Mercurial > repos > galaxyp > blast_plus_remote_blastp
changeset 5:22a767177ac9 draft
planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
| author | galaxyp |
|---|---|
| date | Fri, 20 Jan 2017 16:00:56 -0500 |
| parents | a51980bc0ffe |
| children | e9975de58321 |
| files | README.md blast_plus_remote_blastp.xml test-data/.gitkeep test-data/four_human_proteins.fasta test-data/rhodopsin_proteins.fasta tool-data/blastdb_p.loc.sample tool_data_table_conf.xml.sample tools/blast_plus_remote_blastp.xml tools/repository_dependencies.xml tools/tool_dependencies.xml |
| diffstat | 9 files changed, 754 insertions(+), 571 deletions(-) [+] |
line wrap: on
line diff
--- a/README.md Mon May 04 09:58:57 2015 -0500 +++ b/README.md Fri Jan 20 16:00:56 2017 -0500 @@ -1,7 +1,7 @@ GalaxyP - NCBI BLAST+ remote blastp =================================== -* Home: <https://bitbucket.org/galaxyp/blast_plus_remote_blastp> +* Home: <https://github.com/galaxyproteomics/tools-galaxyp/> * Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/blast_plus_remote_blastp> * Tool ID: `blast_plus_remote_blastp` @@ -15,9 +15,9 @@ GalaxyP Community ----------------- -Current governing community policies for [GalaxyP](https://bitbucket.org/galaxyp/) and other information can be found at: +Current governing community policies for [GalaxyP](https://github.com/galaxyproteomics/) and other information can be found at: -<https://bitbucket.org/galaxyp/galaxyp> +<https://github.com/galaxyproteomics> License @@ -35,7 +35,7 @@ Contributing ------------ -Contributions to this repository are reviewed through pull requests. If you would like your work acknowledged, please also add yourself to the Authors section. If your pull request is accepted, you will also be acknowledged in <https://bitbucket.org/galaxyp/galaxyp/CONTRIBUTORS.md> unless you opt-out. +Contributions to this repository are reviewed through pull requests. If you would like your work acknowledged, please also add yourself to the Authors section. If your pull request is accepted, you will also be acknowledged in <https://github.com/galaxyproteomics/tools-galaxyp/> Authors
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/blast_plus_remote_blastp.xml Fri Jan 20 16:00:56 2017 -0500 @@ -0,0 +1,618 @@ +<tool id="blast_plus_remote_blastp" name="NCBI BLAST+ remote blastp" version="2.6.0"> + <description>Search protein database with protein query sequence(s)</description> + <!-- If job splitting is enabled, break up the query file into parts --> + <!-- + <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="500" merge_outputs="output1" /> + --> + <requirements> + <requirement type="binary">blastp</requirement> + <requirement type="package" version="2.6.0">blast</requirement> + </requirements> + <stdio> + <exit_code range="1" level="fatal" description="Bad input dataset or BLAST options" /> + <exit_code range="2" level="fatal" description="Error in BLAST database" /> + <exit_code range="3" level="fatal" description="Error in BLAST engine" /> + <exit_code range="4" level="fatal" description="Out of Memory" /> + <exit_code range="5:" level="fatal" description="Unknown Error" /> + </stdio> + <version_command>blastp -version</version_command> + <command> +## 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" +#if $db_opts.db_opts_selector == "db": + -db "${db_opts.database.fields.path}" +#elif $db_opts.db_opts_selector == "histdb": + -db "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}" +#elif $db_opts.db_opts_selector == "remote": + -db $db_opts.database + -remote + #set $txids = [] + #set $ntxids = [] + #for $i, $org in enumerate($db_opts.taxid_repeat): + #if $org.exclude: + #set $ntxids = $ntxids + ["txid" + $org.taxid.__str__] + #else + #set $txids = $txids + ["txid" + $org.taxid.__str__] + #end if + #end for + #if (len($txids) + len($ntxids)) > 0: + #set $entrez_query = '' + #if len($txids) > 0: + #set $entrez_query = $entrez_query + '(' + ' OR '.join($txids) + ')' + #end if + #if len($ntxids) > 0: + #set $entrez_query = $entrez_query + ' NOT (' + ' OR '.join($ntxids) + ')' + #end if + -entrez_query '$entrez_query' + #end if +#else: + -subject "$db_opts.subject" +#end if +-task $blast_type +-evalue $evalue_cutoff +-out blast_output +##Set the extended list here so if/when we add things, saved workflows are not affected +#if str($fmt_opt.out_format)=="text": + -outfmt "$fmt_opt.outfmt" $fmt_opt.html $fmt_opt.show_gis + #if $fmt_opt.num_descriptions.__str__.strip() != '': + -num_descriptions $fmt_opt.num_descriptions + #end if + #if $fmt_opt.num_alignments.__str__.strip() != '': + -num_alignments $fmt_opt.num_alignments + #end if +#elif str($fmt_opt.out_format)=="cols": + #set cols = (str($fmt_opt.std_cols)+","+str($fmt_opt.ext_cols)+","+str($fmt_opt.ids_cols)+","+str($fmt_opt.misc_cols)+","+str($fmt_opt.tax_cols)).replace("None", "").replace(",,", ",").replace(",", " ").strip() + -outfmt "6 $cols" + #if $fmt_opt.max_target_seqs.__str__.strip() != '': + -max_target_seqs $fmt_opt.max_target_seqs + #end if +#else: + -outfmt "$fmt_opt.outfmt" + #if $fmt_opt.max_target_seqs.__str__.strip() != '': + -max_target_seqs $fmt_opt.max_target_seqs + #end if +#end if +#if $db_opts.db_opts_selector != "remote": + -num_threads 8 +#end if +#if $adv_opts.adv_opts_selector=="advanced": + $adv_opts.filter_query + -matrix $adv_opts.scoring.matrix + $adv_opts.scoring.gap_costs + + #if $adv_opts.word_size.__str__.strip() != '': + -word_size $adv_opts.word_size + #end if + + #if $adv_opts.window_size.__str__.strip() != '': + -window_size $adv_opts.window_size + #end if + + #if $adv_opts.threshold.__str__.strip() != '': + -threshold $adv_opts.threshold + #end if + + #if $adv_opts.comp_based_stats.__str__.strip() != '': + -comp_based_stats $adv_opts.comp_based_stats + #end if + + ##Ungapped disabled for now - see comments below + ##$adv_opts.ungapped + $adv_opts.use_sw_tback + $adv_opts.parse_deflines + ## End of advanced options: +#end if + </command> + <inputs> + <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> + <conditional name="db_opts"> + <param name="db_opts_selector" type="select" label="Subject database/sequences"> + <option value="db" selected="True">Local BLAST Database</option> + <option value="histdb">BLAST database from your history</option> + <option value="file">Local FASTA file</option> + <option value="remote">NCBI Remote Database</option> + </param> + <when value="db"> + <param name="database" type="select" label="Protein BLAST database"> + <options from_file="blastdb_p.loc"> + <column name="value" index="0"/> + <column name="name" index="1"/> + <column name="path" index="2"/> + </options> + </param> + <param name="subject" type="hidden" value="" /> + </when> + <when value="histdb"> + <param name="database" type="hidden" value="" /> + <param name="histdb" type="data" format="blastdbp" label="Protein BLAST database" /> + <param name="subject" type="hidden" value="" /> + </when> + <when value="file"> + <param name="database" type="hidden" value="" /> + <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/> + </when> + <when value="remote"> + <param name="database" type="select" label="Protein BLAST database"> + <option value="nr" selected="True">Non-redundant protein sequences (nr)</option> + <option value="refseq_protein">Reference proteins (refseq_protein)</option> + <option value="swissprot">UniProtKB/Swiss-Prot(swissprot)</option> + <option value="pat">Patented protein sequences(pat)</option> + <option value="pdb">Protein Data Bank proteins(pdb)</option> + <option value="env_nr">Metagenomic proteins(env_nr)</option> + </param> + <repeat name="taxid_repeat" title="Search Organism Restriction" min="0"> + <param name="taxid" type="integer" value="" label="NCBI Taxon ID" help="For example: Human is 9606 (see: http://www.ncbi.nlm.nih.gov/taxonomy ) "> + <validator type="in_range" min="0" /> + </param> + <param name="exclude" type="boolean" checked="false" label="Exclude this NCBI Taxon ID" help=""/> + </repeat> + </when> + </conditional> + <param name="blast_type" 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> + </param> + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> + <conditional name="fmt_opt"> + <param name="out_format" type="select" label="Output format"> + <option value="tabular" selected="True">Tabular</option> + <option value="cols">Tabular (select which columns)</option> + <option value="blastxml">BLAST XML</option> + <option value="text">Text Report</option> + </param> + <when value="tabular"> + <param name="outfmt" type="select" label="Tabular columns"> + <option value="6" selected="True">Tabular (standard 12 columns)</option> + <option value="7">Tabular (standard 12 columns) with comments</option> + <option value="6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen">Tabular (extended 24 columns)</option> + <option value="6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen salltitles">Tabular (extended 25 columns)</option> + </param> + <param name="max_target_seqs" type="integer" value="500" optional="true" label="Maximum hits to show" help="Use zero for default limits"> + <validator type="in_range" min="0" /> + </param> + </when> + <when value="cols"> + <param name="std_cols" type="select" multiple="true" display="checkboxes" label="Standard columns"> + <option selected="true" value="qseqid">qseqid = Query Seq-id (ID of your sequence)</option> + <option selected="true" value="sseqid">sseqid = Subject Seq-id (ID of the database hit)</option> + <option selected="true" value="pident">pident = Percentage of identical matches</option> + <option selected="true" value="length">length = Alignment length</option> + <option selected="true" value="mismatch">mismatch = Number of mismatches</option> + <option selected="true" value="gapopen">gapopen = Number of gap openings</option> + <option selected="true" value="qstart">qstart = Start of alignment in query</option> + <option selected="true" value="qend">qend = End of alignment in query</option> + <option selected="true" value="sstart">sstart = Start of alignment in subject (database hit)</option> + <option selected="true" value="send">send = End of alignment in subject (database hit)</option> + <option selected="true" value="evalue">evalue = Expectation value (E-value)</option> + <option selected="true" value="bitscore">bitscore = Bit score</option> + </param> + <param name="ext_cols" type="select" multiple="true" display="checkboxes" label="Extended columns"> + <option value="sallseqid">sallseqid = All subject Seq-id(s), separated by a ';'</option> + <option value="score">score = Raw score</option> + <option value="nident">nident = Number of identical matches</option> + <option value="positive">positive = Number of positive-scoring matches</option> + <option value="gaps">gaps = Total number of gaps</option> + <option value="ppos">ppos = Percentage of positive-scoring matches</option> + <option value="qframe">qframe = Query frame</option> + <option value="sframe">sframe = Subject frame</option> + <option value="qseq">qseq = Aligned part of query sequence</option> + <option value="sseq">sseq = Aligned part of subject sequence</option> + <option value="qlen">qlen = Query sequence length</option> + <option value="slen">slen = Subject sequence length</option> + <option value="salltitles">salltitles = All subject title(s), separated by a '<>'</option> + </param> + <param name="ids_cols" type="select" multiple="true" display="checkboxes" label="Other identifier columns"> + <option value="qgi">qgi = Query GI</option> + <option value="qacc">qacc = Query accesion</option> + <option value="qaccver">qaccver = Query accesion.version</option> + <option value="sallseqid">sallseqid = All subject Seq-id(s), separated by a ';'</option> + <option value="sgi">sgi = Subject GI</option> + <option value="sallgi">sallgi = All subject GIs</option> + <option value="sacc">sacc = Subject accession</option> + <option value="saccver">saccver = Subject accession.version</option> + <option value="sallacc">sallacc = All subject accessions</option> + <option value="stitle">stitle = Subject Title</option> + </param> + <param name="misc_cols" type="select" multiple="true" display="checkboxes" label="Miscellaneous columns"> + <option value="sstrand">sstrand = Subject Strand</option> + <!-- Is it really worth including 'frames' given have 'qframe' and 'sframe'? --> + <option value="frames">frames = Query and subject frames separated by a '/'</option> + <option value="btop">btop = Blast traceback operations (BTOP)</option> + <option value="qcovs">qcovs = Query Coverage Per Subject</option> + <option value="qcovhsp">qcovhsp = Query Coverage Per HSP</option> + </param> + <param name="tax_cols" type="select" multiple="true" display="checkboxes" label="Taxonomy columns"> + <option value="staxids">staxids = unique Subject Taxonomy ID(s), separated by a ';' (in numerical order)</option> + <!-- TODO, how to handle the taxonomy data file dependency? If missing these give N/A --> + <option value="sscinames">sscinames = unique Subject Scientific Name(s), separated by a ';'</option> + <option value="scomnames">scomnames = unique Subject Common Name(s), separated by a ';'</option> + <option value="sblastnames">sblastnames = unique Subject Blast Name(s), separated by a ';' (in alphabetical order)</option> + <option value="sskingdoms">sskingdoms = unique Subject Super Kingdom(s), separated by a ';' (in alphabetical order)</option> + </param> + <param name="max_target_seqs" type="integer" value="500" optional="true" label="Maximum hits to show" help="Use zero for default limits"> + <validator type="in_range" min="0" /> + </param> + </when> + <when value="blastxml"> + <param name="outfmt" type="hidden" value="5"/> + <param name="max_target_seqs" type="integer" value="500" optional="true" label="Maximum hits to show" help="Use zero for default limits"> + <validator type="in_range" min="0" /> + </param> + </when> + <when value="text"> + <param name="outfmt" type="select" label="Text format"> + <option value="0">Pairwise text</option> + <option value="1">Query-anchored text showing identitites</option> + <option value="2">Query-anchored text</option> + <option value="3">Flat query-anchored text showing identitites</option> + <option value="4">Flat query-anchored text</option> + </param> + <param name="html" type="boolean" label="Html" truevalue="-html" falsevalue="" checked="true" /> + <param name="show_gis" type="boolean" label="NCBI-gis" truevalue="-show_gis" falsevalue="" checked="false" + help="Show the NCBI gis in the Subject def lines"/> + <param name="num_descriptions" type="integer" value="500" optional="true" label="Maximum Decriptions to show" help="Show one-line descriptions for this number of database sequences."> + <validator type="in_range" min="0" /> + </param> + <param name="num_alignments" type="integer" value="250" optional="true" label="Maximum alignments to show" help="Show alignments for this number of database sequences."> + <validator type="in_range" min="0" /> + </param> + </when> + </conditional> + <conditional name="adv_opts"> + <param name="adv_opts_selector" type="select" label="Advanced Options"> + <option value="basic" selected="True">Hide Advanced Options</option> + <option value="advanced">Show Advanced Options</option> + </param> + <when value="basic" /> + <when value="advanced"> + <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="false" /> + <conditional name="scoring"> + <param name="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="BLOSUM45">BLOSUM45</option> + <option value="PAM250">PAM250</option> + <option value="PAM70">PAM70</option> + <option value="PAM30">PAM30</option> + </param> + <when value="BLOSUM90"> + <param name="gap_costs" type="select" label="Gap Costs"> + <option value="">Use Defaults</option> + <option value="-gapopen 9 -gapextend 2">Existense: 9 Extension: 2</option> + <option value="-gapopen 8 -gapextend 2">Existense: 8 Extension: 2</option> + <option value="-gapopen 7 -gapextend 2">Existense: 7 Extension: 2</option> + <option value="-gapopen 6 -gapextend 2">Existense: 6 Extension: 2</option> + <option value="-gapopen 11 -gapextend 1">Existense: 11 Extension: 1</option> + <option value="-gapopen 10 -gapextend 1" selected="True">Existense: 10 Extension: 1 (default)</option> + <option value="-gapopen 9 -gapextend 1">Existense: 9 Extension: 1</option> + </param> + + </when> + <when value="BLOSUM80"> + <param name="gap_costs" type="select" label="Gap Costs"> + <option value="">Use Defaults</option> + <option value="-gapopen 8 -gapextend 2">Existense: 8 Extension: 2</option> + <option value="-gapopen 7 -gapextend 2">Existense: 7 Extension: 2</option> + <option value="-gapopen 6 -gapextend 2">Existense: 6 Extension: 2</option> + <option value="-gapopen 11 -gapextend 1">Existense: 11 Extension: 1</option> + <option value="-gapopen 10 -gapextend 1" selected="True">Existense: 10 Extension: 1 (default)</option> + <option value="-gapopen 9 -gapextend 1">Existense: 9 Extension: 1</option> + </param> + </when> + <when value="BLOSUM62"> + <param name="gap_costs" type="select" label="Gap Costs"> + <option value="">Use Defaults</option> + <option value="-gapopen 11 -gapextend 2">Existense: 11 Extension: 2</option> + <option value="-gapopen 10 -gapextend 2">Existense: 10 Extension: 2</option> + <option value="-gapopen 9 -gapextend 2">Existense: 9 Extension: 2</option> + <option value="-gapopen 8 -gapextend 2">Existense: 8 Extension: 2</option> + <option value="-gapopen 7 -gapextend 2">Existense: 7 Extension: 2</option> + <option value="-gapopen 6 -gapextend 2">Existense: 6 Extension: 2</option> + <option value="-gapopen 13 -gapextend 1">Existense: 13 Extension: 1</option> + <option value="-gapopen 12 -gapextend 1">Existense: 12 Extension: 1</option> + <option value="-gapopen 11 -gapextend 1" selected="True">Existense: 11 Extension: 1 (default)</option> + <option value="-gapopen 10 -gapextend 1">Existense: 10 Extension: 1</option> + <option value="-gapopen 9 -gapextend 1">Existense: 9 Extension: 1</option> + </param> + + </when> + <when value="BLOSUM50"> + <param name="gap_costs" type="select" label="Gap Costs"> + <option value="">Use Defaults</option> + <option value="-gapopen 13 -gapextend 3">Existense: 13 Extension: 3</option> + <option value="-gapopen 12 -gapextend 3">Existense: 12 Extension: 3</option> + <option value="-gapopen 11 -gapextend 3">Existense: 11 Extension: 3</option> + <option value="-gapopen 10 -gapextend 3">Existense: 10 Extension: 3</option> + <option value="-gapopen 9 -gapextend 3">Existense: 9 Extension: 3</option> + <option value="-gapopen 16 -gapextend 2">Existense: 16 Extension: 2</option> + <option value="-gapopen 15 -gapextend 2">Existense: 15 Extension: 2</option> + <option value="-gapopen 14 -gapextend 2">Existense: 14 Extension: 2</option> + <option value="-gapopen 13 -gapextend 2" selected="True">Existense: 13 Extension: 2 (default)</option> + <option value="-gapopen 12 -gapextend 2">Existense: 12 Extension: 2</option> + <option value="-gapopen 19 -gapextend 1">Existense: 19 Extension: 1</option> + <option value="-gapopen 18 -gapextend 1">Existense: 18 Extension: 1</option> + <option value="-gapopen 17 -gapextend 1">Existense: 17 Extension: 1</option> + <option value="-gapopen 16 -gapextend 1">Existense: 16 Extension: 1</option> + <option value="-gapopen 15 -gapextend 1">Existense: 15 Extension: 1</option> + </param> + + </when> + <when value="BLOSUM45"> + <param name="gap_costs" type="select" label="Gap Costs"> + <option value="">Use Defaults</option> + <option value="-gapopen 13 -gapextend 3">Existense: 13 Extension: 3</option> + <option value="-gapopen 12 -gapextend 3">Existense: 12 Extension: 3</option> + <option value="-gapopen 11 -gapextend 3">Existense: 11 Extension: 3</option> + <option value="-gapopen 10 -gapextend 3">Existense: 10 Extension: 3</option> + <option value="-gapopen 15 -gapextend 2" selected="True">Existense: 15 Extension: 2 (default)</option> + <option value="-gapopen 14 -gapextend 2">Existense: 14 Extension: 2</option> + <option value="-gapopen 13 -gapextend 2">Existense: 13 Extension: 2</option> + <option value="-gapopen 12 -gapextend 2">Existense: 12 Extension: 2</option> + <option value="-gapopen 19 -gapextend 1">Existense: 19 Extension: 1</option> + <option value="-gapopen 18 -gapextend 1">Existense: 18 Extension: 1</option> + <option value="-gapopen 17 -gapextend 1">Existense: 17 Extension: 1</option> + <option value="-gapopen 16 -gapextend 1">Existense: 16 Extension: 1</option> + </param> + </when> + <when value="PAM250"> + <param name="gap_costs" type="select" label="Gap Costs"> + <option value="">Use Defaults</option> + <option value="-gapopen 15 -gapextend 3">Existense: 15 Extension: 3</option> + <option value="-gapopen 14 -gapextend 3">Existense: 14 Extension: 3</option> + <option value="-gapopen 13 -gapextend 3">Existense: 13 Extension: 3</option> + <option value="-gapopen 12 -gapextend 3">Existense: 12 Extension: 3</option> + <option value="-gapopen 17 -gapextend 2">Existense: 17 Extension: 2</option> + <option value="-gapopen 16 -gapextend 2">Existense: 16 Extension: 2</option> + <option value="-gapopen 15 -gapextend 2">Existense: 15 Extension: 2</option> + <option value="-gapopen 14 -gapextend 2" selected="True">Existense: 14 Extension: 2 (default)</option> + <option value="-gapopen 13 -gapextend 2">Existense: 13 Extension: 2</option> + <option value="-gapopen 21 -gapextend 1">Existense: 21 Extension: 1</option> + <option value="-gapopen 20 -gapextend 1">Existense: 20 Extension: 1</option> + <option value="-gapopen 19 -gapextend 1">Existense: 19 Extension: 1</option> + <option value="-gapopen 18 -gapextend 1">Existense: 18 Extension: 1</option> + <option value="-gapopen 17 -gapextend 1">Existense: 17 Extension: 1</option> + </param> + + </when> + <when value="PAM70"> + <param name="gap_costs" type="select" label="Gap Costs"> + <option value="">Use Defaults</option> + <option value="-gapopen 8 -gapextend 2">Existense: 8 Extension: 2</option> + <option value="-gapopen 7 -gapextend 2">Existense: 7 Extension: 2</option> + <option value="-gapopen 6 -gapextend 2">Existense: 6 Extension: 2</option> + <option value="-gapopen 11 -gapextend 1">Existense: 11 Extension: 1</option> + <option value="-gapopen 10 -gapextend 1" selected="True">Existense: 10 Extension: 1 (default)</option> + <option value="-gapopen 9 -gapextend 1">Existense: 9 Extension: 1</option> + </param> + + </when> + <when value="PAM30"> + <param name="gap_costs" type="select" label="Gap Costs"> + <option value="">Use Defaults</option> + <option value="-gapopen 7 -gapextend 2">Existense: 7 Extension: 2</option> + <option value="-gapopen 6 -gapextend 2">Existense: 6 Extension: 2</option> + <option value="-gapopen 5 -gapextend 2">Existense: 5 Extension: 2</option> + <option value="-gapopen 10 -gapextend 1">Existense: 10 Extension: 1</option> + <option value="-gapopen 9 -gapextend 1" selected="True">Existense: 9 Extension: 1 (default)</option> + <option value="-gapopen 8 -gapextend 1">Existense: 8 Extension: 1</option> + </param> + </when> + </conditional> + + <param name="word_size" type="integer" value="" optional="true" label="Word size for wordfinder algorithm" help="Recommended: blastp 3, blastp-short 2"> + <validator type="in_range" min="2" /> + </param> + <param name="window_size" type="integer" value="" optional="true" label="Multiple hits window size, use 0 to specify 1-hit algorithm." help="Recommended: blastp 40, blastp-short 15"> + <validator type="in_range" min="0" /> + </param> + <param name="threshold" type="integer" value="" optional="true" label="Threshold: Minimum score to add a word to the BLAST lookup table." help="Recommended: blastp 11, blastp-short 16"> + <validator type="in_range" min="1" /> + </param> + <param name="comp_based_stats" type="select" optional="true" label="Use composition-based statistics" + help="Recommended: blastp: 2 blastp-short: 0"> + <option value="">Leave Unspecified</option> + <option value="0">0 or F (No composition-based statistics)</option> + <option value="1">1 (Composition-based statistics as in NAR 29:2994-3005, 2001)</option> + <option value="2">2, T, or D (Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties)</option> + <option value="3">3 (Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally)</option> + </param> + + <param name="use_sw_tback" type="boolean" label="Compute locally optimal Smith-Waterman alignments?" truevalue="-use_sw_tback" falsevalue="" checked="false" /> + + <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"/> + </when> + </conditional> + </inputs> + <outputs> + <data name="output_tabular" format="tabular" label="${blast_type} on ${db_opts.db_opts_selector} ${db_opts.database}" from_work_dir="blast_output"> + <filter>fmt_opt['out_format'] in ("tabular","cols")</filter> + </data> + <data name="output_xml" format="blastxml" label="${blast_type} on ${db_opts.db_opts_selector} ${db_opts.database}" from_work_dir="blast_output"> + <filter>fmt_opt['out_format'] == "blastxml"</filter> + </data> + <data name="output_txt" format="txt" label="${blast_type} on ${db_opts.db_opts_selector} ${db_opts.database}" from_work_dir="blast_output"> + <filter>fmt_opt['out_format'] == "text" and not fmt_opt['html']</filter> + </data> + <data name="output_html" format="html" label="${blast_type} on ${db_opts.db_opts_selector} ${db_opts.database}" from_work_dir="blast_output"> + <filter>fmt_opt['out_format'] == "text" and fmt_opt['html']</filter> + </data> + </outputs> + <tests> + <test> + <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="rhodopsin_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="blastxml" /> + <param name="outfmt" value="5" /> + <param name="adv_opts_selector" value="advanced" /> + <param name="filter_query" value="False" /> + <param name="matrix" value="BLOSUM62" /> + <param name="max_target_seqs" value="" /> + <param name="word_size" value="" /> + <param name="parse_deflines" value="False" /> + <output name="output_xml"> + <assert_contents> + <has_text text="sp|Q9BS26|ERP44_HUMAN"/> + </assert_contents> + </output> + </test> + <test> + <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="rhodopsin_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="tabular" /> + <param name="outfmt" value="6" /> + <param name="adv_opts_selector" value="advanced" /> + <param name="filter_query" value="False" /> + <param name="matrix" value="BLOSUM62" /> + <param name="max_target_seqs" value="" /> + <param name="word_size" value="" /> + <param name="parse_deflines" value="False" /> + <output name="output_tabular"> + <assert_contents> + <has_text_matching expression="sp.P08100.OPSD_HUMAN\tgi.283855846.gb.ADB45242.1.\t\d+.\d+\t\d+\t\d+\t0\t\d+\t\d+\t\d+\t\d+\t\S+\t\s*\d+" /> + <has_text text="BAB21486.1"/> + </assert_contents> + </output> + </test> + <test> + <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="rhodopsin_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="tabular" /> + <param name="outfmt" value="6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" /> + <param name="adv_opts_selector" value="advanced" /> + <param name="filter_query" value="False" /> + <param name="matrix" value="BLOSUM62" /> + <param name="max_target_seqs" value="" /> + <param name="word_size" value="" /> + <param name="parse_deflines" value="False" /> + <output name="output_tabular"> + <assert_contents> + <has_text_matching expression="sp.P08100.OPSD_HUMAN\tgi.283855846.gb.ADB45242.1.\t\d+.\d+\t\d+\t\d+\t\d+\t\d+\t\d+\t\d+\t\d+\t\S+\t\s*\d+\t\S+\t\d+\t\d+\t\d+\t\d+\t\S+\t\d+\t\d+\t\S+\t\S+\t\d+\t\d+" /> + </assert_contents> + </output> + </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="tabular" /> + <param name="outfmt" value="6" /> + <param name="adv_opts_selector" value="basic" /> + <output name="output_tabular"> + <assert_contents> + <has_text_matching expression="gi.283855846.gb.ADB45242.1.\tsp.P08100.OPSD_HUMAN\t\d+.\d+\t\d+\t\d+\t0\t\d+\t\d+\t\d+\t\d+\t\S+\t\s*\d+" /> + <has_text text="BAB21486.1"/> + </assert_contents> + </output> + </test> + </tests> + <help> + +.. class:: warningmark + +**Note**. Database searches may take a substantial amount of time. +For large input datasets it is advisable to allow overnight processing. + +----- + +**What it does** + +Search a *protein database* using a *protein query*, +using the NCBI BLAST+ blastp command line tool. + +The search can be performed using a local database, against a sequence supplied in a fasta file, +or the blast can be performed remotely at NCBI. + +The remote operation allows searches to be targeted at specific organisms. + +----- + +**Output format** + +Because Galaxy focuses on processing tabular data, the default output of this +tool is tabular. The standard BLAST+ tabular output contains 12 columns: + +====== ========= ============================================ +Column NCBI name Description +------ --------- -------------------------------------------- + 1 qseqid Query Seq-id (ID of your sequence) + 2 sseqid Subject Seq-id (ID of the database hit) + 3 pident Percentage of identical matches + 4 length Alignment length + 5 mismatch Number of mismatches + 6 gapopen Number of gap openings + 7 qstart Start of alignment in query + 8 qend End of alignment in query + 9 sstart Start of alignment in subject (database hit) + 10 send End of alignment in subject (database hit) + 11 evalue Expectation value (E-value) + 12 bitscore Bit score +====== ========= ============================================ + +The BLAST+ tools can optionally output additional columns of information, +but this takes longer to calculate. Most (but not all) of these columns are +included by selecting the extended tabular output. The extra columns are +included *after* the standard 12 columns. This is so that you can write +workflow filtering steps that accept either the 12 or 24 column tabular +BLAST output. + +====== ============= =========================================== +Column NCBI name Description +------ ------------- ------------------------------------------- + 13 sallseqid All subject Seq-id(s), separated by a ';' + 14 score Raw score + 15 nident Number of identical matches + 16 positive Number of positive-scoring matches + 17 gaps Total number of gaps + 18 ppos Percentage of positive-scoring matches + 19 qframe Query frame + 20 sframe Subject frame + 21 qseq Aligned part of query sequence + 22 sseq Aligned part of subject sequence + 23 qlen Query sequence length + 24 slen Subject sequence length + 25 salltitles All subject title(s), separated by a '<>' +====== ============= =========================================== + +The third option is BLAST XML output, which is designed to be parsed by +another program, and is understood by some Galaxy tools. + +You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). +The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. +The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. +The two query anchored outputs show a multiple sequence alignment between the query and all the matches, +and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). + +------- + +**References** + +Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. + +Schaffer et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. 2001. Nucleic Acids Res. 29:2994-3005. + + </help> + <citations> + <citation type="doi">10.1186/1471-2105-10-421</citation> + <citation type="doi">10.1186/s13742-015-0080-7</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/four_human_proteins.fasta Fri Jan 20 16:00:56 2017 -0500 @@ -0,0 +1,48 @@ +>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 +MHPAVFLSLPDLRCSLLLLVTWVFTPVTTEITSLDTENIDEILNNADVALVNFYADWCRFSQMLHPIFEEASDVIKEEFP +NENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGMMMKREYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSK +RNIIGYFEQKDSDNYRVFERVANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPDMVYLGAMTNFDVTYNWIQDK +CVPLVREITFENGEELTEEGLPFLILFHMKEDTESLEIFQNEVARQLISEKGTINFLHADCDKFRHPLLHIQKTPADCPV +IAIDSFRHMYVFGDFKDVLIPGKLKQFVFDLHSGKLHREFHHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLL +RDRDEL +>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 +MKKFSRMPKSEGGSGGGAAGGGAGGAGAGAGCGSGGSSVGVRVFAVGRHQVTLEESLAEGGFSTVFLVRTHGGIRCALKR +MYVNNMPDLNVCKREITIMKELSGHKNIVGYLDCAVNSISDNVWEVLILMEYCRAGQVVNQMNKKLQTGFTEPEVLQIFC +DTCEAVARLHQCKTPIIHRDLKVENILLNDGGNYVLCDFGSATNKFLNPQKDGVNVVEEEIKKYTTLSYRAPEMINLYGG +KPITTKADIWALGCLLYKLCFFTLPFGESQVAICDGNFTIPDNSRYSRNIHCLIRFMLEPDPEHRPDIFQVSYFAFKFAK +KDCPVSNINNSSIPSALPEPMTASEAAARKSQIKARITDTIGPTETSIAPRQRPKANSATTATPSVLTIQSSATPVKVLA +PGEFGNHRPKGALRPGNGPEILLGQGPPQQPPQQHRVLQQLQQGDWRLQQLHLQHRHPHQQQQQQQQQQQQQQQQQQQQQ +QQQQQQHHHHHHHHLLQDAYMQQYQHATQQQQMLQQQFLMHSVYQPQPSASQYPTMMPQYQQAFFQQQMLAQHQPSQQQA +SPEYLTSPQEFSPALVSYTSSLPAQVGTIMDSSYSANRSVADKEAIANFTNQKNISNPPDMSGWNPFGEDNFSKLTEEEL +LDREFDLLRSNRLEERASSDKNVDSLSAPHNHPPEDPFGSVPFISHSGSPEKKAEHSSINQENGTANPIKNGKTSPASKD +QRTGKKTSVQGQVQKGNDESESDFESDPPSPKSSEEEEQDDEEVLQGEQGDFNDDDTEPENLGHRPLLMDSEDEEEEEKH +SSDSDYEQAKAKYSDMSSVYRDRSGSGPTQDLNTILLTSAQLSSDVAVETPKQEFDVFGAVPFFAVRAQQPQQEKNEKNL +PQHRFPAAGLEQEEFDVFTKAPFSKKVNVQECHAVGPEAHTIPGYPKSVDVFGSTPFQPFLTSTSKSESNEDLFGLVPFD +EITGSQQQKVKQRSLQKLSSRQRRTKQDMSKSNGKRHHGTPTSTKKTLKPTYRTPERARRHKKVGRRDSQSSNEFLTISD +SKENISVALTDGKDRGNVLQPEESLLDPFGAKPFHSPDLSWHPPHQGLSDIRADHNTVLPGRPRQNSLHGSFHSADVLKM +DDFGAVPFTELVVQSITPHQSQQSQPVELDPFGAAPFPSKQ +>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 +MATGGRRGAAAAPLLVAVAALLLGAAGHLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPK +LIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDW +SRILDSVEDNYIVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECL +GNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYT +MNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRS +YALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQE +RNDIALKTNGDQASCENELLKFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQNVTEFDGQDACGSNSWTVVD +IDPPLRSNDPKSQNHPGWLMRGLKPWTQYAIFVKTLVTFSDERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIIL +KWKPPSDPNGNITHYLVFWERQAEDSELFELDYCLKGLKLPSRTWSPPFESEDSQKHNQSEYEDSAGECCSCPKTDSQIL +KELEESSFRKTFEDYLHNVVFVPRKTSSGTGAEDPRPSRKRRSLGDVGNVTVAVPTVAAFPNTSSTSVPTSPEEHRPFEK +VVNKESLVISGLRHFTGYRIELQACNQDTPEERCSVAAYVSARTMPEAKADDIVGPVTHEIFENNVVHLMWQEPKEPNGL +IVLYEVSYRRYGDEELHLCVSRKHFALERGCRLRGLSPGNYSVRIRATSLAGNGSWTEPTYFYVTDYLDVPSNIAKIIIG +PLIFVFLFSVVIGSIYLFLRKRQPDGPLGPLYASSNPEYLSASDVFPCSVYVPDEWEVSREKITLLRELGQGSFGMVYEG +NARDIIKGEAETRVAVKTVNESASLRERIEFLNEASVMKGFTCHHVVRLLGVVSKGQPTLVVMELMAHGDLKSYLRSLRP +EAENNPGRPPPTLQEMIQMAAEIADGMAYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTRDIYETDYYRKGGKGLLPV +RWMAPESLKDGVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQVLKFVMDGGYLDQPDNCPERVTDLMRMCWQFNPKMR +PTFLEIVNLLKDDLHPSFPEVSFFHSEENKAPESEELEMEFEDMENVPLDRSSHCQREEAGGRDGGSSLGFKRSYEEHIP +YTHMNGGKKNGRILTLPRSNPS +>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 +MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLA +VADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFT +WVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQES +ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTT +ICCGKNPLGDDEASATVSKTETSQVAPA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rhodopsin_proteins.fasta Fri Jan 20 16:00:56 2017 -0500 @@ -0,0 +1,43 @@ +>gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus] +MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT +PLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVC +KPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVV +HFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQG +SNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA + +>gi|3024260|sp|P56514.1|OPSD_BUFBU RecName: Full=Rhodopsin +MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRT +PLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVC +KPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVV +HFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQG +SEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTEASSVSSSQ +VSPA + +>gi|283855846|gb|ADB45242.1| rhodopsin [Cynopterus brachyotis] +VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLA +VADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGE +NHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIF +FCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTL +PAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS + +>gi|283855823|gb|ADB45229.1| rhodopsin [Myotis pilosus] +VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLA +VANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGE +NHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIF +FCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTI +PAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS + +>gi|223523|prf||0811197A rhodopsin [Bos taurus] +MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRT +PLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVC +KPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYTPHEETNNESFVIYMFVVH +FIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGS +DFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA + +>gi|12583665|dbj|BAB21486.1| fresh water form rod opsin [Conger myriaster] +MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRT +PLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVC +KPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTC +HFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQG +STFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTEASSVSSSS +VSPA
--- a/tool-data/blastdb_p.loc.sample Mon May 04 09:58:57 2015 -0500 +++ b/tool-data/blastdb_p.loc.sample Fri Jan 20 16:00:56 2017 -0500 @@ -1,32 +1,45 @@ #NOTE: This file comes from the tool galaxyp/blast_plus_remote_blastp +# This is a sample file distributed with Galaxy that is used to define a +# list of protein BLAST databases, using three columns tab separated: # -#This is a sample file distributed with Galaxy that is used to define a -#list of protein BLAST databases, using three columns tab separated -#(longer whitespace are TAB characters): +# <unique_id>{tab}<database_caption>{tab}<base_name_path> +# +# The captions typically contain spaces and might end with the build date. +# It is important that the actual database name does not have a space in +# it, and that there are only two tabs on each line. # -#<unique_id> <database_caption> <base_name_path> +# You can download the NCBI provided protein databases like NR from here: +# ftp://ftp.ncbi.nlm.nih.gov/blast/db/ # -#The captions typically contain spaces and might end with the build date. -#It is important that the actual database name does not have a space in -#it, and that there are only two tabs on each line. -# -#So, for example, if your database is NR and the path to your base name -#is /data/blastdb/nr, then the blastdb_p.loc entry would look like this: +# For simplicity, many Galaxy servers are configured to offer just a live +# version of each NCBI BLAST database (updated with the NCBI provided +# Perl scripts or similar). In this case, we recommend using the case +# sensistive base-name of the NCBI BLAST databases as the unique id. +# Consistent naming is important for sharing workflows between Galaxy +# servers. # -#nr{tab}NCBI NR (non redundant){tab}/data/blastdb/nr +# For example, consider the NCBI "non-redundant" protein BLAST database +# where you have downloaded and decompressed the files under /data/blastdb/ +# meaning at the command line BLAST+ would be run with something like +# which would look at the files /data/blastdb/nr.p*: # -#and your /data/blastdb directory would contain all of the files associated -#with the database, /data/blastdb/nr.*. +# $ blastp -db /data/blastdb/nr -query ... # -#Your blastdb_p.loc file should include an entry per line for each "base name" -#you have stored. For example: +# In this case use nr (lower case to match the NCBI file naming) as the +# unique id in the first column of blastdb_p.loc, giving an entry like +# this: +# +# nr{tab}NCBI non-redundant (nr){tab}/data/blastdb/nr # -#nr_05Jun2010 NCBI NR (non redundant) 05 Jun 2010 /data/blastdb/05Jun2010/nr -#nr_15Aug2010 NCBI NR (non redundant) 15 Aug 2010 /data/blastdb/15Aug2010/nr -#...etc... +# Alternatively, rather than a "live" mirror of the NCBI databases which +# are updated automatically, for full reproducibility the Galaxy Team +# recommend saving date-stamped copies of the databases. In this case +# your blastdb_p.loc file should include an entry per line for each +# version you have stored. For example: # -#You can download the NCBI provided protein databases like NR from here: -#ftp://ftp.ncbi.nlm.nih.gov/blast/db/ +# nr_05Jun2010{tab}NCBI NR (non redundant) 05 Jun 2010{tab}/data/blastdb/05Jun2010/nr +# nr_15Aug2010{tab}NCBI NR (non redundant) 15 Aug 2010{tab}/data/blastdb/15Aug2010/nr +# ...etc... # -#See also blastdb.loc which is for any nucleotide BLAST database, and -#blastdb_d.loc which is for any protein domains databases (like CDD). +# See also blastdb.loc which is for any nucleotide BLAST database, and +# blastdb_d.loc which is for any protein domains databases (like CDD).
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Jan 20 16:00:56 2017 -0500 @@ -0,0 +1,6 @@ +<tables> + <table name="blastdb_p" comment_char="#" allow_duplicate_entries="False"> + <columns>value, name, path</columns> + <file path="tool-data/blastdb_p.loc" /> + </table> +</tables>
--- a/tools/blast_plus_remote_blastp.xml Mon May 04 09:58:57 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,534 +0,0 @@ -<tool id="blast_plus_remote_blastp" name="NCBI BLAST+ remote blastp" version="1.0.1"> - <description>Search protein database with protein query sequence(s)</description> - <parallelism method="multi" split_inputs="query" split_mode="number_of_parts" split_size="4" shared_inputs="subject" merge_outputs="output1"></parallelism> - <version_command>blastp -version</version_command> - <requirements> - <requirement type="binary">blastp</requirement> - <requirement type="package" version="2.2.29">blast+</requirement> - </requirements> - <command> -## 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" -#if $db_opts.db_opts_selector == "db": - -db "${db_opts.database.fields.path}" -#elif $db_opts.db_opts_selector == "remote": - -db $db_opts.database - -remote - #set $txids = [] - #set $ntxids = [] - #for $i, $org in enumerate($db_opts.taxid_repeat): - #if $org.exclude: - #set $ntxids = $ntxids + ["txid" + $org.taxid.__str__] - #else - #set $txids = $txids + ["txid" + $org.taxid.__str__] - #end if - #end for - #if (len($txids) + len($ntxids)) > 0: - #set $entrez_query = '' - #if len($txids) > 0: - #set $entrez_query = $entrez_query + '(' + ' OR '.join($txids) + ')' - #end if - #if len($ntxids) > 0: - #set $entrez_query = $entrez_query + ' NOT (' + ' OR '.join($ntxids) + ')' - #end if - -entrez_query '$entrez_query' - #end if -#else: - -subject "$db_opts.subject" -#end if --task $blast_type --evalue $evalue_cutoff --out blast_output -##Set the extended list here so if/when we add things, saved workflows are not affected -#if str($fmt_opt.out_format)=="text": - -outfmt "$fmt_opt.outfmt" $fmt_opt.html $fmt_opt.show_gis - #if $fmt_opt.num_descriptions.__str__.strip() != '': - -num_descriptions $fmt_opt.num_descriptions - #end if - #if $fmt_opt.num_alignments.__str__.strip() != '': - -num_alignments $fmt_opt.num_alignments - #end if -#else: - -outfmt "$fmt_opt.outfmt" - #if $fmt_opt.max_target_seqs.__str__.strip() != '': - -max_target_seqs $fmt_opt.max_target_seqs - #end if -#end if -#if $db_opts.db_opts_selector != "remote": - -num_threads 8 -#end if -#if $adv_opts.adv_opts_selector=="advanced": - $adv_opts.filter_query - -matrix $adv_opts.scoring.matrix - $adv_opts.scoring.gap_costs - - #if $adv_opts.word_size.__str__.strip() != '': - -word_size $adv_opts.word_size - #end if - - #if $adv_opts.window_size.__str__.strip() != '': - -window_size $adv_opts.window_size - #end if - - #if $adv_opts.threshold.__str__.strip() != '': - -threshold $adv_opts.threshold - #end if - - #if $adv_opts.comp_based_stats.__str__.strip() != '': - -comp_based_stats $adv_opts.comp_based_stats - #end if - - ##Ungapped disabled for now - see comments below - ##$adv_opts.ungapped - $adv_opts.use_sw_tback - $adv_opts.parse_deflines - ## End of advanced options: -#end if - </command> - <inputs> - <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> - <conditional name="db_opts"> - <param name="db_opts_selector" type="select" label="Subject database/sequences"> - <option value="db" selected="True">Local BLAST Database</option> - <option value="file">Local FASTA file</option> - <option value="remote">NCBI Remote Database</option> - </param> - <when value="db"> - <param name="database" type="select" label="Protein BLAST database"> - <options from_file="blastdb_p.loc"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <column name="path" index="2"/> - </options> - </param> - <param name="subject" type="hidden" value="" /> - </when> - <when value="file"> - <param name="database" type="hidden" value="" /> - <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/> - </when> - <when value="remote"> - <param name="database" type="select" label="Protein BLAST database"> - <option value="nr" selected="selected" >Non-redundant protein sequences (nr)</option> - <option value="refseq_protein" >Reference proteins (refseq_protein)</option> - <option value="swissprot" >UniProtKB/Swiss-Prot(swissprot)</option> - <option value="pat" >Patented protein sequences(pat)</option> - <option value="pdb" >Protein Data Bank proteins(pdb)</option> - <option value="env_nr" >Metagenomic proteins(env_nr)</option> - </param> - <repeat name="taxid_repeat" title="Search Organism Restriction" min="0"> - <param name="taxid" type="integer" value="" label="NCBI Taxon ID" help="For example: Human is 9606 (see: http://www.ncbi.nlm.nih.gov/taxonomy ) "> - <dsvalidator type="in_range" min="0" /> - </param> - <param name="exclude" type="boolean" checked="false" label="Exclude this NCBI Taxon ID" help=""/> - </repeat> - </when> - </conditional> - <param name="blast_type" type="select" display="radio" label="Type of BLAST"> - <option value="blastp">blastp</option> - <option value="blastp-short">blastp-short</option> - </param> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> - <conditional name="fmt_opt"> - <param name="out_format" type="select" label="Output format"> - <option value="tabular" selected="True">Tabular</option> - <option value="blastxml">BLAST XML</option> - <option value="text">Text Report</option> - </param> - <when value="tabular"> - <param name="outfmt" type="select" label="Tabular columns"> - <option value="6" selected="True">Tabular (standard 12 columns)</option> - <option value="7">Tabular (standard 12 columns) with comments</option> - <option value="6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen">Tabular (extended 24 columns)</option> - </param> - <param name="max_target_seqs" type="integer" value="500" optional="true" label="Maximum hits to show" help="Use zero for default limits"> - <validator type="in_range" min="0" /> - </param> - </when> - <when value="blastxml"> - <param name="outfmt" type="hidden" value="5"/> - <param name="max_target_seqs" type="integer" value="500" optional="true" label="Maximum hits to show" help="Use zero for default limits"> - <validator type="in_range" min="0" /> - </param> - </when> - <when value="text"> - <param name="outfmt" type="select" label="Text format"> - <option value="0">Pairwise text</option> - <option value="1">Query-anchored text showing identitites</option> - <option value="2">Query-anchored text</option> - <option value="3">Flat query-anchored text showing identitites</option> - <option value="4">Flat query-anchored text</option> - </param> - <param name="html" type="boolean" label="Html" truevalue="-html" falsevalue="" checked="true" /> - <param name="show_gis" type="boolean" label="NCBI-gis" truevalue="-show_gis" falsevalue="" checked="false" - help="Show the NCBI gis in the Subject def lines"/> - <param name="num_descriptions" type="integer" value="500" optional="true" label="Maximum Decriptions to show" help="Show one-line descriptions for this number of database sequences."> - <validator type="in_range" min="0" /> - </param> - <param name="num_alignments" type="integer" value="250" optional="true" label="Maximum alignments to show" help="Show alignments for this number of database sequences."> - <validator type="in_range" min="0" /> - </param> - </when> - </conditional> - <conditional name="adv_opts"> - <param name="adv_opts_selector" type="select" label="Advanced Options"> - <option value="basic" selected="True">Hide Advanced Options</option> - <option value="advanced">Show Advanced Options</option> - </param> - <when value="basic" /> - <when value="advanced"> - <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="false" /> - <conditional name="scoring"> - <param name="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="BLOSUM45">BLOSUM45</option> - <option value="PAM250">PAM250</option> - <option value="PAM70">PAM70</option> - <option value="PAM30">PAM30</option> - </param> - <when value="BLOSUM90"> - <param name="gap_costs" type="select" label="Gap Costs"> - <option value="">Use Defaults</option> - <option value="-gapopen 9 -gapextend 2">Existense: 9 Extension: 2</option> - <option value="-gapopen 8 -gapextend 2">Existense: 8 Extension: 2</option> - <option value="-gapopen 7 -gapextend 2">Existense: 7 Extension: 2</option> - <option value="-gapopen 6 -gapextend 2">Existense: 6 Extension: 2</option> - <option value="-gapopen 11 -gapextend 1">Existense: 11 Extension: 1</option> - <option value="-gapopen 10 -gapextend 1" selected="true">Existense: 10 Extension: 1 (default)</option> - <option value="-gapopen 9 -gapextend 1">Existense: 9 Extension: 1</option> - </param> - - </when> - <when value="BLOSUM80"> - <param name="gap_costs" type="select" label="Gap Costs"> - <option value="">Use Defaults</option> - <option value="-gapopen 8 -gapextend 2">Existense: 8 Extension: 2</option> - <option value="-gapopen 7 -gapextend 2">Existense: 7 Extension: 2</option> - <option value="-gapopen 6 -gapextend 2">Existense: 6 Extension: 2</option> - <option value="-gapopen 11 -gapextend 1">Existense: 11 Extension: 1</option> - <option value="-gapopen 10 -gapextend 1" selected="true">Existense: 10 Extension: 1 (default)</option> - <option value="-gapopen 9 -gapextend 1">Existense: 9 Extension: 1</option> - </param> - </when> - <when value="BLOSUM62"> - <param name="gap_costs" type="select" label="Gap Costs"> - <option value="">Use Defaults</option> - <option value="-gapopen 11 -gapextend 2">Existense: 11 Extension: 2</option> - <option value="-gapopen 10 -gapextend 2">Existense: 10 Extension: 2</option> - <option value="-gapopen 9 -gapextend 2">Existense: 9 Extension: 2</option> - <option value="-gapopen 8 -gapextend 2">Existense: 8 Extension: 2</option> - <option value="-gapopen 7 -gapextend 2">Existense: 7 Extension: 2</option> - <option value="-gapopen 6 -gapextend 2">Existense: 6 Extension: 2</option> - <option value="-gapopen 13 -gapextend 1">Existense: 13 Extension: 1</option> - <option value="-gapopen 12 -gapextend 1">Existense: 12 Extension: 1</option> - <option value="-gapopen 11 -gapextend 1" selected="true">Existense: 11 Extension: 1 (default)</option> - <option value="-gapopen 10 -gapextend 1">Existense: 10 Extension: 1</option> - <option value="-gapopen 9 -gapextend 1">Existense: 9 Extension: 1</option> - </param> - - </when> - <when value="BLOSUM50"> - <param name="gap_costs" type="select" label="Gap Costs"> - <option value="">Use Defaults</option> - <option value="-gapopen 13 -gapextend 3">Existense: 13 Extension: 3</option> - <option value="-gapopen 12 -gapextend 3">Existense: 12 Extension: 3</option> - <option value="-gapopen 11 -gapextend 3">Existense: 11 Extension: 3</option> - <option value="-gapopen 10 -gapextend 3">Existense: 10 Extension: 3</option> - <option value="-gapopen 9 -gapextend 3">Existense: 9 Extension: 3</option> - <option value="-gapopen 16 -gapextend 2">Existense: 16 Extension: 2</option> - <option value="-gapopen 15 -gapextend 2">Existense: 15 Extension: 2</option> - <option value="-gapopen 14 -gapextend 2">Existense: 14 Extension: 2</option> - <option value="-gapopen 13 -gapextend 2" selected="true">Existense: 13 Extension: 2 (default)</option> - <option value="-gapopen 12 -gapextend 2">Existense: 12 Extension: 2</option> - <option value="-gapopen 19 -gapextend 1">Existense: 19 Extension: 1</option> - <option value="-gapopen 18 -gapextend 1">Existense: 18 Extension: 1</option> - <option value="-gapopen 17 -gapextend 1">Existense: 17 Extension: 1</option> - <option value="-gapopen 16 -gapextend 1">Existense: 16 Extension: 1</option> - <option value="-gapopen 15 -gapextend 1">Existense: 15 Extension: 1</option> - </param> - - </when> - <when value="BLOSUM45"> - <param name="gap_costs" type="select" label="Gap Costs"> - <option value="">Use Defaults</option> - <option value="-gapopen 13 -gapextend 3">Existense: 13 Extension: 3</option> - <option value="-gapopen 12 -gapextend 3">Existense: 12 Extension: 3</option> - <option value="-gapopen 11 -gapextend 3">Existense: 11 Extension: 3</option> - <option value="-gapopen 10 -gapextend 3">Existense: 10 Extension: 3</option> - <option value="-gapopen 15 -gapextend 2" selected="true">Existense: 15 Extension: 2 (default)</option> - <option value="-gapopen 14 -gapextend 2">Existense: 14 Extension: 2</option> - <option value="-gapopen 13 -gapextend 2">Existense: 13 Extension: 2</option> - <option value="-gapopen 12 -gapextend 2">Existense: 12 Extension: 2</option> - <option value="-gapopen 19 -gapextend 1">Existense: 19 Extension: 1</option> - <option value="-gapopen 18 -gapextend 1">Existense: 18 Extension: 1</option> - <option value="-gapopen 17 -gapextend 1">Existense: 17 Extension: 1</option> - <option value="-gapopen 16 -gapextend 1">Existense: 16 Extension: 1</option> - </param> - </when> - <when value="PAM250"> - <param name="gap_costs" type="select" label="Gap Costs"> - <option value="">Use Defaults</option> - <option value="-gapopen 15 -gapextend 3">Existense: 15 Extension: 3</option> - <option value="-gapopen 14 -gapextend 3">Existense: 14 Extension: 3</option> - <option value="-gapopen 13 -gapextend 3">Existense: 13 Extension: 3</option> - <option value="-gapopen 12 -gapextend 3">Existense: 12 Extension: 3</option> - <option value="-gapopen 17 -gapextend 2">Existense: 17 Extension: 2</option> - <option value="-gapopen 16 -gapextend 2">Existense: 16 Extension: 2</option> - <option value="-gapopen 15 -gapextend 2">Existense: 15 Extension: 2</option> - <option value="-gapopen 14 -gapextend 2" selected="true">Existense: 14 Extension: 2 (default)</option> - <option value="-gapopen 13 -gapextend 2">Existense: 13 Extension: 2</option> - <option value="-gapopen 21 -gapextend 1">Existense: 21 Extension: 1</option> - <option value="-gapopen 20 -gapextend 1">Existense: 20 Extension: 1</option> - <option value="-gapopen 19 -gapextend 1">Existense: 19 Extension: 1</option> - <option value="-gapopen 18 -gapextend 1">Existense: 18 Extension: 1</option> - <option value="-gapopen 17 -gapextend 1">Existense: 17 Extension: 1</option> - </param> - - </when> - <when value="PAM70"> - <param name="gap_costs" type="select" label="Gap Costs"> - <option value="">Use Defaults</option> - <option value="-gapopen 8 -gapextend 2">Existense: 8 Extension: 2</option> - <option value="-gapopen 7 -gapextend 2">Existense: 7 Extension: 2</option> - <option value="-gapopen 6 -gapextend 2">Existense: 6 Extension: 2</option> - <option value="-gapopen 11 -gapextend 1">Existense: 11 Extension: 1</option> - <option value="-gapopen 10 -gapextend 1" selected="true">Existense: 10 Extension: 1 (default)</option> - <option value="-gapopen 9 -gapextend 1">Existense: 9 Extension: 1</option> - </param> - - </when> - <when value="PAM30"> - <param name="gap_costs" type="select" label="Gap Costs"> - <option value="">Use Defaults</option> - <option value="-gapopen 7 -gapextend 2">Existense: 7 Extension: 2</option> - <option value="-gapopen 6 -gapextend 2">Existense: 6 Extension: 2</option> - <option value="-gapopen 5 -gapextend 2">Existense: 5 Extension: 2</option> - <option value="-gapopen 10 -gapextend 1">Existense: 10 Extension: 1</option> - <option value="-gapopen 9 -gapextend 1" selected="true">Existense: 9 Extension: 1 (default)</option> - <option value="-gapopen 8 -gapextend 1">Existense: 8 Extension: 1</option> - </param> - </when> - </conditional> - - <param name="word_size" type="integer" value="" optional="true" label="Word size for wordfinder algorithm" help="Recommended: blastp 3, blastp-short 2"> - <validator type="in_range" min="2" /> - </param> - <param name="window_size" type="integer" value="" optional="true" label="Multiple hits window size, use 0 to specify 1-hit algorithm." help="Recommended: blastp 40, blastp-short 15"> - <validator type="in_range" min="0" /> - </param> - <param name="threshold" type="integer" value="" optional="true" label="Threshold: Minimum score to add a word to the BLAST lookup table." help="Recommended: blastp 11, blastp-short 16"> - <validator type="in_range" min="1" /> - </param> - <param name="comp_based_stats" type="select" optional="true" label="Use composition-based statistics" - help="Recommended: blastp: 2 blastp-short: 0"> - <option value="">Leave Unspecified</option> - <option value="0">0 or F (No composition-based statistics)</option> - <option value="1">1 (Composition-based statistics as in NAR 29:2994-3005, 2001)</option> - <option value="2">2, T, or D (Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties)</option> - <option value="3">3 (Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally)</option> - </param> - - <param name="use_sw_tback" type="boolean" label="Compute locally optimal Smith-Waterman alignments?" truevalue="-use_sw_tback" falsevalue="" checked="false" /> - - <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"/> - </when> - </conditional> - </inputs> - - <outputs> - <data name="output_tabular" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector} ${db_opts.database}" from_work_dir="blast_output"> - <filter>fmt_opt['out_format'] == "tabular"</filter> - </data> - <data name="output_xml" format="blastxml" label="${blast_type.value_label} on ${db_opts.db_opts_selector} ${db_opts.database}" from_work_dir="blast_output"> - <filter>fmt_opt['out_format'] == "blastxml"</filter> - </data> - <data name="output_txt" format="txt" label="${blast_type.value_label} on ${db_opts.db_opts_selector} ${db_opts.database}" from_work_dir="blast_output"> - <filter>fmt_opt['out_format'] == "text" and not fmt_opt['html']</filter> - </data> - <data name="output_html" format="html" label="${blast_type.value_label} on ${db_opts.db_opts_selector} ${db_opts.database}" from_work_dir="blast_output"> - <filter>fmt_opt['out_format'] == "text" and fmt_opt['html']</filter> - </data> - </outputs> - - <stdio> - <exit_code range="1" level="fatal" description="Bad input dataset or BLAST options" /> - <exit_code range="2" level="fatal" description="Error in BLAST database" /> - <exit_code range="3" level="fatal" description="Error in BLAST engine" /> - <exit_code range="4" level="fatal" description="Out of Memory" /> - <exit_code range="5:" level="fatal" description="Unknown Error" /> - </stdio> - - <tests> - <test> - <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="rhodopsin_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="blastxml" /> - <param name="outfmt" value="5" /> - <param name="adv_opts_selector" value="advanced" /> - <param name="filter_query" value="False" /> - <param name="matrix" value="BLOSUM62" /> - <param name="max_target_seqs" value="" /> - <param name="word_size" value="" /> - <param name="parse_deflines" value="True" /> - <output name="output_xml"> - <assert_contents> - <has_text text="sp|Q9BS26|ERP44_HUMAN"/> - </assert_contents> - </output> - </test> - <test> - <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="rhodopsin_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="tabular" /> - <param name="outfmt" value="6" /> - <param name="adv_opts_selector" value="advanced" /> - <param name="filter_query" value="False" /> - <param name="matrix" value="BLOSUM62" /> - <param name="max_target_seqs" value="" /> - <param name="word_size" value="" /> - <param name="parse_deflines" value="True" /> - <output name="output_tabular"> - <assert_contents> - <has_text_matching expression="sp.P08100.OPSD_HUMAN\tgi.283855846.gb.ADB45242.1.\t\d+.\d+\t\d+\t\d+\t0\t\d+\t\d+\t\d+\t\d+\t\S+\t\s*\d+" /> - <has_text text="BAB21486.1"/> - </assert_contents> - </output> - </test> - <test> - <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="rhodopsin_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="tabular" /> - <param name="outfmt" value="6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" /> - <param name="adv_opts_selector" value="advanced" /> - <param name="filter_query" value="False" /> - <param name="matrix" value="BLOSUM62" /> - <param name="max_target_seqs" value="" /> - <param name="word_size" value="" /> - <param name="parse_deflines" value="True" /> - <output name="output_tabular"> - <assert_contents> - <has_text_matching expression="sp.P08100.OPSD_HUMAN\tgi.283855846.gb.ADB45242.1.\t\d+.\d+\t\d+\t\d+\t\d+\t\d+\t\d+\t\d+\t\d+\t\S+\t\s*\d+\t\S+\t\d+\t\d+\t\d+\t\d+\t\S+\t\d+\t\d+\t\S+\t\S+\t\d+\t\d+" /> - </assert_contents> - </output> - </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="tabular" /> - <param name="outfmt" value="6" /> - <param name="adv_opts_selector" value="basic" /> - <output name="output_tabular"> - <assert_contents> - <has_text_matching expression="gi.283855846.gb.ADB45242.1.\tsp.P08100.OPSD_HUMAN\t\d+.\d+\t\d+\t\d+\t0\t\d+\t\d+\t\d+\t\d+\t\S+\t\s*\d+" /> - <has_text text="BAB21486.1"/> - </assert_contents> - </output> - </test> - </tests> - <help> - -.. class:: warningmark - -**Note**. Database searches may take a substantial amount of time. -For large input datasets it is advisable to allow overnight processing. - ------ - -**What it does** - -Search a *protein database* using a *protein query*, -using the NCBI BLAST+ blastp command line tool. - -The search can be performed using a local database, against a sequence supplied in a fasta file, -or the blast can be performed remotely at NCBI. - -The remote operation allows searches to be targeted at specific organisms. - ------ - -**Output format** - -Because Galaxy focuses on processing tabular data, the default output of this -tool is tabular. The standard BLAST+ tabular output contains 12 columns: - -====== ========= ============================================ -Column NCBI name Description ------- --------- -------------------------------------------- - 1 qseqid Query Seq-id (ID of your sequence) - 2 sseqid Subject Seq-id (ID of the database hit) - 3 pident Percentage of identical matches - 4 length Alignment length - 5 mismatch Number of mismatches - 6 gapopen Number of gap openings - 7 qstart Start of alignment in query - 8 qend End of alignment in query - 9 sstart Start of alignment in subject (database hit) - 10 send End of alignment in subject (database hit) - 11 evalue Expectation value (E-value) - 12 bitscore Bit score -====== ========= ============================================ - -The BLAST+ tools can optionally output additional columns of information, -but this takes longer to calculate. Most (but not all) of these columns are -included by selecting the extended tabular output. The extra columns are -included *after* the standard 12 columns. This is so that you can write -workflow filtering steps that accept either the 12 or 24 column tabular -BLAST output. - -====== ============= =========================================== -Column NCBI name Description ------- ------------- ------------------------------------------- - 13 sallseqid All subject Seq-id(s), separated by a ';' - 14 score Raw score - 15 nident Number of identical matches - 16 positive Number of positive-scoring matches - 17 gaps Total number of gaps - 18 ppos Percentage of positive-scoring matches - 19 qframe Query frame - 20 sframe Subject frame - 21 qseq Aligned part of query sequence - 22 sseq Aligned part of subject sequence - 23 qlen Query sequence length - 24 slen Subject sequence length -====== ============= =========================================== - -The third option is BLAST XML output, which is designed to be parsed by -another program, and is understood by some Galaxy tools. - -You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). -The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. -The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. -The two query anchored outputs show a multiple sequence alignment between the query and all the matches, -and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). - -------- - -**References** - -Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. - -Schaffer et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. 2001. Nucleic Acids Res. 29:2994-3005. - - </help> -</tool>
--- a/tools/repository_dependencies.xml Mon May 04 09:58:57 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -<?xml version="1.0"?> -<repositories> - <repository changeset_revision="f66f8ca7b7b9" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> - <repository changeset_revision="de11e1a921c4" name="blast_datatypes" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> -</repositories>
--- a/tools/tool_dependencies.xml Mon May 04 09:58:57 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="blast+" version="2.2.29"> - <repository changeset_revision="a2ec897aac2c" name="package_blast_plus_2_2_29" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>