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changeset 2:14b2e159b310 draft

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v0.1.7 - Updated citation & misc internal changes
author peterjc
date Fri, 04 Sep 2015 07:06:18 -0400
parents ff0b814c1320
children 9ba8ebb636f4
files test-data/four_human_proteins.fasta tools/blast_rbh/README.rst tools/blast_rbh/blast_rbh.py tools/blast_rbh/blast_rbh.xml
diffstat 4 files changed, 118 insertions(+), 93 deletions(-) [+]
line wrap: on
line diff
--- a/test-data/four_human_proteins.fasta	Fri Nov 21 06:57:14 2014 -0500
+++ b/test-data/four_human_proteins.fasta	Fri Sep 04 07:06:18 2015 -0400
@@ -1,61 +1,48 @@
 >sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1
-MHPAVFLSLPDLRCSLLLLVTWVFTPVTTEITSLDTENIDEILNNADVALVNFYADWCRF
-SQMLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGMMMK
-REYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFER
-VANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPDMVYLGAMTNFDVTYNWIQDK
-CVPLVREITFENGEELTEEGLPFLILFHMKEDTESLEIFQNEVARQLISEKGTINFLHAD
-CDKFRHPLLHIQKTPADCPVIAIDSFRHMYVFGDFKDVLIPGKLKQFVFDLHSGKLHREF
-HHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLLRDRDEL
+MHPAVFLSLPDLRCSLLLLVTWVFTPVTTEITSLDTENIDEILNNADVALVNFYADWCRFSQMLHPIFEEASDVIKEEFP
+NENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGMMMKREYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSK
+RNIIGYFEQKDSDNYRVFERVANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPDMVYLGAMTNFDVTYNWIQDK
+CVPLVREITFENGEELTEEGLPFLILFHMKEDTESLEIFQNEVARQLISEKGTINFLHADCDKFRHPLLHIQKTPADCPV
+IAIDSFRHMYVFGDFKDVLIPGKLKQFVFDLHSGKLHREFHHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLL
+RDRDEL
 >sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2
-MKKFSRMPKSEGGSGGGAAGGGAGGAGAGAGCGSGGSSVGVRVFAVGRHQVTLEESLAEG
-GFSTVFLVRTHGGIRCALKRMYVNNMPDLNVCKREITIMKELSGHKNIVGYLDCAVNSIS
-DNVWEVLILMEYCRAGQVVNQMNKKLQTGFTEPEVLQIFCDTCEAVARLHQCKTPIIHRD
-LKVENILLNDGGNYVLCDFGSATNKFLNPQKDGVNVVEEEIKKYTTLSYRAPEMINLYGG
-KPITTKADIWALGCLLYKLCFFTLPFGESQVAICDGNFTIPDNSRYSRNIHCLIRFMLEP
-DPEHRPDIFQVSYFAFKFAKKDCPVSNINNSSIPSALPEPMTASEAAARKSQIKARITDT
-IGPTETSIAPRQRPKANSATTATPSVLTIQSSATPVKVLAPGEFGNHRPKGALRPGNGPE
-ILLGQGPPQQPPQQHRVLQQLQQGDWRLQQLHLQHRHPHQQQQQQQQQQQQQQQQQQQQQ
-QQQQQQHHHHHHHHLLQDAYMQQYQHATQQQQMLQQQFLMHSVYQPQPSASQYPTMMPQY
-QQAFFQQQMLAQHQPSQQQASPEYLTSPQEFSPALVSYTSSLPAQVGTIMDSSYSANRSV
-ADKEAIANFTNQKNISNPPDMSGWNPFGEDNFSKLTEEELLDREFDLLRSNRLEERASSD
-KNVDSLSAPHNHPPEDPFGSVPFISHSGSPEKKAEHSSINQENGTANPIKNGKTSPASKD
-QRTGKKTSVQGQVQKGNDESESDFESDPPSPKSSEEEEQDDEEVLQGEQGDFNDDDTEPE
-NLGHRPLLMDSEDEEEEEKHSSDSDYEQAKAKYSDMSSVYRDRSGSGPTQDLNTILLTSA
-QLSSDVAVETPKQEFDVFGAVPFFAVRAQQPQQEKNEKNLPQHRFPAAGLEQEEFDVFTK
-APFSKKVNVQECHAVGPEAHTIPGYPKSVDVFGSTPFQPFLTSTSKSESNEDLFGLVPFD
-EITGSQQQKVKQRSLQKLSSRQRRTKQDMSKSNGKRHHGTPTSTKKTLKPTYRTPERARR
-HKKVGRRDSQSSNEFLTISDSKENISVALTDGKDRGNVLQPEESLLDPFGAKPFHSPDLS
-WHPPHQGLSDIRADHNTVLPGRPRQNSLHGSFHSADVLKMDDFGAVPFTELVVQSITPHQ
-SQQSQPVELDPFGAAPFPSKQ
+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
-MATGGRRGAAAAPLLVAVAALLLGAAGHLYPGEVCPGMDIRNNLTRLHELENCSVIEGHL
-QILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYAL
-VIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNYIVLNKDDNE
-ECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECL
-GNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQG
-CHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGC
-TVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETL
-EIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQE
-RNDIALKTNGDQASCENELLKFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQ
-NVTEFDGQDACGSNSWTVVDIDPPLRSNDPKSQNHPGWLMRGLKPWTQYAIFVKTLVTFS
-DERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIILKWKPPSDPNGNITHYLVFWE
-RQAEDSELFELDYCLKGLKLPSRTWSPPFESEDSQKHNQSEYEDSAGECCSCPKTDSQIL
-KELEESSFRKTFEDYLHNVVFVPRKTSSGTGAEDPRPSRKRRSLGDVGNVTVAVPTVAAF
-PNTSSTSVPTSPEEHRPFEKVVNKESLVISGLRHFTGYRIELQACNQDTPEERCSVAAYV
-SARTMPEAKADDIVGPVTHEIFENNVVHLMWQEPKEPNGLIVLYEVSYRRYGDEELHLCV
-SRKHFALERGCRLRGLSPGNYSVRIRATSLAGNGSWTEPTYFYVTDYLDVPSNIAKIIIG
-PLIFVFLFSVVIGSIYLFLRKRQPDGPLGPLYASSNPEYLSASDVFPCSVYVPDEWEVSR
-EKITLLRELGQGSFGMVYEGNARDIIKGEAETRVAVKTVNESASLRERIEFLNEASVMKG
-FTCHHVVRLLGVVSKGQPTLVVMELMAHGDLKSYLRSLRPEAENNPGRPPPTLQEMIQMA
-AEIADGMAYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTRDIYETDYYRKGGKGLLPV
-RWMAPESLKDGVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQVLKFVMDGGYLDQPDN
-CPERVTDLMRMCWQFNPKMRPTFLEIVNLLKDDLHPSFPEVSFFHSEENKAPESEELEME
-FEDMENVPLDRSSHCQREEAGGRDGGSSLGFKRSYEEHIPYTHMNGGKKNGRILTLPRSN
-PS
+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
-MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY
-VTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG
-GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIP
-EGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQES
-ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAI
-YNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA
+MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLA
+VADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFT
+WVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQES
+ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTT
+ICCGKNPLGDDEASATVSKTETSQVAPA
--- a/tools/blast_rbh/README.rst	Fri Nov 21 06:57:14 2014 -0500
+++ b/tools/blast_rbh/README.rst	Fri Sep 04 07:06:18 2015 -0400
@@ -1,7 +1,7 @@
 Find BLAST Reciprocal Best Hits (RBH), with Galaxy wrapper
 ==========================================================
 
-This tool is copyright 2011-2014 by Peter Cock, The James Hutton Institute
+This tool is copyright 2011-2015 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below.
 
@@ -16,6 +16,23 @@
 http://toolshed.g2.bx.psu.edu/view/peterjc/blast_rbh
 
 
+Citation
+========
+
+Please cite the following paper:
+
+NCBI BLAST+ integrated into Galaxy.
+P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo
+*GigaScience* 2015, 4:39
+DOI: http://dx.doi.org/10.1186/s13742-015-0080-7
+
+You should also cite the NCBI BLAST+ tools:
+
+BLAST+: architecture and applications.
+C. Camacho et al. *BMC Bioinformatics* 2009, 10:421.
+DOI: http://dx.doi.org/10.1186/1471-2105-10-421
+
+
 Automated Installation
 ======================
 
@@ -62,6 +79,11 @@
           not treating this as an error, leading to confusing RBH output).
 v0.1.5  - Clarify documentation for using the Python script outside Galaxy.
         - Updated to depend on NCBI BLAST+ 2.2.30 via ToolShed install.
+v0.1.6  - Offer the new blastp-fast task added in BLAST+ 2.2.30.
+        - Added "NCBI BLAST+ integrated into Galaxy" preprint citation.
+v0.1.7  - Reorder XML elements (internal change only).
+        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
+        - Updated citation information with GigaScience paper.
 ======= ======================================================================
 
 
@@ -71,31 +93,40 @@
 This tool is developed on the following GitHub repository:
 https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh
 
-For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
-the following command from the Galaxy root folder::
+For pushing a release to the test or main "Galaxy Tool Shed", use the following
+Planemo commands (which requires you have set your Tool Shed access details in
+``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
+
+    $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/galaxy_blast/tools/blast_rbh/
+    ...
 
-    $ tar -czf blast_rbh.tar.gz tools/blast_rbh/README.rst tools/blast_rbh/blast_rbh.xml tools/blast_rbh/blast_rbh.py tools/blast_rbh/tool_dependencies.xml test-data/rhodopsin_nucs.fasta test-data/rhodopsin_proteins.fasta test-data/three_human_mRNA.fasta test-data/four_human_proteins.fasta test-data/k12_edited_proteins.fasta test-data/k12_ten_proteins.fasta test-data/rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular test-data/rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular test-data/rbh_blastp_four_human_vs_rhodopsin_proteins.tabular test-data/rbh_none.tabular test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular test-data/rbh_blastp_k12.tabular test-data/rbh_blastp_k12_self.tabular
+or::
+
+    $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/galaxy_blast/tools/blast_rbh/
+    ...
+
+To just build and check the tar ball, use::
 
-Check this worked::
-
-    $ tar -tzf blast_rbh.tar.gz
-    tools/blast_rbh/README.rst
-    tools/blast_rbh/blast_rbh.xml
-    tools/blast_rbh/blast_rbh.py
-    tools/blast_rbh/tool_dependencies.xml
+    $ planemo shed_upload --tar_only  ~/repositories/galaxy_blast/tools/blast_rbh/
+    ...
+    $ tar -tzf shed_upload.tar.gz 
+    test-data/four_human_proteins.fasta
+    test-data/k12_edited_proteins.fasta
+    test-data/k12_ten_proteins.fasta
+    test-data/rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular
+    test-data/rbh_blastp_four_human_vs_rhodopsin_proteins.tabular
+    test-data/rbh_blastp_k12.tabular
+    test-data/rbh_blastp_k12_self.tabular
+    test-data/rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular
+    test-data/rbh_none.tabular
+    test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular
     test-data/rhodopsin_nucs.fasta
     test-data/rhodopsin_proteins.fasta
     test-data/three_human_mRNA.fasta
-    test-data/four_human_proteins.fasta
-    test-data/k12_edited_proteins.fasta
-    test-data/k12_ten_proteins.fasta
-    test-data/rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular
-    test-data/rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular
-    test-data/rbh_blastp_four_human_vs_rhodopsin_proteins.tabular
-    test-data/rbh_none.tabular
-    test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular
-    test-data/rbh_blastp_k12.tabular
-    test-data/rbh_blastp_k12_self.tabular
+    tools/blast_rbh/README.rst
+    tools/blast_rbh/blast_rbh.py
+    tools/blast_rbh/blast_rbh.xml
+    tools/blast_rbh/tool_dependencies.xml
 
 
 Licence (MIT)
--- a/tools/blast_rbh/blast_rbh.py	Fri Nov 21 06:57:14 2014 -0500
+++ b/tools/blast_rbh/blast_rbh.py	Fri Sep 04 07:06:18 2015 -0400
@@ -14,6 +14,9 @@
 """
 
 # TODO - Output more columns, e.g. pident, qcovs, descriptions?
+# TODO - Use new -qcov_hsp_perc option in BLAST+ 2.2.30 to filter
+#        results, rather than doing minimum HSP coverage in Python.
+#        [Not doing this right now as would break on older BLAST+]
 
 import os
 import sys
@@ -32,7 +35,7 @@
 
 if "--version" in sys.argv[1:]:
     #TODO - Capture version of BLAST+ binaries too?
-    print "BLAST RBH v0.1.5"
+    print "BLAST RBH v0.1.6"
     sys.exit(0)
 
 #Parse Command Line
@@ -107,7 +110,7 @@
     else:
         stop_err("Invalid BLAST type for BLASTN: %r" % blast_type)
 elif dbtype == "prot":
-    if blast_type not in ["blastp", "blastp-short"]:
+    if blast_type not in ["blastp", "blastp-fast", "blastp-short"]:
         stop_err("Invalid BLAST type for BLASTP: %r" % blast_type)
     blast_cmd = "blastp -task %s" % blast_type
 else:
@@ -329,7 +332,7 @@
 outfile.close()
 print "Done, %i RBH found" % count
 if tie_warning:
-    sys.stderr.write("Warning: Sequencies with tied best hits found, you may have duplicates/clusters\n")
+    sys.stderr.write("Warning: Sequences with tied best hits found, you may have duplicates/clusters\n")
 
 #Remove temp files...
 shutil.rmtree(base_path)
--- a/tools/blast_rbh/blast_rbh.xml	Fri Nov 21 06:57:14 2014 -0500
+++ b/tools/blast_rbh/blast_rbh.xml	Fri Sep 04 07:06:18 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="blast_reciprocal_best_hits" name="BLAST Reciprocal Best Hits (RBH)" version="0.1.5">
+<tool id="blast_reciprocal_best_hits" name="BLAST Reciprocal Best Hits (RBH)" version="0.1.7">
     <description>from two FASTA files</description>
     <requirements>
         <requirement type="package" version="1.64">biopython</requirement>
@@ -8,6 +8,11 @@
         <requirement type="binary">blastn</requirement>
         <requirement type="package" version="2.2.30">blast+</requirement>
     </requirements>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
     <version_command interpreter="python">
 blast_rbh.py --version
     </version_command>
@@ -24,11 +29,6 @@
 -c $q_cover
 -o "$output"
     </command>
-    <stdio>
-        <!-- Anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
     <inputs>
         <!-- Galaxy does not have sub-types for protein vs nucletide FASTA -->
         <param name="fasta_a" type="data" format="fasta"
@@ -45,6 +45,7 @@
             <when value="prot">
                 <param name="prot_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 - Uses longer words as described by Shiryev et al (2007)</option>
                     <option value="blastp-short">blastp-short - BLASTP optimized for queries shorter than 30 residues</option>
                 </param>
             </when>
@@ -71,8 +72,6 @@
     <outputs>
         <data name="output" format="tabular" label="BLAST RBH: $fasta_a.name vs $fasta_b.name" />
     </outputs>
-    <requirements>
-    </requirements>
     <tests>
         <test>
             <param name="fasta_a" value="four_human_proteins.fasta" ftype="fasta"/>
@@ -163,7 +162,7 @@
             <param name="fasta_a" value="k12_edited_proteins.fasta" ftype="fasta"/>
             <param name="fasta_b" value="k12_edited_proteins.fasta" ftype="fasta"/>
             <param name="dbtype" value="prot"/>
-            <param name="nucl_type" value="blastp"/>
+            <param name="nucl_type" value="blastp-fast"/>
             <param name="identity" value="80.0"/>
             <param name="q_cover" value="80.0"/>
             <output name="output" file="rbh_blastp_k12_self.tabular" ftype="tabular"/>
@@ -235,11 +234,16 @@
 
 **References**
 
-A specific paper covering this tool is planned, but please also cite:
+Please cite:
+
+P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo (2015).
+NCBI BLAST+ integrated into Galaxy.
+*GigaScience* 4:39
+http://dx.doi.org/10.1186/s13742-015-0080-7
 
 Christiam Camacho et al. (2009).
 BLAST+: architecture and applications.
-BMC Bioinformatics. 15;10:421.
+*BMC Bioinformatics* 15;10:421.
 http://dx.doi.org/10.1186/1471-2105-10-421
 
 This wrapper is available to install into other Galaxy Instances via the Galaxy
@@ -247,6 +251,6 @@
     </help>
     <citations>
         <citation type="doi">10.1186/1471-2105-10-421</citation>
-        <!-- TODO: Add BibTeX entry / preprint DOI for Galaxy BLAST+ paper -->
+        <citation type="doi">10.1186/s13742-015-0080-7</citation>
     </citations>
 </tool>