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Changeset 14:2fe07f50a41e (2014-12-01)

Previous changeset 13:623f727cdff1 (2014-03-14) Next changeset 15:c16c30e9ad5b (2015-07-05)

Commit message:
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.

added:
test-data/cd00003.smp
test-data/cd00003_and_cd00008.aux
test-data/cd00003_and_cd00008.freq
test-data/cd00003_and_cd00008.loo
test-data/cd00003_and_cd00008.phr
test-data/cd00003_and_cd00008.pin
test-data/cd00003_and_cd00008.psd
test-data/cd00003_and_cd00008.psi
test-data/cd00003_and_cd00008.psq
test-data/cd00003_and_cd00008.rps
test-data/cd00008.smp
test-data/empty_file.dat
tools/ncbi_blast_plus/ncbi_makeprofiledb.xml

diff -r 623f727cdff1 -r 2fe07f50a41e test-data/cd00003.smp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cd00003.smp Mon Dec 01 05:59:16 2014 -0500

b'@@ -0,0 +1,19957 @@\n+PssmWithParameters ::= {\n+ pssm {\n+ isProtein TRUE,\n+ numRows 28,\n+ numColumns 234,\n+ byRow FALSE,\n+ query seq {\n+ id {\n+ general {\n+ db "CDD",\n+ tag id 237977\n+ }\n+ },\n+ descr {\n+ title "cd00003, PNPsynthase, Pyridoxine 5\'-phosphate (PNP) synthase\n+ domain; pyridoxal 5\'-phosphate is the active form of vitamin B6 that acts as\n+ an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria,\n+ formation of pyridoxine 5\'-phosphate is a step in the biosynthesis of vitamin\n+ B6. PNP synthase, a homooctameric enzyme, catalyzes the final step in PNP\n+ biosynthesis, the condensation of 1-amino-acetone 3-phosphate and\n+ 1-deoxy-D-xylulose 5-phosphate. PNP synthase adopts a TIM barrel topology,\n+ intersubunit contacts are mediated by three \'\'extra\'\' helices, generating a\n+ tetramer of symmetric dimers with shared active sites; the open state has\n+ been proposed to accept substrates and to release products, while most of the\n+ catalytic events are likely to occur in the closed state; a hydrophilic\n+ channel running through the center of the barrel was identified as the\n+ essential structural feature that enables PNP synthase to release water\n+ molecules produced during the reaction from the closed, solvent-shielded\n+ active site."\n+ },\n+ inst {\n+ repr raw,\n+ mol aa,\n+ length 234,\n+ seq-data ncbieaa "RLGVNIDHVATLRNARGTNYPDPVEAALLAEKAGADGITVHLREDRRHIQDR\n+DVRLLRELVRTELNLEMAPTEEMLEIALEVKPHQVTLVPEKREELTTEGGLDVAGQAEKLKPIIERLKDAGIRVSLFI\n+DPDPEQIEAAKEVGADRVELHTGPYANAYDKAEREAELERIAKAAKLARELGLGVNAGHGLNYENVKPIAKIPGIAEL\n+NIGHAIISRALFVGLEEAVREMKDLI"\n+ }\n+ },\n+ intermediateData {\n+ weightedResFreqsPerPos {\n+ { 0, 10, 0 },\n+ { 575880368388257, 10, -16 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 663632240275508, 10, -16 },\n+ { 18974024208621, 10, -15 },\n+ { 435260939968393, 10, -16 },\n+ { 0, 10, 0 },\n+ { 231579235547631, 10, -16 },\n+ { 217943087911858, 10, -16 },\n+ { 197347688751049, 10, -15 },\n+ { 149575209809135, 10, -15 },\n+ { 0, 10, 0 },\n+ { 373639929584932, 10, -16 },\n+ { 0, 10, 0 },\n+ { 454596950735964, 10, -16 },\n+ { 280508357667036, 10, -15 },\n+ { 0, 10, 0 },\n+ { 276040598748792, 10, -16 },\n+ { 187780737233597, 10, -16 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 119593107246649, 10, -16 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 355209907721631, 10, -16 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 925910073190528, 10, -15 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 385689360373084, 10, -16 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 526473206870828, 10, -16 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 499042712921408, 10, -15 },\n+ { 160105971725447, 10, -16 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 217340080528288, 10, -16 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 38877105237495, 10, -14 },\n+ { 0, 10, 0 },\n+ { 217943087911858, 10, -16 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ '..b'-414,\n+ -399,\n+ -460,\n+ 5,\n+ 352,\n+ 16,\n+ -587,\n+ -100,\n+ -494,\n+ -32768,\n+ -32768,\n+ -400,\n+ -32768,\n+ -32768,\n+ -32768,\n+ -195,\n+ -32768,\n+ -409,\n+ -650,\n+ -589,\n+ -382,\n+ -651,\n+ -647,\n+ 402,\n+ -562,\n+ -63,\n+ -221,\n+ -629,\n+ -572,\n+ -558,\n+ -589,\n+ -496,\n+ -335,\n+ 665,\n+ -607,\n+ -100,\n+ -446,\n+ -32768,\n+ -32768,\n+ -400,\n+ -32768,\n+ -32768,\n+ -32768,\n+ -24,\n+ -32768,\n+ -591,\n+ -46,\n+ -272,\n+ -576,\n+ -277,\n+ -37,\n+ -291,\n+ 283,\n+ -138,\n+ -402,\n+ -350,\n+ -488,\n+ 369,\n+ 578,\n+ -203,\n+ -174,\n+ -491,\n+ -587,\n+ -100,\n+ -483,\n+ -32768,\n+ -32768,\n+ -400,\n+ -32768,\n+ -32768,\n+ -32768,\n+ 7,\n+ -32768,\n+ -616,\n+ 241,\n+ 528,\n+ -606,\n+ -496,\n+ -367,\n+ -230,\n+ 196,\n+ -343,\n+ -105,\n+ -331,\n+ -454,\n+ 43,\n+ 272,\n+ -194,\n+ -392,\n+ -502,\n+ -619,\n+ -100,\n+ -523,\n+ -32768,\n+ -32768,\n+ -400,\n+ -32768,\n+ -32768,\n+ -32768,\n+ -446,\n+ -32768,\n+ -500,\n+ -647,\n+ -538,\n+ 178,\n+ -619,\n+ -325,\n+ -106,\n+ -485,\n+ -175,\n+ 921,\n+ -550,\n+ -602,\n+ -404,\n+ -481,\n+ -486,\n+ -420,\n+ -288,\n+ -277,\n+ -100,\n+ 627,\n+ -32768,\n+ -32768,\n+ -400,\n+ -32768,\n+ -32768,\n+ -32768,\n+ -165,\n+ -32768,\n+ -534,\n+ -503,\n+ -358,\n+ -453,\n+ -555,\n+ -452,\n+ -144,\n+ 482,\n+ 287,\n+ -280,\n+ -440,\n+ -508,\n+ -91,\n+ 361,\n+ -409,\n+ -396,\n+ 122,\n+ -575,\n+ -100,\n+ -472,\n+ -32768,\n+ -32768,\n+ -400,\n+ -32768,\n+ -32768,\n+ -32768,\n+ 149,\n+ -32768,\n+ -567,\n+ 385,\n+ 307,\n+ -606,\n+ -460,\n+ -383,\n+ -292,\n+ 51,\n+ -396,\n+ -460,\n+ -145,\n+ -458,\n+ 207,\n+ 304,\n+ -90,\n+ -107,\n+ -277,\n+ -625,\n+ -100,\n+ -526,\n+ -32768,\n+ -32768,\n+ -400,\n+ -32768,\n+ -32768,\n+ -32768,\n+ 176,\n+ -32768,\n+ 31,\n+ -605,\n+ -520,\n+ -357,\n+ -572,\n+ -562,\n+ 483,\n+ -473,\n+ 369,\n+ -197,\n+ -576,\n+ -553,\n+ -44,\n+ -69,\n+ -433,\n+ -185,\n+ 8,\n+ -549,\n+ -100,\n+ -456,\n+ -32768,\n+ -32768,\n+ -400,\n+ -32768,\n+ -32768,\n+ -32768,\n+ -154,\n+ -32768,\n+ 387,\n+ -646,\n+ -594,\n+ -334,\n+ -636,\n+ -593,\n+ 485,\n+ -545,\n+ 343,\n+ 529,\n+ -604,\n+ -586,\n+ -513,\n+ -556,\n+ -479,\n+ -56,\n+ 41,\n+ -533,\n+ -100,\n+ -450,\n+ -32768,\n+ -32768,\n+ -400,\n+ -32768,\n+ -32768\n+ },\n+ lambda { 267, 10, -3 },\n+ kappa { 695502437462053, 10, -16 },\n+ h { 14, 10, -2 },\n+ scalingFactor 100,\n+ lambdaUngapped { 315181590957692, 10, -15 },\n+ kappaUngapped { 22723615854819, 10, -14 },\n+ hUngapped { 852942415611443, 10, -15 }\n+ }\n+ },\n+ params {\n+ pseudocount 10,\n+ rpsdbparams {\n+ matrixName "BLOSUM62"\n+ }\n+ }\n+}\n'

diff -r 623f727cdff1 -r 2fe07f50a41e test-data/cd00003_and_cd00008.aux
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cd00003_and_cd00008.aux Mon Dec 01 05:59:16 2014 -0500

@@ -0,0 +1,12 @@
+BLOSUM62
+11
+1
+0.000000e+00
+0.000000e+00
+0
+0
+100.000000
+234
+6.955024e-02
+160
+4.862535e-02

diff -r 623f727cdff1 -r 2fe07f50a41e test-data/cd00003_and_cd00008.freq

Binary file test-data/cd00003_and_cd00008.freq has changed

diff -r 623f727cdff1 -r 2fe07f50a41e test-data/cd00003_and_cd00008.loo

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diff -r 623f727cdff1 -r 2fe07f50a41e test-data/cd00003_and_cd00008.phr

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diff -r 623f727cdff1 -r 2fe07f50a41e test-data/cd00003_and_cd00008.pin

Binary file test-data/cd00003_and_cd00008.pin has changed

diff -r 623f727cdff1 -r 2fe07f50a41e test-data/cd00003_and_cd00008.psd
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cd00003_and_cd00008.psd Mon Dec 01 05:59:16 2014 -0500

@@ -0,0 +1,2 @@
+gnl|cdd|1890191
+gnl|cdd|2379770

diff -r 623f727cdff1 -r 2fe07f50a41e test-data/cd00003_and_cd00008.psi

Binary file test-data/cd00003_and_cd00008.psi has changed

diff -r 623f727cdff1 -r 2fe07f50a41e test-data/cd00003_and_cd00008.psq

Binary file test-data/cd00003_and_cd00008.psq has changed

diff -r 623f727cdff1 -r 2fe07f50a41e test-data/cd00003_and_cd00008.rps

Binary file test-data/cd00003_and_cd00008.rps has changed

diff -r 623f727cdff1 -r 2fe07f50a41e test-data/cd00008.smp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cd00008.smp Mon Dec 01 05:59:16 2014 -0500

b'@@ -0,0 +1,13679 @@\n+PssmWithParameters ::= {\n+ pssm {\n+ isProtein TRUE,\n+ numRows 28,\n+ numColumns 160,\n+ byRow FALSE,\n+ query seq {\n+ id {\n+ general {\n+ db "CDD",\n+ tag id 189019\n+ }\n+ },\n+ descr {\n+ title "cd00008, PIN_53EXO-like, PIN domains of the 5\'-3\' exonucleases\n+ of DNA polymerase I, bacteriophage T4 RNase H and T5-5\' nucleases, and\n+ homologs. PIN (PilT N terminus) domains of the 5\'-3\' exonucleases (53EXO) of\n+ mutli-domain DNA polymerase I and single domain protein homologs, as well as,\n+ the PIN domains of bacteriophage T5-5\'nuclease (T5FEN or 5\'-3\'exonuclease),\n+ bacteriophage T4 RNase H (T4FEN), bacteriophage T3 (T3 phage\n+ exodeoxyribonuclease) and other similar nucleases are included in this\n+ family. The 53EXO of DNA polymerase I recognizes and endonucleolytically\n+ cleaves a structure-specific DNA substrate that has a bifurcated downstream\n+ duplex and an upstream template-primer duplex that overlaps the downstream\n+ duplex by 1 bp. The T5-5\'nuclease is a 5\'-3\'exodeoxyribonuclease that also\n+ exhibits endonucleolytic activity on flap structures (branched duplex DNA\n+ containing a free single-stranded 5\'end). T4 RNase H, which removes the RNA\n+ primers that initiate lagging strand fragments, has 5\'- 3\'exonuclease\n+ activity on DNA/DNA and RNA/DNA duplexes and has endonuclease activity on\n+ flap or forked DNA structures. These nucleases are members of the\n+ structure-specific, 5\' nuclease family that catalyzes hydrolysis of DNA\n+ duplex-containing nucleic acid structures during DNA replication, repair, and\n+ recombination. They contain a PIN domain with a helical arch/clamp region (I\n+ domain) of variable length (approximately 16 to 30 residues in 53EXO-like PIN\n+ domains) and a H3TH (helix-3-turn-helix) domain, an atypical\n+ helix-hairpin-helix-2-like region. Both the H3TH domain (not included here)\n+ and the helical arch/clamp region are involved in DNA binding. The active\n+ site of the 53EXO of Taq DNA polymerase I includes a set of conserved acidic\n+ residues that are essential for binding three divalent metal ions (two Mn2+\n+ ions and one Zn2+ ion) required for nuclease activity. T5-5\'nuclease requires\n+ at least two bound divalent metal ions for nuclease activity and is reported\n+ to be able to use Mg2+, Mn2+ or Co2+ as co-factors."\n+ },\n+ inst {\n+ repr raw,\n+ mol aa,\n+ length 160,\n+ seq-data ncbieaa "LMLVDGTNLAFRTKHNNSKKKEKINLSPFASSYVSSIQSLAKSYSARTTIVL\n+GDKGKSVFRLEHLPEYKGNRDEKYAEEKALDEQFFEYLKDAFELCKATTFPTFTIRGYEADDMAAYLVKKIGHEGDHV\n+WIISTDGDWDQLLTDKVSRFSPTTRREYHL"\n+ }\n+ },\n+ intermediateData {\n+ weightedResFreqsPerPos {\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 338020833333333, 10, -15 },\n+ { 0, 10, 0 },\n+ { 328645833333333, 10, -15 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 333333333333333, 10, -15 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 338020833333333, 10, -15 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 333333333333333, 10, -15 },\n+ { 328645833333333, 10, -15 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0, 10, 0 },\n+ { 0'..b' -307,\n+ 704,\n+ -250,\n+ -309,\n+ -192,\n+ -207,\n+ -249,\n+ -197,\n+ -100,\n+ -12,\n+ -32768,\n+ -32768,\n+ -399,\n+ -32768,\n+ -32768,\n+ -32768,\n+ -64,\n+ -32768,\n+ -122,\n+ -145,\n+ -113,\n+ -102,\n+ -157,\n+ -140,\n+ -20,\n+ -97,\n+ 17,\n+ 497,\n+ -93,\n+ -116,\n+ -65,\n+ -112,\n+ -12,\n+ 327,\n+ -19,\n+ -149,\n+ -100,\n+ -121,\n+ -32768,\n+ -32768,\n+ -399,\n+ -32768,\n+ -32768,\n+ -32768,\n+ -142,\n+ -32768,\n+ -302,\n+ -51,\n+ 332,\n+ -282,\n+ -264,\n+ 602,\n+ -290,\n+ -70,\n+ -294,\n+ -205,\n+ -45,\n+ -211,\n+ 22,\n+ -107,\n+ -28,\n+ 303,\n+ -228,\n+ -332,\n+ -100,\n+ -69,\n+ -32768,\n+ -32768,\n+ -399,\n+ -32768,\n+ -32768,\n+ -32768,\n+ -121,\n+ -32768,\n+ -379,\n+ -186,\n+ -84,\n+ -383,\n+ 340,\n+ -157,\n+ -394,\n+ 351,\n+ -349,\n+ -246,\n+ -95,\n+ -242,\n+ -9,\n+ 403,\n+ -102,\n+ -177,\n+ -341,\n+ -352,\n+ -100,\n+ -289,\n+ -32768,\n+ -32768,\n+ -399,\n+ -32768,\n+ -32768,\n+ -32768,\n+ -196,\n+ -32768,\n+ -375,\n+ -234,\n+ -82,\n+ -9,\n+ -299,\n+ -9,\n+ -301,\n+ 349,\n+ -256,\n+ -192,\n+ -143,\n+ -264,\n+ -2,\n+ 405,\n+ -146,\n+ -178,\n+ -268,\n+ -72,\n+ -100,\n+ 490,\n+ -32768,\n+ -32768,\n+ -399,\n+ -32768,\n+ -32768,\n+ -32768,\n+ -226,\n+ -32768,\n+ -301,\n+ -157,\n+ 297,\n+ -71,\n+ -349,\n+ -222,\n+ -123,\n+ -172,\n+ 207,\n+ -46,\n+ -277,\n+ -314,\n+ -71,\n+ -214,\n+ -226,\n+ -213,\n+ -167,\n+ 856,\n+ -100,\n+ -25,\n+ -32768,\n+ -32768,\n+ -399,\n+ -32768,\n+ -32768,\n+ -32768,\n+ -167,\n+ -32768,\n+ -210,\n+ -396,\n+ -331,\n+ 65,\n+ -415,\n+ -122,\n+ 350,\n+ -300,\n+ 9,\n+ -12,\n+ -350,\n+ -347,\n+ -284,\n+ -313,\n+ -261,\n+ -135,\n+ 320,\n+ -71,\n+ -100,\n+ 490,\n+ -32768,\n+ -32768,\n+ -399,\n+ -32768,\n+ -32768,\n+ -32768,\n+ -136,\n+ -32768,\n+ -287,\n+ -161,\n+ -56,\n+ -281,\n+ -243,\n+ 591,\n+ -274,\n+ 318,\n+ -281,\n+ -184,\n+ -43,\n+ -206,\n+ -7,\n+ 7,\n+ -29,\n+ 308,\n+ -222,\n+ -337,\n+ -100,\n+ -69,\n+ -32768,\n+ -32768,\n+ -399,\n+ -32768,\n+ -32768,\n+ -32768,\n+ -187,\n+ -32768,\n+ -240,\n+ -339,\n+ -301,\n+ -129,\n+ -391,\n+ -351,\n+ 323,\n+ -269,\n+ 251,\n+ 24,\n+ -362,\n+ 495,\n+ -275,\n+ -318,\n+ -249,\n+ -165,\n+ 48,\n+ -331,\n+ -100,\n+ -238,\n+ -32768,\n+ -32768,\n+ -399,\n+ -32768,\n+ -32768\n+ },\n+ lambda { 267, 10, -3 },\n+ kappa { 486253485452101, 10, -16 },\n+ h { 14, 10, -2 },\n+ scalingFactor 100,\n+ lambdaUngapped { 318588052238909, 10, -15 },\n+ kappaUngapped { 158869858915243, 10, -15 },\n+ hUngapped { 43477934178065, 10, -14 }\n+ }\n+ },\n+ params {\n+ pseudocount 10,\n+ rpsdbparams {\n+ matrixName "BLOSUM62"\n+ }\n+ }\n+}\n'

diff -r 623f727cdff1 -r 2fe07f50a41e tools/ncbi_blast_plus/README.rst
--- a/tools/ncbi_blast_plus/README.rst Fri Mar 14 07:40:46 2014 -0400
+++ b/tools/ncbi_blast_plus/README.rst Mon Dec 01 05:59:16 2014 -0500

b'@@ -1,10 +1,13 @@\n Galaxy wrappers for NCBI BLAST+ suite\n =====================================\n \n-These wrappers are copyright 2010-2013 by Peter Cock (The James Hutton Institute,\n-UK) and additional contributors. All rights reserved. See the licence text below.\n+These wrappers are copyright 2010-2014 by Peter Cock (The James Hutton Institute,\n+UK) and additional contributors including Edward Kirton, John Chilton,\n+Nicola Soranzo, Jim Johnson, and Bjoern Gruening.\n \n-Currently tested with NCBI BLAST 2.2.28+ (i.e. version 2.2.28 of BLAST+),\n+See the licence text below.\n+\n+Currently tested with NCBI BLAST 2.2.29+ (i.e. version 2.2.29 of BLAST+),\n and does not work with the NCBI \'legacy\' BLAST suite (e.g. ``blastall``).\n \n Note that these wrappers (and the associated datatypes) were originally\n@@ -21,9 +24,9 @@\n ======================\n \n Galaxy should be able to automatically install the dependencies, i.e. the\n-``blast_datatypes`` repository which defines the BLAST XML file format\n-(``blastxml``) and protein and nucleotide BLAST databases (``blastdbp`` and\n-``blastdbn``).\n+BLAST+ binaries and the ``blast_datatypes`` repository which defines the\n+BLAST XML file format (``blastxml``), protein and nucleotide BLAST databases\n+(``blastdbp`` and ``blastdbn``), and so on.\n \n See the configuration notes below.\n \n@@ -47,12 +50,12 @@\n <tool file="ncbi_blast_plus/ncbi_blastdbcmd_info.xml" />\n <tool file="ncbi_blast_plus/ncbi_rpsblast_wrapper.xml" />\n <tool file="ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml" />\n+ <tool file="ncbi_blast_plus/ncbi_makeprofiledb.xml" />\n <tool file="ncbi_blast_plus/blastxml_to_tabular.xml" />\n </section>\n \n You will also need to install ``blast_datatypes`` from the Tool Shed. This\n-defines the BLAST XML file format (``blastxml``) and protein and nucleotide\n-BLAST databases composite file formats (``blastdbp`` and ``blastdbn``):\n+defines the BLAST XML file format (``blastxml``), BLAST databases, etc:\n \n * http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes\n \n@@ -61,7 +64,7 @@\n files.\n \n You must install the NCBI BLAST+ standalone tools somewhere on the system\n-path. Currently the unit tests are written using "BLAST 2.2.28+".\n+path. Currently the unit tests are written using BLAST 2.2.29+.\n \n Run the functional tests (adjusting the section identifier to match your\n ``tool_conf.xml.sample`` file)::\n@@ -72,10 +75,10 @@\n =============\n \n You must tell Galaxy about any system level BLAST databases using configuration\n-files blastdb.loc (nucleotide databases like NT) and blastdb_p.loc (protein\n-databases like NR), and blastdb_d.loc (protein domain databases like CDD or\n-SMART) which are located in the tool-data/ folder. Sample files are included\n-which explain the tab-based format to use.\n+files ``blastdb.loc`` (nucleotide databases like NT) and ``blastdb_p.loc``\n+(protein databases like NR), and ``blastdb_d.loc`` (protein domain databases\n+like CDD or SMART) which are located in the ``tool-data/`` folder. Sample\n+files are included which explain the tab-based format to use.\n \n You can download the NCBI provided databases as tar-balls from here:\n \n@@ -91,9 +94,9 @@\n will appear as ``N/A`` in the tabular output.\n \n The BLAST+ binaries support multi-threaded operation, which is handled via the\n-$GALAXY_SLOTS environment variable. This should be set automatically by Galaxy\n-via your job runner settings, which allows you to (for example) allocate four\n-cores to each BLAST job.\n+``$GALAXY_SLOTS`` environment variable. This should be set automatically by\n+Galaxy via your job runner settings, which allows you to (for example) allocate\n+four cores to each BLAST job.\n \n In addition, the BLAST+ wrappers also support high level parallelism by task\n splitting if ``use_tasked_jobs = True`` is enabled in your ``universe_wsgi.ini``\n@@ -111,25 +114,25 @@\n v0.0.11 - Final revision as part of the Galaxy main repository, and the\n first release via the Tool Shed\n v0.0.12 - Implements genetic code op'..b"y option to BLASTN.\n - Fallback on ElementTree if cElementTree missing in XML to tabular.\n - Link to Tool Shed added to help text and this documentation.\n- - Tweak dependency on blast_datatypes to also work on Test Tool Shed.\n- - Dependency on new package_blast_plus_2_2_26 in Tool Shed.\n+ - Tweak dependency on ``blast_datatypes`` to also work on Test Tool Shed.\n+ - Dependency on new ``package_blast_plus_2_2_26`` in Tool Shed.\n - Adopted standard MIT License.\n - Development moved to GitHub, https://github.com/peterjc/galaxy_blast\n - Updated citation information (Cock et al. 2013).\n-v0.0.21 - Use macros to simplify the XML wrappers.\n+v0.0.21 - Use macros to simplify the XML wrappers (by John Chilton).\n - Added wrapper for dustmasker.\n- - Enabled masking for makeblastdb.\n- - Requires 'maskinfo-asn1' and 'maskinfo-asn1-binary' datatypes.\n- defined in updated blast_datatypes on Galaxy ToolShed.\n+ - Enabled masking for makeblastdb (Nicola Soranzo).\n+ - Requires ``maskinfo-asn1`` and ``maskinfo-asn1-binary`` datatypes,\n+ defined in ``blast_datatypes`` v0.0.17 on Galaxy ToolShed.\n - Tests updated for BLAST+ 2.2.27 instead of BLAST+ 2.2.26.\n- - Now depends on package_blast_plus_2_2_27 in ToolShed.\n-v0.0.22 - More use macros to simplify the wrappers.\n- - Set number of threads via $GALAXY_SLOTS environment variable.\n+ - Now depends on ``package_blast_plus_2_2_27`` in ToolShed.\n+v0.0.22 - More use of macros to simplify the wrappers.\n+ - Set number of threads via ``$GALAXY_SLOTS`` environment variable.\n - More descriptive default output names.\n- - Tests require updated BLAST DB definitions (blast_datatypes v0.0.18).\n+ - Tests require updated BLAST DB definitions (``blast_datatypes`` v0.0.18).\n - Pre-check for duplicate identifiers in makeblastdb wrapper.\n - Tests updated for BLAST+ 2.2.28 instead of BLAST+ 2.2.27.\n- - Now depends on package_blast_plus_2_2_28 in ToolShed.\n+ - Now depends on ``package_blast_plus_2_2_28`` in ToolShed.\n - Extended tabular output includes 'salltitles' as column 25.\n-v0.1.00 - Now depends on package_blast_plus_2_2_29 in ToolShed.\n- - Tabular output now includes option to pick specific columns,\n- including previously unavailable taxonomy columns.\n- - BLAST XML to tabular tool supports multiple input files.\n+v0.1.00 - Now depends on ``package_blast_plus_2_2_29`` in ToolShed.\n+ - Tabular output now includes option to pick specific columns\n+ (based on contribution from Jim Johnson), including previously\n+ unavailable taxonomy columns.\n+ - BLAST XML to tabular tool supports multiple input files\n+ (based on contribution from Jim Johnson).\n - More detailed descriptions for BLASTN and BLASTP task option.\n- - Wrappers for segmasker, dustmasker and convert2blastmask.\n+ - Wrappers for segmasker, dustmasker and convert2blastmask\n+ (contribution from Bjoern Gruening).\n - Supports using maskinfo with makeblastdb wrapper.\n - Supports setting a taxonomy ID in makeblastdb wrapper.\n - Subtle changes like new conditional settings will require some old\n- workflows be updated to cope. \n+ workflows be updated to cope.\n+v0.1.01 - Requires ``blastdbd`` datatype (``blast_datatypes`` v0.0.19).\n+ - Wrapper for makeprofiledb added to create protein domain databases\n+ (based on contribution from Bjoern Gruening).\n+ - The RPS-BLAST and RPS-TBLASTN wrappers support using a protein\n+ domain database from the user's history.\n+ - Tool definitions now embed citation information (by John Chilton).\n+ - BLAST tools support GI and SeqID filters (added by Bjoern Gruening).\n ======= ======================================================================\n \n \n"

diff -r 623f727cdff1 -r 2fe07f50a41e tools/ncbi_blast_plus/blastxml_to_tabular.py
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.py Fri Mar 14 07:40:46 2014 -0400
+++ b/tools/ncbi_blast_plus/blastxml_to_tabular.py Mon Dec 01 05:59:16 2014 -0500

[

@@ -66,7 +66,7 @@
from optparse import OptionParser

if "-v" in sys.argv or "--version" in sys.argv:
-    print "v0.1.00"
+    print "v0.1.01"
     sys.exit(0)

if sys.version_info[:2] >= ( 2, 5 ):
@@ -85,7 +85,20 @@

if len(sys.argv) == 4 and sys.argv[3] in ["std", "x22", "ext"]:
     #False positive if user really has a BLAST XML file called 'std' or 'ext'...
-    stop_err("ERROR: The script API has changed, sorry.")
+    stop_err("""ERROR: The script API has changed, sorry.
+
+Instead of the old style:
+
+$ python blastxml_to_tabular.py input.xml output.tabular std
+
+Please use:
+
+$ python blastxml_to_tabular.py -o output.tabular -c std input.xml
+
+For more information, use:
+
+$ python blastxml_to_tabular.py -h
+""")

usage = """usage: %prog [options] blastxml[,...]

diff -r 623f727cdff1 -r 2fe07f50a41e tools/ncbi_blast_plus/blastxml_to_tabular.xml
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml Fri Mar 14 07:40:46 2014 -0400
+++ b/tools/ncbi_blast_plus/blastxml_to_tabular.xml Mon Dec 01 05:59:16 2014 -0500

@@ -1,4 +1,4 @@
-<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.1.00">
+<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.1.01">
     <description>Convert BLAST XML output to tabular</description>
     <version_command interpreter="python">blastxml_to_tabular.py --version</version_command>
     <command interpreter="python">
@@ -209,4 +209,7 @@
This wrapper is available to install into other Galaxy Instances via the Galaxy
Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus
     </help>
+    <citations>
+      <citation type="doi">10.7717/peerj.167</citation>
+    </citations>
</tool>

diff -r 623f727cdff1 -r 2fe07f50a41e tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml
--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Fri Mar 14 07:40:46 2014 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Mon Dec 01 05:59:16 2014 -0500

@@ -1,4 +1,4 @@
-<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.1.00">
+<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.1.01">
     <description>Show BLAST database information from blastdbcmd</description>
     <macros>
         <token name="@BINARY@">blastdbcmd</token>
@@ -32,4 +32,5 @@

@REFERENCES@
     </help>
+    <expand macro="blast_citations" />
</tool>

diff -r 623f727cdff1 -r 2fe07f50a41e tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Fri Mar 14 07:40:46 2014 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Mon Dec 01 05:59:16 2014 -0500

@@ -1,4 +1,4 @@
-<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="0.1.00">
+<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="0.1.01">
     <description>Extract sequence(s) from BLAST database</description>
     <macros>
         <token name="@BINARY@">blastdbcmd</token>
@@ -104,4 +104,5 @@

@REFERENCES@
     </help>
+    <expand macro="blast_citations" />
</tool>

diff -r 623f727cdff1 -r 2fe07f50a41e tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Fri Mar 14 07:40:46 2014 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Mon Dec 01 05:59:16 2014 -0500

@@ -1,4 +1,4 @@
-<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.1.00">
+<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.1.01">
     <description>Search nucleotide database with nucleotide query sequence(s)</description>
     
     <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1"></parallelism>
@@ -24,6 +24,7 @@
-perc_identity $adv_opts.identity_cutoff
#end if
$adv_opts.ungapped
+@ADV_ID_LIST_FILTER@
## End of advanced options:
#end if
     </command>
@@ -62,6 +63,7 @@
             </param>
             <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" />
             <expand macro="input_parse_deflines" />
+            <expand macro="advanced_optional_id_files" />
         </expand>
     </inputs>
     <outputs>
@@ -128,4 +130,5 @@

@REFERENCES@
     </help>
+    <expand macro="blast_citations" />
</tool>

diff -r 623f727cdff1 -r 2fe07f50a41e tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Fri Mar 14 07:40:46 2014 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Mon Dec 01 05:59:16 2014 -0500

@@ -1,4 +1,4 @@
-<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.1.00">
+<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.1.01">
     <description>Search protein database with protein query sequence(s)</description>
     
     <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1" />
@@ -22,6 +22,7 @@
@ADVANCED_OPTIONS@
##Ungapped disabled for now - see comments below
##$adv_opts.ungapped
+@ADV_ID_LIST_FILTER@
## End of advanced options:
#end if
     </command>
@@ -52,6 +53,7 @@
             <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" />
             -->
             <expand macro="input_parse_deflines" />
+            <expand macro="advanced_optional_id_files" />
         </expand>
     </inputs>
     <outputs>
@@ -144,4 +146,5 @@

@REFERENCES@
     </help>
+    <expand macro="blast_citations" />
</tool>

diff -r 623f727cdff1 -r 2fe07f50a41e tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Fri Mar 14 07:40:46 2014 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Mon Dec 01 05:59:16 2014 -0500

@@ -1,4 +1,4 @@
-<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.1.00">
+<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.1.01">
     <description>Search protein database with translated nucleotide query sequence(s)</description>
     
     <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1"></parallelism>
@@ -22,6 +22,7 @@
-matrix $adv_opts.matrix
@ADVANCED_OPTIONS@
$adv_opts.ungapped
+@ADV_ID_LIST_FILTER@
## End of advanced options:
#end if
     </command>
@@ -45,6 +46,7 @@
             <expand macro="input_word_size" />
             <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" />
             <expand macro="input_parse_deflines" />
+            <expand macro="advanced_optional_id_files" />
         </expand>
     </inputs>
     <outputs>
@@ -123,4 +125,5 @@

@REFERENCES@
     </help>
+    <expand macro="blast_citations" />
</tool>

diff -r 623f727cdff1 -r 2fe07f50a41e tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml Fri Mar 14 07:40:46 2014 -0400
+++ b/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml Mon Dec 01 05:59:16 2014 -0500

@@ -1,4 +1,4 @@
-<tool id="ncbi_convert2blastmask_wrapper" name="NCBI BLAST+ convert2blastmask" version="0.1.00">
+<tool id="ncbi_convert2blastmask_wrapper" name="NCBI BLAST+ convert2blastmask" version="0.1.01">
     <description>Convert masking information in lower-case masked FASTA input to file formats suitable for makeblastdb</description>
     <macros>
         <token name="@BINARY@">convert2blastmask</token>
@@ -84,4 +84,5 @@

@REFERENCES@
     </help>
+    <expand macro="blast_citations" />
</tool>

diff -r 623f727cdff1 -r 2fe07f50a41e tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml Fri Mar 14 07:40:46 2014 -0400
+++ b/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml Mon Dec 01 05:59:16 2014 -0500

@@ -1,4 +1,4 @@
-<tool id="ncbi_dustmasker_wrapper" name="NCBI BLAST+ dustmasker" version="0.1.00">
+<tool id="ncbi_dustmasker_wrapper" name="NCBI BLAST+ dustmasker" version="0.1.01">
     
     <description>masks low complexity regions</description>
     <macros>
@@ -96,4 +96,5 @@

@REFERENCES@
     </help>
+    <expand macro="blast_citations" />
</tool>

diff -r 623f727cdff1 -r 2fe07f50a41e tools/ncbi_blast_plus/ncbi_macros.xml
--- a/tools/ncbi_blast_plus/ncbi_macros.xml Fri Mar 14 07:40:46 2014 -0400
+++ b/tools/ncbi_blast_plus/ncbi_macros.xml Mon Dec 01 05:59:16 2014 -0500

@@ -113,8 +113,9 @@
         <stdio>
             
             <exit_code range="1:" />
+            
             <exit_code range=":-1" />
-            
+            
             <regex match="Error:" />
             <regex match="Exception:" />
         </stdio>
@@ -228,10 +229,8 @@
     <xml name="input_conditional_pssm">
         <conditional name="db_opts">
             <param name="db_opts_selector" type="select" label="Protein domain database (PSSM)">
-              <option value="db" selected="True">Locally installed BLAST database</option>
-              
             </param>
             <when value="db">
                 <param name="database" type="select" label="Protein domain database">
@@ -244,13 +243,11 @@
                 <param name="histdb" type="hidden" value="" />
                 <param name="subject" type="hidden" value="" />
             </when>
-            
         </conditional>
     </xml>
     <xml name="input_conditional_choose_db_type">
@@ -325,8 +322,42 @@
             <when value="advanced">
                 <yield />
             </when>
-        </conditional>
+        </conditional>
     </xml>
+    <xml name="advanced_optional_id_files">
+        <conditional name="adv_optional_id_files_opts">
+            <param name="adv_optional_id_files_opts_selector" type="select"
+                   label="Restrict search of database to a given set of ID's"
+    help="This feature provides a means to exclude ID's from a BLAST database search. The expectation values in the BLAST results are based upon the sequences actually searched, and not on the underlying database. Note this cannot be used when comparing against a FASTA file.">
+                <option value="none" selected="True">No restriction, search the entire database</option>
+                <option value="gilist">GI identifers</option>
+                <option value="negative_gilist">Negative GI identifers</option>
+                <option value="seqidlist">Sequence identifers (SeqId's)</option>
+            </param>
+            <when value="none" />
+            <when value="gilist">
+                <param name="gilist" type="data" format="txt" label="Restrict search of database to GI's listed in this file"
+                       help="This option is only available for database searches."/>
+            </when>
+            <when value="negative_gilist">
+                <param name="negative_gilist" type="data" format="txt" label="Restrict search of database to everything except the GI's listed in this file"
+                       help="This option is only available for database searches."/>
+            </when>
+            <when value="seqidlist">
+                <param name="seqidlist" type="data" format="txt" label=" Restrict search of database to list of SeqId's"
+                       help="This option is only available for database searches."/>
+            </when>
+        </conditional>
+    </xml>
+    <token name="@ADV_ID_LIST_FILTER@">
+#if $adv_opts.adv_optional_id_files_opts.adv_optional_id_files_opts_selector == 'negative_gilist':
+    -negative_gilist $adv_opts.adv_optional_id_files_opts.negative_gilist
+#elif $adv_opts.adv_optional_id_files_opts.adv_optional_id_files_opts_selector == 'gilist':
+    -gilist $adv_opts.adv_optional_id_files_opts.gilist
+#elif $adv_opts.adv_optional_id_files_opts.adv_optional_id_files_opts_selector == 'seqidlist':
+    -seqidlist $adv_opts.adv_optional_id_files_opts.seqidlist
+#end if
+    </token>
     <token name="@THREADS@">-num_threads "\${GALAXY_SLOTS:-8}"</token>
     <token name="@BLAST_DB_SUBJECT@">
#if $db_opts.db_opts_selector == "db":
@@ -383,6 +414,13 @@
This wrapper is available to install into other Galaxy Instances via the Galaxy
Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus
     </token>
+    <xml name="blast_citations">
+        <citations>
+            <citation type="doi">10.1186/1471-2105-10-421</citation>
+            <citation type="doi">10.7717/peerj.167</citation>
+            
+        </citations>
+    </xml>
     <token name="@OUTPUT_FORMAT@">**Output format**

Because Galaxy focuses on processing tabular data, the default output of this

diff -r 623f727cdff1 -r 2fe07f50a41e tools/ncbi_blast_plus/ncbi_makeblastdb.xml
--- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Fri Mar 14 07:40:46 2014 -0400
+++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Mon Dec 01 05:59:16 2014 -0500

@@ -1,4 +1,4 @@
-<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.1.00">
+<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.1.01">
     <description>Make BLAST database</description>
     <macros>
         <token name="@BINARY@">makeblastdb</token>
@@ -180,4 +180,5 @@

@REFERENCES@
     </help>
+    <expand macro="blast_citations" />
</tool>

diff -r 623f727cdff1 -r 2fe07f50a41e tools/ncbi_blast_plus/ncbi_makeprofiledb.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml Mon Dec 01 05:59:16 2014 -0500

@@ -0,0 +1,128 @@
+<tool id="ncbi_makeprofiledb" name="NCBI BLAST+ makeprofiledb" version="0.1.01">
+    <description>Make profile database</description>
+    <macros>
+        <token name="@BINARY@">makeprofiledb</token>
+        <import>ncbi_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command>
+##Unlike makeblastdb, makeprofiledb needs directory to exist already:
+mkdir -p $outfile.extra_files_path &&
+makeprofiledb -out "${os.path.join($outfile.extra_files_path,'blastdb')}"
+
+##We turn $infile_list into $infiles with a configfile entry defined below
+-in $infiles
+
+#if $title:
+-title "$title"
+#else:
+##Would default to being based on the cryptic Galaxy filenames, which is unhelpful
+-title "Profile Database"
+#end if
+
+-threshold $threshold
+
+#if str($contain_pssm_scores.contain_pssm_scores_type) == 'no':
+    -gapopen $contain_pssm_scores.gapopen
+    -gapextend $contain_pssm_scores.gapextend
+    -scale $contain_pssm_scores.scale
+    -matrix $contain_pssm_scores.matrix
+#end if
+
+-obsr_threshold $obsr_threshold
+-exclude_invalid $exclude_invalid
+
+-logfile "$outfile"
+    </command>
+    <expand macro="stdio" />
+    <inputs>
+        <param name="input_file" type="data" multiple="true" optional="false" format="pssm-asn1"
+        label="Input PSSM files(s)"
+        help="One or NCBI PSSM ASN.1 format scoremat files (often named *.smp)" />
+        <param name="infile_list" type="data" multiple="true" format="pssm-asn1" />
+
+        <param name="title" type="text" value="" label="Title for the profile database" help="This is the database name shown in BLAST search output" />
+        <param name="threshold" type="float" size="5" value="9.82" label="Minimum word score to add a word to the lookup table" />
+
+        
+        
+
+        <conditional name="contain_pssm_scores">
+            <param name="contain_pssm_scores_type" type="select" label="Does your input file contain PSSM scores?">
+              <option value="yes" selected="True">Yes</option>
+              <option value="no">No</option>
+            </param>
+            <when value="yes" />
+            <when value="no">
+                <param name="gapopen" type="integer" size="5" value="" label="Cost to open a gap" />
+                <param name="gapextend" type="integer" size="5" value="" label="Cost to extend a gap" />
+                <param name="scale" type="float" size="5" value="" label="PSSM scale factor" />
+                <expand macro="input_scoring_matrix" />
+            </when>
+        </conditional>
+
+        
+        <param name="exclude_invalid" type="boolean" truevalue="true" falsevalue="false" checked="true"
+            label="Exclude invalid domains?"
+            help="Exclude domains that do not pass validation test" />
+        <param name="obsr_threshold" type="float" size="5" value="6.0"
+            label="Observation threshold"
+            help="Exclude domains with with maximum number of independent observations below this threshold" />
+    </inputs>
+    <configfiles>
+        <configfile name="infiles">
+#for $infile in $input_file
+${infile}
+#end for
+        </configfile>
+    </configfiles>
+    <outputs>
+        <data name="outfile" format="blastdbd" label="RPS database from ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" value="cd00003.smp,cd00008.smp" ftype="pssm-asn1" />
+            <param name="title" value="Just 2 PSSM matrices" />
+            <param name="contain_pssm_scores_type" value="yes" />
+            <output name="out_file" file="empty_file.dat" ftype="blastdbd" >
+                <extra_files type="file" value="cd00003_and_cd00008.phr" name="blastdb.phr" />
+                <extra_files type="file" value="cd00003_and_cd00008.pin" name="blastdb.pin" lines_diff="2" />
+                <extra_files type="file" value="cd00003_and_cd00008.psq" name="blastdb.psq" />
+                <extra_files type="file" value="cd00003_and_cd00008.freq" name="blastdb.freq" />
+                <extra_files type="file" value="cd00003_and_cd00008.loo" name="blastdb.loo" />
+                <extra_files type="file" value="cd00003_and_cd00008.psd" name="blastdb.psd" />
+                <extra_files type="file" value="cd00003_and_cd00008.psi" name="blastdb.psi" />
+                <extra_files type="file" value="cd00003_and_cd00008.rps" name="blastdb.rps" />
+                <extra_files type="file" value="cd00003_and_cd00008.aux" name="blastdb.aux" />
+            </output>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Make a protein domain profile database (for use with RPS-BLAST or RSP-TBLASTN)
+from one or more Position Specific Scoring Matrices (PSSM) files in the NCBI
+"scoremat" ASN.1 format (usually named ``*.smp``).
+
+This is a wrapper for the NCBI BLAST+ tool 'makeprofiledb'.
+
+More information about makeprofiledb can be found in the `BLAST Command Line Applications User Manual`_.
+
+.. _BLAST Command Line Applications User Manual: http://www.ncbi.nlm.nih.gov/books/NBK1763/
+
+
+**References**
+
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following papers:
+
+@REFERENCES@
+    </help>
+    <expand macro="blast_citations" />
+</tool>

diff -r 623f727cdff1 -r 2fe07f50a41e tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Fri Mar 14 07:40:46 2014 -0400
+++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Mon Dec 01 05:59:16 2014 -0500

@@ -1,4 +1,4 @@
-<tool id="ncbi_rpsblast_wrapper" name="NCBI BLAST+ rpsblast" version="0.1.00">
+<tool id="ncbi_rpsblast_wrapper" name="NCBI BLAST+ rpsblast" version="0.1.01">
     <description>Search protein domain database (PSSMs) with protein query sequence(s)</description>
     
     <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1" />
@@ -104,4 +104,5 @@

@REFERENCES@
     </help>
+    <expand macro="blast_citations" />
</tool>

diff -r 623f727cdff1 -r 2fe07f50a41e tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Fri Mar 14 07:40:46 2014 -0400
+++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Mon Dec 01 05:59:16 2014 -0500

@@ -1,4 +1,4 @@
-<tool id="ncbi_rpstblastn_wrapper" name="NCBI BLAST+ rpstblastn" version="0.1.00">
+<tool id="ncbi_rpstblastn_wrapper" name="NCBI BLAST+ rpstblastn" version="0.1.01">
     <description>Search protein domain database (PSSMs) with translated nucleotide query sequence(s)</description>
     
     <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1"></parallelism>
@@ -102,4 +102,5 @@

@REFERENCES@
     </help>
+    <expand macro="blast_citations" />
</tool>

diff -r 623f727cdff1 -r 2fe07f50a41e tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml Fri Mar 14 07:40:46 2014 -0400
+++ b/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml Mon Dec 01 05:59:16 2014 -0500

@@ -1,4 +1,4 @@
-<tool id="ncbi_segmasker_wrapper" name="NCBI BLAST+ segmasker" version="0.1.00">
+<tool id="ncbi_segmasker_wrapper" name="NCBI BLAST+ segmasker" version="0.1.01">
     <description>low-complexity regions in protein sequences</description>
     <macros>
         <token name="@BINARY@">segmasker</token>
@@ -98,4 +98,5 @@

@REFERENCES@
     </help>
+    <expand macro="blast_citations" />
</tool>

diff -r 623f727cdff1 -r 2fe07f50a41e tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Fri Mar 14 07:40:46 2014 -0400
+++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Mon Dec 01 05:59:16 2014 -0500

@@ -1,4 +1,4 @@
-<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.1.00">
+<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.1.01">
     <description>Search translated nucleotide database with protein query sequence(s)</description>
     
     <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1"></parallelism>
@@ -22,6 +22,7 @@
@ADVANCED_OPTIONS@
##Ungapped disabled for now - see comments below
##$adv_opts.ungapped
+@ADV_ID_LIST_FILTER@
## End of advanced options:
#end if
     </command>
@@ -49,6 +50,7 @@
             <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" />
             -->
             <expand macro="input_parse_deflines" />
+            <expand macro="advanced_optional_id_files" />
         </expand>
     </inputs>
     <outputs>
@@ -158,4 +160,5 @@

@REFERENCES@
     </help>
+    <expand macro="blast_citations" />
</tool>

diff -r 623f727cdff1 -r 2fe07f50a41e tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Fri Mar 14 07:40:46 2014 -0400
+++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Mon Dec 01 05:59:16 2014 -0500

@@ -1,4 +1,4 @@
-<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.1.00">
+<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.1.01">
     <description>Search translated nucleotide database with translated nucleotide query sequence(s)</description>
     
     <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1"></parallelism>
@@ -24,6 +24,7 @@
## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
## Note -max_target_seqs overrides -num_descriptions and -num_alignments
@ADVANCED_OPTIONS@
+@ADV_ID_LIST_FILTER@
## End of advanced options:
#end if
     </command>
@@ -49,6 +50,7 @@
             
             <expand macro="input_word_size" />
             <expand macro="input_parse_deflines" />
+            <expand macro="advanced_optional_id_files" />
         </expand>
     </inputs>
     <outputs>
@@ -74,7 +76,7 @@

**What it does**

-Search a *translated nucleotide database* using a *protein query*,
+Search a *translated nucleotide database* using a *translated nucleotide query*,
using the NCBI BLAST+ tblastx command line tool.

@FASTA_WARNING@
@@ -92,4 +94,5 @@

@REFERENCES@
     </help>
+    <expand macro="blast_citations" />
</tool>

diff -r 623f727cdff1 -r 2fe07f50a41e tools/ncbi_blast_plus/repository_dependencies.xml
--- a/tools/ncbi_blast_plus/repository_dependencies.xml Fri Mar 14 07:40:46 2014 -0400
+++ b/tools/ncbi_blast_plus/repository_dependencies.xml Mon Dec 01 05:59:16 2014 -0500

@@ -1,4 +1,4 @@
<?xml version="1.0"?>
<repositories description="This requires the BLAST datatype definitions (e.g. the BLAST XML format).">
- <repository changeset_revision="de11e1a921c4" name="blast_datatypes" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+ <repository changeset_revision="2bda64d39931" name="blast_datatypes" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
</repositories>

diff -r 623f727cdff1 -r 2fe07f50a41e tools/ncbi_blast_plus/tool_dependencies.xml
--- a/tools/ncbi_blast_plus/tool_dependencies.xml Fri Mar 14 07:40:46 2014 -0400
+++ b/tools/ncbi_blast_plus/tool_dependencies.xml Mon Dec 01 05:59:16 2014 -0500

@@ -1,6 +1,6 @@
<?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" />
+        <repository changeset_revision="a2ec897aac2c" name="package_blast_plus_2_2_29" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
</tool_dependency>