Mercurial > repos > devteam > ncbi_blast_plus
changeset 23:9e483194ebf6 draft
planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit befaf16290a437209109c06c20d0deb170925d16-dirty
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--- a/tools/ncbi_blast_plus/README.rst Fri May 19 06:04:55 2017 -0400 +++ b/tools/ncbi_blast_plus/README.rst Fri Sep 15 07:52:22 2017 -0400 @@ -244,6 +244,9 @@ (internal change only). v0.2.01 - Use ``<command detect_errors="aggressive">`` (internal change only). - Single quote command line arguments (internal change only). + - Show the BLAST option corresponding to each tool parameter + - Add ``-max_hsps`` option + - Add ``-use_sw_tback`` option for BLASTP ======= ====================================================================== @@ -280,7 +283,7 @@ $ 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
--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Fri May 19 06:04:55 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Fri Sep 15 07:52:22 2017 -0400 @@ -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">
--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Fri May 19 06:04:55 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Fri Sep 15 07:52:22 2017 -0400 @@ -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**
--- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Fri May 19 06:04:55 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Fri Sep 15 07:52:22 2017 -0400 @@ -17,23 +17,23 @@ @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> @@ -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>
--- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Fri May 19 06:04:55 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Fri Sep 15 07:52:22 2017 -0400 @@ -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**
--- a/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml Fri May 19 06:04:55 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml Fri Sep 15 07:52:22 2017 -0400 @@ -17,22 +17,22 @@ -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_xml">maskinfo_xml</option>
--- a/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml Fri May 19 06:04:55 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml Fri Sep 15 07:52:22 2017 -0400 @@ -22,10 +22,10 @@ </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 -->
--- a/tools/ncbi_blast_plus/ncbi_macros.xml Fri May 19 06:04:55 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_macros.xml Fri Sep 15 07:52:22 2017 -0400 @@ -23,7 +23,7 @@ </xml> <xml name="input_out_format"> <conditional name="output"> - <param name="out_format" type="select" label="Output format"> + <param name="out_format" argument="-outfmt" type="select" label="Output format"> <option value="6">Tabular (standard 12 columns)</option> <option value="ext" selected="true">Tabular (extended 25 columns)</option> <option value="cols">Tabular (select which columns)</option> @@ -109,11 +109,11 @@ </conditional> </xml> <xml name="input_scoring_matrix"> - <param name="matrix" type="select" label="Scoring matrix"> + <param argument="-matrix" type="select" label="Scoring matrix"> <option value="BLOSUM90">BLOSUM90</option> <option value="BLOSUM80">BLOSUM80</option> <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option> - <option value="BLOSUM50">BLOSUM50</option> + <option value="BLOSUM50">BLOSUM50</option> <option value="BLOSUM45">BLOSUM45</option> <option value="PAM250">PAM250</option> <option value="PAM70">PAM70</option> @@ -121,7 +121,7 @@ </param> </xml> <xml name="input_query_gencode"> - <param name="query_gencode" type="select" label="Query genetic code"> + <param argument="-query_gencode" type="select" label="Query genetic code"> <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details --> <option value="1" selected="true">1. Standard</option> <option value="2">2. Vertebrate Mitochondrial</option> @@ -144,7 +144,7 @@ </param> </xml> <xml name="input_db_gencode"> - <param name="db_gencode" type="select" label="Database/subject genetic code"> + <param argument="-db_gencode" type="select" label="Database/subject genetic code"> <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details --> <option value="1" selected="true">1. Standard</option> <option value="2">2. Vertebrate Mitochondrial</option> @@ -178,7 +178,7 @@ <options from_data_table="blastdb" /> </param> <param name="histdb" type="hidden" value="" /> - <param name="subject" type="hidden" value="" /> + <param name="subject" type="hidden" value="" /> </when> <when value="histdb"> <param name="database" type="hidden" value="" /> @@ -188,7 +188,7 @@ <when value="file"> <param name="database" type="hidden" value="" /> <param name="histdb" type="hidden" value="" /> - <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> + <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> </when> </conditional> </xml> @@ -214,7 +214,7 @@ <when value="file"> <param name="database" type="hidden" value="" /> <param name="histdb" type="hidden" value="" /> - <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/> + <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/> </when> </conditional> </xml> @@ -257,36 +257,33 @@ </conditional> </xml> <xml name="input_parse_deflines"> - <param name="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"/> + <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" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="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" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="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" value="0" label="Maximum hits to show" help="Use zero for default limits"> - <validator type="in_range" min="0" /> - </param> + <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" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> + <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 name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2."> - <validator type="in_range" min="0" /> - </param> + <param argument="-word_size" type="integer" min="0" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2" /> </xml> <xml name="input_strand"> - <param name="strand" type="select" label="Query strand(s) to search against database/subject"> + <param argument="-strand" type="select" label="Query strand(s) to search against database/subject"> <option value="-strand both">Both</option> <option value="-strand plus">Plus (forward)</option> <option value="-strand minus">Minus (reverse complement)</option> </param> </xml> <xml name="input_qcov_hsp_perc"> - <param name="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"/> + <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="advanced_options"> <conditional name="adv_opts"> @@ -312,15 +309,15 @@ </param> <when value="none" /> <when value="gilist"> - <param name="gilist" type="data" format="txt" label="Restrict search of database to GI's listed in this file" + <param argument="-gilist" type="data" format="txt" label="Restrict search of database to GI's listed in this file" help="This option is only available for database searches."/> </when> <when value="negative_gilist"> - <param name="negative_gilist" type="data" format="txt" label="Restrict search of database to everything except the GI's listed in this file" + <param argument="-negative_gilist" type="data" format="txt" label="Restrict search of database to everything except the GI's listed in this file" help="This option is only available for database searches."/> </when> <when value="seqidlist"> - <param name="seqidlist" type="data" format="txt" label=" Restrict search of database to list of SeqId's" + <param argument="-seqidlist" type="data" format="txt" label=" Restrict search of database to list of SeqId's" help="This option is only available for database searches."/> </when> </conditional> @@ -369,13 +366,16 @@ ## Note -max_target_seqs used to simply override -num_descriptions and -num_alignments ## but this was changed in BLAST+ 2.2.27 onwards to force their use (raised with NCBI) #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): -#if str($output.out_format) in ["6", "ext", "cols", "5"]: -## Most output formats use this, including tabular and XML: --max_target_seqs $adv_opts.max_hits -#else -## Text and HTML output formats 0-4 currently need this instead: --num_descriptions $adv_opts.max_hits -num_alignments $adv_opts.max_hits + #if str($output.out_format) in ["6", "ext", "cols", "5"]: + ## Most output formats use this, including tabular and XML: + -max_target_seqs $adv_opts.max_hits + #else + ## Text and HTML output formats 0-4 currently need this instead: + -num_descriptions $adv_opts.max_hits -num_alignments $adv_opts.max_hits + #end if #end if +#if str($adv_opts.max_hsps) + -max_hsps $adv_opts.max_hsps #end if </token> <token name="@ADV_WORD_SIZE@"> @@ -483,7 +483,7 @@ <token name="@SEARCH_TIME_WARNING@">.. class:: warningmark **Note**. Database searches may take a substantial amount of time. -For large input datasets it is advisable to allow overnight processing. +For large input datasets it is advisable to allow overnight processing. ----- </token>
--- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Fri May 19 06:04:55 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Fri Sep 15 07:52:22 2017 -0400 @@ -49,7 +49,7 @@ > "$outfile" </command> <inputs> - <param name="dbtype" type="select" display="radio" label="Molecule type of input"> + <param argument="-dbtype" type="select" display="radio" label="Molecule type of input"> <option value="prot">protein</option> <option value="nucl">nucleotide</option> </param> @@ -57,13 +57,13 @@ NOTE Double check the new database would be self contained first --> <!-- Note this is a mandatory parameter - default should be most recent FASTA file --> - <param name="input_file" type="data" multiple="true" optional="false" format="fasta" label="Input FASTA files(s)" help="One or more FASTA files" /> - <param name="title" type="text" value="" label="Title for BLAST database" help="This is the database name shown in BLAST search output" /> - <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" /> - <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." /> + <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" /> + <param argument="-title" type="text" value="" label="Title for BLAST database" help="This is the database name shown in BLAST search output" /> + <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" /> + <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." /> <!-- SEQUENCE MASKING OPTIONS --> <!-- Note this is an optional parameter - default should be NO files --> - <param name="mask_data_file" type="data" multiple="true" optional="true" value="" format="maskinfo-asn1,maskinfo-asn1-binary" label="Optional ASN.1 file(s) containing masking data" help="As produced by NCBI masking applications (e.g. dustmasker, segmasker, windowmasker)" /> + <param name="mask_data_file" argument="-mask_data" type="data" multiple="true" optional="true" value="" format="maskinfo-asn1,maskinfo-asn1-binary" label="Optional ASN.1 file(s) containing masking data" help="As produced by NCBI masking applications (e.g. dustmasker, segmasker, windowmasker)" /> <!-- TODO - Option to create GI indexed masking data? via -gi_mask and -gi_mask_name? --> <!-- TAXONOMY OPTIONS --> <conditional name="tax"> @@ -77,11 +77,11 @@ <when value=""> </when> <when value="id"> - <param name="taxid" type="integer" value="" label="NCBI taxonomy ID" help="Integer >=0, e.g. 9606 for Homo sapiens" min="0" /> + <param argument="-taxid" type="integer" min="0" value="" label="NCBI taxonomy ID" help="Integer >=0, e.g. 9606 for Homo sapiens" /> </when> <!-- TODO: File format? <when value="map"> - <param name="taxmap" type="data" format="txt" label="Seq ID : Tax ID mapping file" help="Format: SequenceId TaxonomyId" /> + <param name="taxmap" argument="-taxid_map" type="data" format="txt" label="Seq ID : Tax ID mapping file" help="Format: SequenceId TaxonomyId" /> </when> --> </conditional>
--- a/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml Fri May 19 06:04:55 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml Fri Sep 15 07:52:22 2017 -0400 @@ -10,7 +10,7 @@ mkdir -p $outfile.files_path && makeprofiledb -out '${os.path.join($outfile.files_path, "blastdb")}' -##We turn $infile_list into $infiles with a configfile entry defined below +##We turn $input_file into $infiles with a configfile entry defined below -in '$infiles' #if $title: @@ -42,13 +42,12 @@ </configfile> </configfiles> <inputs> - <param name="input_file" type="data" multiple="true" optional="false" 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="infile_list" type="data" multiple="true" format="pssm-asn1" /> - <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 @@ -66,19 +65,19 @@ </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>
--- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Fri May 19 06:04:55 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Fri Sep 15 07:52:22 2017 -0400 @@ -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
--- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Fri May 19 06:04:55 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Fri Sep 15 07:52:22 2017 -0400 @@ -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
--- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Fri May 19 06:04:55 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Fri Sep 15 07:52:22 2017 -0400 @@ -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**
--- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Fri May 19 06:04:55 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Fri Sep 15 07:52:22 2017 -0400 @@ -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**