_human_proteins_masked.fasta" ftype="fasta" /> <param name="masking_algorithm" value="seg" /> <param name="masking_options" value="window=12; locut=2.2; hicut=2.5" /> - <param name="parse_seqids" value="True" /> + <param name="parse_seqids" value="true" /> <param name="outformat" value="maskinfo_asn1_text" /> <output name="outfile" file="convert2blastmask_four_human_masked.maskinfo-asn1" /> </test> |
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| diff -r 7538e2bfcd41 -r 6f386c5dc4fb tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml Wed Apr 19 05:27:19 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml Mon Sep 18 06:21:27 2017 -0400 |
| b |
| @@ -6,26 +6,26 @@ <import>ncbi_macros.xml</import> </macros> <expand macro="preamble" /> - <command> + <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 dustmasker #if $db_opts.db_opts_selector == "db": - -in "${db_opts.database.fields.path}" -infmt blastdb + -in '${db_opts.database.fields.path}' -infmt blastdb #elif $db_opts.db_opts_selector == "histdb": - -in "${os.path.join($db_opts.histdb.files_path, 'blastdb')}" -infmt blastdb + -in '${os.path.join($db_opts.histdb.files_path, "blastdb")}' -infmt blastdb #else: - -in "$subject" -infmt fasta + -in '$subject' -infmt fasta #end if --out "$outfile" +-out '$outfile' -window $window -level $level -linker $linker -outfmt $outformat </command> <inputs> <expand macro="input_conditional_nucleotide_db" /> - <param name="window" type="integer" value="64" label="DUST window length" /> - <param name="level" type="integer" value="20" label="DUST level" help="Score threshold for subwindows" /> - <param name="linker" type="integer" value="1" label="DUST linker" help="How close masked intervals should be to get merged together" /> - <param name="outformat" type="select" label="Output format"> + <param argument="-window" type="integer" value="64" label="DUST window length" /> + <param argument="-level" type="integer" value="20" label="DUST level" help="Score threshold for subwindows" /> + <param argument="-linker" type="integer" value="1" label="DUST linker" help="How close masked intervals should be to get merged together" /> + <param name="outformat" argument="-outfmt" type="select" label="Output format"> <!-- seqloc_* formats are not very useful and what BLAST+ calls 'interval' is not what Galaxy calls interval format --> @@ -40,9 +40,9 @@ <change_format> <when input="outformat" value="fasta" format="fasta" /> <when input="outformat" value="maskinfo_asn1_bin" format="maskinfo-asn1-binary" /> - <!-- + <!-- <when input="outformat" value="maskinfo_asn1_text" format="maskinfo-asn1" /> - --> + --> <when input="outformat" value="maskinfo_xml" format="xml" /> </change_format> </data> |
| b |
| diff -r 7538e2bfcd41 -r 6f386c5dc4fb tools/ncbi_blast_plus/ncbi_macros.xml --- a/tools/ncbi_blast_plus/ncbi_macros.xml Wed Apr 19 05:27:19 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_macros.xml Mon Sep 18 06:21:27 2017 -0400 |
| [ |
| b'@@ -1,5 +1,5 @@\n <macros>\n- <token name="@WRAPPER_VERSION@">0.2.00</token>\n+ <token name="@WRAPPER_VERSION@">0.2.01</token>\n <xml name="parallelism">\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@@ -8,15 +8,6 @@\n <requirements>\n <requirement type="package" version="2.5.0">blast</requirement>\n </requirements>\n- <stdio>\n- <!-- Anything other than zero is an error -->\n- <exit_code range="1:" />\n- <!-- Might see negative return codes for Unix signals via Python subprocess -->\n- <exit_code range=":-1" />\n- <!-- In case the return code has not been set properly check stderr too -->\n- <regex match="Error:" />\n- <regex match="Exception:" />\n- </stdio>\n <version_command>@BINARY@ -version</version_command>\n </xml>\n <xml name="output_change_format">\n@@ -32,9 +23,9 @@\n </xml>\n <xml name="input_out_format">\n <conditional name="output">\n- <param name="out_format" type="select" label="Output format">\n+ <param name="out_format" argument="-outfmt" type="select" label="Output format">\n <option value="6">Tabular (standard 12 columns)</option>\n- <option value="ext" selected="True">Tabular (extended 25 columns)</option>\n+ <option value="ext" selected="true">Tabular (extended 25 columns)</option>\n <option value="cols">Tabular (select which columns)</option>\n <option value="5">BLAST XML</option>\n <option value="0">Pairwise text</option>\n@@ -118,11 +109,11 @@\n </conditional>\n </xml>\n <xml name="input_scoring_matrix">\n- <param name="matrix" type="select" label="Scoring matrix">\n+ <param argument="-matrix" type="select" label="Scoring matrix">\n <option value="BLOSUM90">BLOSUM90</option>\n <option value="BLOSUM80">BLOSUM80</option>\n <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option>\n- <option value="BLOSUM50">BLOSUM50</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@@ -130,9 +121,9 @@\n </param>\n </xml>\n <xml name="input_query_gencode">\n- <param name="query_gencode" type="select" label="Query genetic code">\n+ <param argument="-query_gencode" type="select" label="Query genetic code">\n <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details -->\n- <option value="1" selected="True">1. Standard</option>\n+ <option value="1" selected="true">1. Standard</option>\n <option value="2">2. Vertebrate Mitochondrial</option>\n <option value="3">3. Yeast Mitochondrial</option>\n <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>\n@@ -153,9 +144,9 @@\n </param>\n </xml>\n <xml name="input_db_gencode">\n- <param name="db_gencode" type="select" label="Database/subject genetic code">\n+ <param argument="-db_gencode" type="select" label="Database/subject genetic code">\n <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details -->\n- <option value="1" selected="True">1. Standard</option>\n+ <option value="1" selected="true">1. Standard</option>\n <option value="2">2. Vertebrate Mitochondrial</option>\n <option value="3">3. Yeast Mitochondrial</option>\n <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>\n@@ -176,9 +167,10 @@\n'..b'for database searches."/>\n </when>\n <when value="seqidlist">\n- <param name="seqidlist" type="data" format="txt" label=" Restrict search of database to list of SeqId\'s"\n+ <param argument="-seqidlist" type="data" format="txt" label=" Restrict search of database to list of SeqId\'s"\n help="This option is only available for database searches."/>\n </when>\n </conditional>\n@@ -351,23 +341,24 @@\n <token name="@THREADS@">-num_threads "\\${GALAXY_SLOTS:-8}"</token>\n <token name="@BLAST_DB_SUBJECT@">\n #if $db_opts.db_opts_selector == "db":\n- -db "${\' \'.join(str( $db_opts.database.fields.path ).split( \',\' ))}"\n+ -db \'${" ".join(str($db_opts.database.fields.path).split(","))}\'\n #elif $db_opts.db_opts_selector == "histdb":\n- -db "${os.path.join($db_opts.histdb.extra_files_path,\'blastdb\')}"\n+ -db \'${os.path.join($db_opts.histdb.extra_files_path, "blastdb")}\'\n #else:\n- -subject "$db_opts.subject"\n+ -subject \'$db_opts.subject\'\n #end if\n </token>\n- <token name="@BLAST_OUTPUT@">-out "$output1"\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- -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen salltitles"\n+ -outfmt \'6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen salltitles\'\n #elif str($output.out_format)=="cols"\n ##Pick your own columns. Galaxy gives us it comma separated, BLAST+ wants space separated:\n ##TODO - Can we catch the user picking no columns and raise an error here?\n #set cols = (str($output.std_cols)+","+str($output.ext_cols)+","+str($output.ids_cols)+","+str($output.misc_cols)+","+str($output.tax_cols)).replace("None", "").replace(",,", ",").replace(",", " ").strip()\n- -outfmt "6 $cols"\n+ -outfmt \'6 $cols\'\n #else:\n+## Note do not quote this as can be \'0 -html\' which is really two arguments\n -outfmt $output.out_format\n #end if\n </token>\n@@ -377,13 +368,16 @@\n ## Note -max_target_seqs used to simply override -num_descriptions and -num_alignments\n ## but this was changed in BLAST+ 2.2.27 onwards to force their use (raised with NCBI)\n #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):\n-#if str($output.out_format) in ["6", "ext", "cols", "5"]:\n-## Most output formats use this, including tabular and XML:\n--max_target_seqs $adv_opts.max_hits\n-#else\n-## Text and HTML output formats 0-4 currently need this instead:\n--num_descriptions $adv_opts.max_hits -num_alignments $adv_opts.max_hits\n+ #if str($output.out_format) in ["6", "ext", "cols", "5"]:\n+ ## Most output formats use this, including tabular and XML:\n+ -max_target_seqs $adv_opts.max_hits\n+ #else\n+ ## Text and HTML output formats 0-4 currently need this instead:\n+ -num_descriptions $adv_opts.max_hits -num_alignments $adv_opts.max_hits\n+ #end if\n #end if\n+#if str($adv_opts.max_hsps)\n+ -max_hsps $adv_opts.max_hsps\n #end if\n </token>\n <token name="@ADV_WORD_SIZE@">\n@@ -394,11 +388,11 @@\n </token>\n <!-- @ON_DB_SUBJECT@ is for use with @BLAST_DB_SUBJECT@ -->\n <token name="@ON_DB_SUBJECT@">#if str($db_opts.db_opts_selector)==\'db\'\n-${db_opts.database}\n+\'${db_opts.database}\'\n #elif str($db_opts.db_opts_selector)==\'histdb\'\n-${db_opts.histdb.name}\n+\'${db_opts.histdb.name}\'\n #else\n-${db_opts.subject.name}\n+\'${db_opts.subject.name}\'\n #end if</token>\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@@ -491,7 +485,7 @@\n <token name="@SEARCH_TIME_WARNING@">.. class:: warningmark\n \n **Note**. Database searches may take a substantial amount of time.\n-For large input datasets it is advisable to allow overnight processing. \n+For large input datasets it is advisable to allow overnight processing.\n \n -----\n </token>\n' |
| b |
| diff -r 7538e2bfcd41 -r 6f386c5dc4fb tools/ncbi_blast_plus/ncbi_makeblastdb.xml --- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Wed Apr 19 05:27:19 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Mon Sep 18 06:21:27 2017 -0400 |
| b |
| b'@@ -5,23 +5,24 @@\n <import>ncbi_macros.xml</import>\n </macros>\n <expand macro="preamble" />\n- <command interpreter="python">check_no_duplicates.py\n+ <command detect_errors="aggressive" strict="true">\n+python $__tool_directory__/check_no_duplicates.py\n ##First check for duplicates (since BLAST+ 2.2.28 fails to do so)\n ##and abort (via the ampersand ampersand trick) if any are found.\n-#for i in $input_file#"${i}" #end for#\n+#for i in $input_file#\'${i}\' #end for#\n &&\n-makeblastdb -out "${os.path.join($outfile.files_path,\'blastdb\')}"\n+makeblastdb -out \'${os.path.join($outfile.files_path, "blastdb")}\'\n $parse_seqids\n $hash_index\n ## Single call to -in with multiple filenames space separated with outer quotes\n ## (presumably any filenames with spaces would be a problem). Note this gives\n ## some extra spaces, e.g. -in "file1 file2 file3 " but BLAST seems happy:\n--in "#for i in $input_file#${i} #end for#"\n+-in \'#for i in $input_file#${i} #end for#\'\n #if $title:\n--title "$title"\n+-title \'$title\'\n #else:\n ##Would default to being based on the cryptic Galaxy filenames, which is unhelpful\n--title "BLAST Database"\n+-title \'BLAST Database\'\n #end if\n -dbtype $dbtype\n ## --------------------------------------------------------------------\n@@ -31,7 +32,7 @@\n ## See Trello issue https://trello.com/c/lp5YmA1O\n #if \' \'.join( map(str, $mask_data_file) ) != \'None\':\n #for i in $mask_data_file:\n--mask_data "${i}"\n+-mask_data \'${i}\'\n #end for\n #end if\n ## --------------------------------------------------------------------\n@@ -48,7 +49,7 @@\n > "$outfile"\n </command>\n <inputs>\n- <param name="dbtype" type="select" display="radio" label="Molecule type of input">\n+ <param argument="-dbtype" type="select" display="radio" label="Molecule type of input">\n <option value="prot">protein</option>\n <option value="nucl">nucleotide</option>\n </param>\n@@ -56,13 +57,13 @@\n NOTE Double check the new database would be self contained first\n -->\n <!-- Note this is a mandatory parameter - default should be most recent FASTA file -->\n- <param name="input_file" type="data" multiple="true" optional="false" format="fasta" label="Input FASTA files(s)" help="One or more FASTA files" />\n- <param name="title" type="text" value="" label="Title for BLAST database" help="This is the database name shown in BLAST search output" />\n- <param name="parse_seqids" type="boolean" truevalue="-parse_seqids" falsevalue="" checked="False" label="Parse the sequence identifiers" help="This is only advised if your FASTA file follows the NCBI naming conventions using pipe \'|\' symbols" />\n- <param name="hash_index" type="boolean" truevalue="-hash_index" falsevalue="" checked="true" label="Enable the creation of sequence hash values" help="These hash values can then be used to quickly determine if a given sequence data exists in this BLAST database." />\n+ <param name="input_file" argument="-in" type="data" multiple="true" optional="false" format="fasta" label="Input FASTA files(s)" help="One or more FASTA files" />\n+ <param argument="-title" type="text" value="" label="Title for BLAST database" help="This is the database name shown in BLAST search output" />\n+ <param argument="-parse_seqids" type="boolean" truevalue="-parse_seqids" falsevalue="" checked="false" label="Parse the sequence identifiers" help="This is only advised if your FASTA file follows the NCBI naming conventions using pipe \'|\' symbols" />\n+ <param argument="-hash_index" type="boolean" truevalue="-hash_index" falsevalue="" checked="true" label="Enable the creation of sequence hash values" help="These hash values can then be used to quickly determine if a given sequence data exists in this BLAST database." />\n <!-- SEQUENCE MASKING OPTIONS -->\n <!-- Note this is an optional parameter - default should be NO files -->\n- <param name="mask_data_'..b'TODO - Option to create GI indexed masking data? via -gi_mask and -gi_mask_name? -->\n <!-- TAXONOMY OPTIONS -->\n <conditional name="tax">\n@@ -76,11 +77,11 @@\n <when value="">\n </when>\n <when value="id">\n- <param name="taxid" type="integer" value="" label="NCBI taxonomy ID" help="Integer >=0, e.g. 9606 for Homo sapiens" min="0" />\n+ <param argument="-taxid" type="integer" min="0" value="" label="NCBI taxonomy ID" help="Integer >=0, e.g. 9606 for Homo sapiens" />\n </when>\n <!-- TODO: File format?\n <when value="map">\n- <param name="taxmap" type="data" format="txt" label="Seq ID : Tax ID mapping file" help="Format: SequenceId TaxonomyId" />\n+ <param name="taxmap" argument="-taxid_map" type="data" format="txt" label="Seq ID : Tax ID mapping file" help="Format: SequenceId TaxonomyId" />\n </when>\n -->\n </conditional>\n@@ -107,7 +108,7 @@\n <param name="title" value="Just 4 human proteins" />\n <param name="parse_seqids" value="" />\n <param name="hash_index" value="true" />\n- <output name="out_file" compare="contains" file="four_human_proteins.fasta.log.txt" ftype="blastdbp">\n+ <output name="outfile" compare="contains" file="four_human_proteins.fasta.log.txt" ftype="blastdbp">\n <extra_files type="file" value="four_human_proteins.fasta.phr" name="blastdb.phr" />\n <extra_files type="file" value="four_human_proteins.fasta.pin" name="blastdb.pin" lines_diff="2" />\n <extra_files type="file" value="four_human_proteins.fasta.psq" name="blastdb.psq" />\n@@ -126,7 +127,7 @@\n <param name="hash_index" value="true" />\n <param name="taxselect" value="id" />\n <param name="taxid" value="9606" />\n- <output name="out_file" compare="contains" file="four_human_proteins_taxid.fasta.log.txt" ftype="blastdbp">\n+ <output name="outfile" compare="contains" file="four_human_proteins_taxid.fasta.log.txt" ftype="blastdbp">\n <extra_files type="file" value="four_human_proteins_taxid.fasta.phr" name="blastdb.phr" />\n <extra_files type="file" value="four_human_proteins_taxid.fasta.pin" name="blastdb.pin" lines_diff="2" />\n <extra_files type="file" value="four_human_proteins_taxid.fasta.psq" name="blastdb.psq" />\n@@ -144,7 +145,7 @@\n <param name="parse_seqids" value="" />\n <param name="hash_index" value="true" />\n <param name="mask_data_file" value="segmasker_four_human.maskinfo-asn1" ftype="maskinfo-asn1" />\n- <output name="out_file" compare="contains" file="four_human_proteins.fasta.log.txt" ftype="blastdbp">\n+ <output name="outfile" compare="contains" file="four_human_proteins.fasta.log.txt" ftype="blastdbp">\n <extra_files type="file" value="four_human_proteins.fasta.phr" name="blastdb.phr" />\n <extra_files type="file" value="four_human_proteins.fasta.pin" name="blastdb.pin" lines_diff="2" />\n <extra_files type="file" value="four_human_proteins.fasta.psq" name="blastdb.psq" />\n@@ -163,7 +164,7 @@\n <param name="hash_index" value="true" />\n <param name="taxselect" value="id" />\n <param name="taxid" value="9606" />\n- <output name="out_file" compare="contains" file="three_human_mRNA.fasta.log.txt" ftype="blastdbn">\n+ <output name="outfile" compare="contains" file="three_human_mRNA.fasta.log.txt" ftype="blastdbn">\n <extra_files type="file" value="three_human_mRNA.fasta.nhr" name="blastdb.nhr" />\n <extra_files type="file" value="three_human_mRNA.fasta.nin" name="blastdb.nin" lines_diff="2" />\n <extra_files type="file" value="three_human_mRNA.fasta.nsq" name="blastdb.nsq" />\n' |
| b |
| diff -r 7538e2bfcd41 -r 6f386c5dc4fb tools/ncbi_blast_plus/ncbi_makeprofiledb.xml --- a/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml Wed Apr 19 05:27:19 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml Mon Sep 18 06:21:27 2017 -0400 |
| b |
| @@ -5,19 +5,19 @@ <import>ncbi_macros.xml</import> </macros> <expand macro="preamble" /> - <command> + <command detect_errors="aggressive" strict="true"> ##Unlike makeblastdb, makeprofiledb needs directory to exist already: mkdir -p $outfile.files_path && -makeprofiledb -out "${os.path.join($outfile.files_path,'blastdb')}" +makeprofiledb -out '${os.path.join($outfile.files_path, "blastdb")}' -##We turn $infile_list into $infiles with a configfile entry defined below --in $infiles +##We turn $input_file into $infiles with a configfile entry defined below +-in '$infiles' #if $title: --title "$title" +-title '$title' #else: ##Would default to being based on the cryptic Galaxy filenames, which is unhelpful --title "Profile Database" +-title 'Profile Database' #end if -threshold $threshold @@ -32,7 +32,7 @@ -obsr_threshold $obsr_threshold -exclude_invalid $exclude_invalid --logfile "$outfile" +-logfile '$outfile' </command> <configfiles> <configfile name="infiles"> @@ -42,13 +42,12 @@ </configfile> </configfiles> <inputs> - <param name="input_file" type="data" multiple="true" optional="false" format="pssm-asn1" - label="Input PSSM files(s)" - help="One or NCBI PSSM ASN.1 format scoremat files (often named *.smp)" /> - <param name="infile_list" type="data" multiple="true" format="pssm-asn1" /> + <param name="input_file" argument="-in" type="data" multiple="true" optional="false" format="pssm-asn1" + label="Input PSSM files(s)" + help="One or NCBI PSSM ASN.1 format scoremat files (often named *.smp)" /> - <param name="title" type="text" value="" label="Title for the profile database" help="This is the database name shown in BLAST search output" /> - <param name="threshold" type="float" size="5" value="9.82" label="Minimum word score to add a word to the lookup table" /> + <param argument="-title" type="text" value="" label="Title for the profile database" help="This is the database name shown in BLAST search output" /> + <param argument="-threshold" type="float" size="5" value="9.82" label="Minimum word score to add a word to the lookup table" /> <!-- output options --> <!-- Initially we're only offering the default, RPS databases for use with rpsblast and rpstblastn @@ -61,24 +60,24 @@ <conditional name="contain_pssm_scores"> <param name="contain_pssm_scores_type" type="select" label="Does your input file contain PSSM scores?"> - <option value="yes" selected="True">Yes</option> + <option value="yes" selected="true">Yes</option> <option value="no">No</option> </param> <when value="yes" /> <when value="no"> - <param name="gapopen" type="integer" size="5" value="" label="Cost to open a gap" /> - <param name="gapextend" type="integer" size="5" value="" label="Cost to extend a gap" /> - <param name="scale" type="float" size="5" value="" label="PSSM scale factor" /> + <param argument="-gapopen" type="integer" size="5" value="" label="Cost to open a gap" /> + <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" /> </when> </conditional> <!-- Delta Blast Options --> - <param name="exclude_invalid" type="boolean" truevalue="true" falsevalue="false" checked="true" + <param argument="-exclude_invalid" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Exclude invalid domains?" help="Exclude domains that do not pass validation test" /> - <param name="obsr_threshold" type="float" size="5" value="6.0" - label="Observation threshold" + <param argument="-obsr_threshold" type="float" size="5" value="6.0" + label="Observation threshold" help="Exclude domains with with maximum number of independent observations below this threshold" /> </inputs> <outputs> @@ -89,7 +88,7 @@ <param name="input_file" value="cd00003.smp,cd00008.smp" ftype="pssm-asn1" /> <param name="title" value="Just 2 PSSM matrices" /> <param name="contain_pssm_scores_type" value="yes" /> - <output name="out_file" file="empty_file.dat" ftype="blastdbd" > + <output name="outfile" file="empty_file.dat" ftype="blastdbd" > <extra_files type="file" value="cd00003_and_cd00008.phr" name="blastdb.phr" /> <extra_files type="file" value="cd00003_and_cd00008.pin" name="blastdb.pin" lines_diff="2" /> <extra_files type="file" value="cd00003_and_cd00008.psq" name="blastdb.psq" /> |
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| diff -r 7538e2bfcd41 -r 6f386c5dc4fb tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Wed Apr 19 05:27:19 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Mon Sep 18 06:21:27 2017 -0400 |
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| @@ -6,15 +6,15 @@ </macros> <expand macro="parallelism" /> <expand macro="preamble" /> - <command> + <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 rpsblast --query "$query" +-query '$query' #if $db_opts.db_opts_selector == "db": - -db "${db_opts.database.fields.path}" + -db '${db_opts.database.fields.path}' #elif $db_opts.db_opts_selector == "histdb": - -db "${os.path.join($db_opts.histdb.files_path,'blastdb')}" + -db '${os.path.join($db_opts.histdb.files_path, "blastdb")}' #end if -evalue $evalue_cutoff @BLAST_OUTPUT@ @@ -27,7 +27,7 @@ #end if </command> <inputs> - <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> + <param argument="-query" type="data" format="fasta" label="Protein query sequence(s)"/> <expand macro="input_conditional_pssm" /> @@ -61,7 +61,7 @@ </test> </tests> <help> - + @SEARCH_TIME_WARNING@ **What it does** @@ -76,7 +76,7 @@ http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#NCBI_curated_domains *Kog* - PSSMs from automatically aligned sequences and sequence -fragments classified in the KOGs resource, the eukaryotic +fragments classified in the KOGs resource, the eukaryotic counterpart to COGs, see http://www.ncbi.nlm.nih.gov/COG/ *Cog* - PSSMs from automatically aligned sequences and sequence |
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| diff -r 7538e2bfcd41 -r 6f386c5dc4fb tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Wed Apr 19 05:27:19 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Mon Sep 18 06:21:27 2017 -0400 |
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| @@ -6,15 +6,15 @@ </macros> <expand macro="parallelism" /> <expand macro="preamble" /> - <command> + <command detect_errors="aggressive"> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces rpstblastn --query "$query" +-query '$query' #if $db_opts.db_opts_selector == "db": - -db "${db_opts.database.fields.path}" + -db '${db_opts.database.fields.path}' #elif $db_opts.db_opts_selector == "histdb": - -db "${os.path.join($db_opts.histdb.files_path,'blastdb')}" + -db '${os.path.join($db_opts.histdb.files_path, "blastdb")}' #end if -evalue $evalue_cutoff @BLAST_OUTPUT@ @@ -28,7 +28,7 @@ #end if </command> <inputs> - <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> + <param argument="-query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> <expand macro="input_conditional_pssm" /> @@ -61,7 +61,7 @@ </test> </tests> <help> - + @SEARCH_TIME_WARNING@ **What it does** @@ -76,7 +76,7 @@ http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#NCBI_curated_domains *Kog* - PSSMs from automatically aligned sequences and sequence -fragments classified in the KOGs resource, the eukaryotic +fragments classified in the KOGs resource, the eukaryotic counterpart to COGs, see http://www.ncbi.nlm.nih.gov/COG/ *Cog* - PSSMs from automatically aligned sequences and sequence |
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| diff -r 7538e2bfcd41 -r 6f386c5dc4fb tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml Wed Apr 19 05:27:19 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml Mon Sep 18 06:21:27 2017 -0400 |
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| @@ -5,18 +5,18 @@ <import>ncbi_macros.xml</import> </macros> <expand macro="preamble" /> - <command> + <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 segmasker #if $db_opts.db_opts_selector == "db": - -in "${db_opts.database.fields.path}" -infmt blastdb + -in '${db_opts.database.fields.path}' -infmt blastdb #elif $db_opts.db_opts_selector == "histdb": - -in "${os.path.join($db_opts.histdb.files_path, 'blastdb')}" -infmt blastdb + -in '${os.path.join($db_opts.histdb.files_path, "blastdb")}' -infmt blastdb #else: - -in "$subject" -infmt fasta + -in '$subject' -infmt fasta #end if --out "$outfile" +-out '$outfile' -window $window -locut $locut -hicut $hicut @@ -42,9 +42,9 @@ <change_format> <when input="outformat" value="fasta" format="fasta" /> <when input="outformat" value="maskinfo_asn1_bin" format="maskinfo-asn1-binary" /> - <!-- + <!-- <when input="outformat" value="maskinfo_asn1_text" format="maskinfo-asn1" /> - --> + --> <when input="outformat" value="maskinfo_xml" format="xml" /> </change_format> </data> |
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| diff -r 7538e2bfcd41 -r 6f386c5dc4fb tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Wed Apr 19 05:27:19 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Mon Sep 18 06:21:27 2017 -0400 |
| b |
| @@ -6,11 +6,11 @@ </macros> <expand macro="parallelism" /> <expand macro="preamble" /> - <command> + <command detect_errors="aggressive"> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces tblastn --query "$query" +-query '$query' @BLAST_DB_SUBJECT@ -task $blast_type -evalue $evalue_cutoff @@ -30,10 +30,10 @@ #end if </command> <inputs> - <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> + <param argument="-query" type="data" format="fasta" label="Protein query sequence(s)"/> <expand macro="input_conditional_nucleotide_db" /> - <param name="blast_type" type="select" display="radio" label="Type of BLAST"> + <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> @@ -51,7 +51,7 @@ 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 name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" /> + <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" /> @@ -144,7 +144,7 @@ </test> </tests> <help> - + @SEARCH_TIME_WARNING@ **What it does** |
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| diff -r 7538e2bfcd41 -r 6f386c5dc4fb tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Wed Apr 19 05:27:19 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Mon Sep 18 06:21:27 2017 -0400 |
| b |
| @@ -6,11 +6,11 @@ </macros> <expand macro="parallelism" /> <expand macro="preamble" /> - <command> + <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 "$query" +-query '$query' @BLAST_DB_SUBJECT@ -query_gencode $query_gencode -evalue $evalue_cutoff @@ -29,7 +29,7 @@ #end if </command> <inputs> - <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> + <param argument="-query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> <expand macro="input_conditional_nucleotide_db" /> <expand macro="input_query_gencode" /> @@ -69,7 +69,7 @@ </test> </tests> <help> - + @SEARCH_TIME_WARNING@ **What it does** |