# HG changeset patch # User galaxyp # Date 1484946056 18000 # Node ID 22a767177ac9d566ba4a283ef27dec497445d59a # Parent a51980bc0ffe48d16eca21279210ca757f5b39fa planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 diff -r a51980bc0ffe -r 22a767177ac9 README.md --- 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: +* Home: * Galaxy Tool Shed: * 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: - + 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 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 Authors diff -r a51980bc0ffe -r 22a767177ac9 blast_plus_remote_blastp.xml --- /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 @@ + + Search protein database with protein query sequence(s) + + + + blastp + blast + + + + + + + + + blastp -version + +## 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + fmt_opt['out_format'] in ("tabular","cols") + + + fmt_opt['out_format'] == "blastxml" + + + fmt_opt['out_format'] == "text" and not fmt_opt['html'] + + + fmt_opt['out_format'] == "text" and fmt_opt['html'] + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +.. 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. + + + + 10.1186/1471-2105-10-421 + 10.1186/s13742-015-0080-7 + + diff -r a51980bc0ffe -r 22a767177ac9 test-data/.gitkeep diff -r a51980bc0ffe -r 22a767177ac9 test-data/four_human_proteins.fasta --- /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 diff -r a51980bc0ffe -r 22a767177ac9 test-data/rhodopsin_proteins.fasta --- /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 diff -r a51980bc0ffe -r 22a767177ac9 tool-data/blastdb_p.loc.sample --- 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): +# {tab}{tab} +# +# 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. # -# +# 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). diff -r a51980bc0ffe -r 22a767177ac9 tool_data_table_conf.xml.sample --- /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 @@ + + + value, name, path + +

+ diff -r a51980bc0ffe -r 22a767177ac9 tools/blast_plus_remote_blastp.xml --- 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 @@ - - Search protein database with protein query sequence(s) - - blastp -version - - blastp - blast+ - - -## 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - fmt_opt['out_format'] == "tabular" - - - fmt_opt['out_format'] == "blastxml" - - - fmt_opt['out_format'] == "text" and not fmt_opt['html'] - - - fmt_opt['out_format'] == "text" and fmt_opt['html'] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -.. 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. - - - diff -r a51980bc0ffe -r 22a767177ac9 tools/repository_dependencies.xml --- 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 @@ - - - - - diff -r a51980bc0ffe -r 22a767177ac9 tools/tool_dependencies.xml --- 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 @@ - - - - - -