# HG changeset patch
# User galaxyp
# Date 1484946042 18000
# Node ID e3ee9f1693c3149bebd7a4a77a0366d3f4824e7a
planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
diff -r 000000000000 -r e3ee9f1693c3 COPYING
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/COPYING Fri Jan 20 16:00:42 2017 -0500
@@ -0,0 +1,121 @@
+Creative Commons Legal Code
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+limitation commercial, advertising or promotional purposes (the
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+applied by Affirmer to the Work. Should any part of the License for any
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diff -r 000000000000 -r e3ee9f1693c3 README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Fri Jan 20 16:00:42 2017 -0500
@@ -0,0 +1,47 @@
+GalaxyP - NCBI BLAST+ remote blastp
+===================================
+
+* Home:
+* Galaxy Tool Shed:
+* Tool ID: `blast_plus_remote_blastp`
+
+
+Description
+-----------
+
+NCBI BLAST+ blastp with additional optional arguments.
+
+
+GalaxyP Community
+-----------------
+
+Current governing community policies for [GalaxyP](https://github.com/galaxyproteomics/) and other information can be found at:
+
+
+
+
+License
+-------
+
+Copyright (c) 2014 Regents of the University of Minnesota and Authors listed below.
+
+To the extent possible under law, the author(s) have dedicated all copyright and related and neighboring rights to this software to the public domain worldwide. This software is distributed without any warranty.
+
+You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see .
+
+You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission.
+
+
+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
+
+
+Authors
+-------
+
+Authors and contributors:
+
+* John Chilton
+* Minnesota Supercomputing Institute, Univeristy of Minnesota
diff -r 000000000000 -r e3ee9f1693c3 blast_plus_remote_blastp.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/blast_plus_remote_blastp.xml Fri Jan 20 16:00:42 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
+
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+ fmt_opt['out_format'] in ("tabular","cols")
+
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+ fmt_opt['out_format'] == "blastxml"
+
+
+ fmt_opt['out_format'] == "text" and not fmt_opt['html']
+
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+ fmt_opt['out_format'] == "text" and fmt_opt['html']
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+.. 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 000000000000 -r e3ee9f1693c3 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 16:00:42 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 000000000000 -r e3ee9f1693c3 test-data/rhodopsin_proteins.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rhodopsin_proteins.fasta Fri Jan 20 16:00:42 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 000000000000 -r e3ee9f1693c3 tool-data/.gitkeep
diff -r 000000000000 -r e3ee9f1693c3 tool-data/blastdb_p.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/blastdb_p.loc.sample Fri Jan 20 16:00:42 2017 -0500
@@ -0,0 +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:
+#
+# {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/
+#
+# 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.
+#
+# 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*:
+#
+# $ blastp -db /data/blastdb/nr -query ...
+#
+# 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
+#
+# 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:
+#
+# 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).
diff -r 000000000000 -r e3ee9f1693c3 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 16:00:42 2017 -0500
@@ -0,0 +1,6 @@
+
+