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changeset 0:c4d9ea0ddd42 draft

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"planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
author guerler
date Mon, 27 Jul 2020 04:37:03 -0400
parents
children a6b54ca2bded
files hhblits.xml test-data/6VYB_A.fasta test-data/6VYB_A.hhr test-data/dbCAN-fam-V8/dbCAN-fam-V8_cs219.ffdata test-data/dbCAN-fam-V8/dbCAN-fam-V8_cs219.ffindex test-data/dbCAN-fam-V8/dbCAN-fam-V8_hhm.ffdata test-data/dbCAN-fam-V8/dbCAN-fam-V8_hhm.ffindex
diffstat 7 files changed, 1519 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hhblits.xml	Mon Jul 27 04:37:03 2020 -0400
@@ -0,0 +1,61 @@
+<tool id="hhblits" name="HH-blits itererative protein sequence searching" version="0.1.0" python_template_version="3.5">
+    <requirements>
+        <requirement type="package" version="3.2.0">hhsuite</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        link $hhm_ffdata hhdb_hhm.ffdata &&
+        link $hhm_ffindex hhdb_hhm.ffindex &&
+        link $cs219_ffdata hhdb_cs219.ffdata &&
+        link $cs219_ffindex hhdb_cs219.ffindex &&
+        hhblits -n $n -e $e -i $input -d hhdb -o $output
+    ]]></command>
+    <inputs>
+        <param format="data" name="input" type="data" label="Query Sequence" help="Single sequence or multiple sequence alignment (MSA)
+                in a3m, a2m, or FASTA format, or HMM in hhm format (-i)"/>
+        <param format="data" name="hhm_ffindex" type="data" label="HHM Index file" help="Database file ending with 'hhm.ffindex'"/>
+        <param format="data" name="hhm_ffdata" type="data" label="HHM Data file" help="Database file ending with 'hhm.ffdata'"/>
+        <param format="data" name="cs219_ffindex" type="data" label="cs219 Index file" help="Database file ending with 'cs219.ffindex'"/>
+        <param format="data" name="cs219_ffdata" type="data" label="cs219 Data file" help="Database file ending with 'cs219.ffdata'"/>
+        <param name="n" type="integer" label="Number of Iterations (-n)" value="2" min="1" max="8"/>
+        <param name="e" type="float" label="E-value cutoff for inclusion in result alignment (-e)" value="0.001" min="0" max="1"/>
+    </inputs>
+    <outputs>
+        <data format="fasta" name="output" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="6VYB_A.fasta"/>
+            <param name="hhm_ffindex" value="dbCAN-fam-V8/dbCAN-fam-V8_hhm.ffindex"/>
+            <param name="hhm_ffdata" value="dbCAN-fam-V8/dbCAN-fam-V8_hhm.ffdata"/>
+            <param name="cs219_ffindex" value="dbCAN-fam-V8/dbCAN-fam-V8_cs219.ffindex"/>
+            <param name="cs219_ffdata" value="dbCAN-fam-V8/dbCAN-fam-V8_cs219.ffdata"/>
+            <output name="output" file="6VYB_A.hhr" lines_diff="4"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+HMM-HMM-based lightning-fast iterative sequence search
+HHblits is a sensitive, general-purpose, iterative sequence search tool that represents
+both query and database sequences by HMMs. You can search HHblits databases starting
+with a single query sequence, a multiple sequence alignment (MSA), or an HMM. HHblits
+prints out a ranked list of database HMMs/MSAs and can also generate an MSA by merging
+the significant database HMMs/MSAs onto the query MSA.
+
+Steinegger M, Meier M, Mirdita M, Vöhringer H, Haunsberger S J, and Söding J (2019)
+HH-suite3 for fast remote homology detection and deep protein annotation.
+bioRxiv, 560029. doi:10.1101/560029
+(c) The HH-suite development team
+
+Download databases from <http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/>.
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@misc{githubhh-suite,
+  author = {Soeding, Johannes},
+  year = {2005},
+  title = {Protein homology detection by HMM-HMM comparison},
+  publisher = {Oxford University Press},
+  journal = {Bioinformatics},
+  url = {https://doi.org/10.1093/bioinformatics/bti125},
+}</citation>
+    </citations>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/6VYB_A.fasta	Mon Jul 27 04:37:03 2020 -0400
@@ -0,0 +1,20 @@
+>6VYB_A
+AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHPVLPFNDG
+VYFASTEKSNIIRGWIFGTTLDSKSLLIVNNATNVVIKVCEFQFCNDPFLG
+VCTFEYVSFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVD
+LPIGINITRFQTLLAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSET
+KCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASV
+YAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFV
+IRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDNYNYLYRLFR
+KSNLKPFERDISTFPLQSYGFQPTNVGYQPYRVVVLSFELLHAPATVCGPK
+KSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDP
+QTLEILDITPCSFGGVSVITPGTNTSNEVAVLYQDVNCTEVNVFQTRAGCL
+IGAEHVNNSYECDIPIGAGICASYQTQSIIAYTMSLGAENSVAYSNNSIAI
+PTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNR
+ALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKSKRSF
+IEDLLFNKVTFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQ
+IPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALG
+KLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLI
+TGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYH
+LMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNG
+THWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDS
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/6VYB_A.hhr	Mon Jul 27 04:37:03 2020 -0400
@@ -0,0 +1,156 @@
+Query         6VYB_A
+Match_columns 966
+No_of_seqs    1 out of 1
+Neff          1
+Searched_HMMs 100
+Date          Sun Jul 26 21:21:46 2020
+Command       hhblits -i test-data/query.fasta -o query.hhr -d test-data/dbCAN-fam-V8/dbCAN-fam-V8 
+
+ No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
+  1 ABN54336.1|CE12|183-378|9.5e-5  17.2     1.1  0.0014   32.1   0.0   13  586-598     1-13  (210)
+  2 ANU56961.1|PL12_2.hmm|1.8e-61|   3.4     9.9   0.013   24.9   0.0   32  900-931    38-69  (131)
+  3 CAX58257.1|CE11|4-276|4.9e-122   2.1      18   0.023   25.0   0.0   38  857-894     6-54  (277)
+  4 APK54672.1|GT103                 2.1      18   0.023   24.9   0.0  168  629-825     1-184 (232)
+  5 AAD04130.1|GT13|24-440|6.3e-18   1.7      23    0.03   25.6   0.0   47  302-349   156-203 (390)
+  6 ACR10769.1|PL1|79-276|1.4e-54    1.3      33   0.041   21.6   0.0   53   59-111    59-115 (196)
+  7 AAR43340.1|GT19|17-374|6.8e-14   1.3      33   0.041   23.4   0.0   14  254-267   116-129 (357)
+  8 BAD47100.1|GH125|74-473|3.2e-1   1.3      32   0.041   24.6   0.0   41   98-138   291-338 (402)
+  9 ACY95489.1|CBM14|33-88|9.4e-16   1.1      38   0.047   18.2   0.0   36  238-277    39-74  (81)
+ 10 AAK92730.1|PL1_1.hmm|3.6e-111|   0.9      49   0.063   21.4   0.0   50  277-326    18-67  (199)
+
+No 1
+>ABN54336.1|CE12|183-378|9.5e-54
+Probab=17.23  E-value=1.1  Score=32.05  Aligned_cols=13  Identities=38%  Similarity=0.705  Sum_probs=11.0  Template_Neff=5.400
+
+Q 6VYB_A          586 TMYICGDSTECSN  598 (966)
+Q Consensus       586 tmyicgdstecsn  598 (966)
+                      |+|||||||-|..
+T Consensus         1 tI~l~GDSTva~~   13 (210)
+T ABN54336.1|CE1    1 TIFLAGDSTVANY   13 (210)
+Confidence            6899999998853
+
+
+No 2
+>ANU56961.1|PL12_2.hmm|1.8e-61|404-534
+Probab=3.41  E-value=9.9  Score=24.92  Aligned_cols=32  Identities=25%  Similarity=0.544  Sum_probs=26.7  Template_Neff=2.600
+
+Q 6VYB_A          900 ICHDGKAHFPREGVFVSNGTHWFVTQRNFYEP  931 (966)
+Q Consensus       900 ichdgkahfpregvfvsngthwfvtqrnfyep  931 (966)
+                      .-++|+-.||..|.||-.|..--..+|+.|..
+T Consensus        38 Lw~~GRnf~PDaG~yvY~Gd~~~~~~R~wfR~   69 (131)
+T ANU56961.1|PL1   38 LWVKGRNFFPDAGSYVYAGDSEINKLRNWFRQ   69 (131)
+Confidence            56899999999999999998866777777753
+
+
+No 3
+>CAX58257.1|CE11|4-276|4.9e-122
+Probab=2.10  E-value=18  Score=25.00  Aligned_cols=38  Identities=32%  Similarity=0.532  Sum_probs=26.5  Template_Neff=4.700
+
+Q 6VYB_A          857 KRVDFCGKGYHL------MSFPQSAPHGVVFLHVT-----YVPAQEKNF  894 (966)
+Q Consensus       857 krvdfcgkgyhl------msfpqsaphgvvflhvt-----yvpaqeknf  894 (966)
+                      +.|.+.|.|.|-      --.|..+.+|++|..+-     .+||.-.+.
+T Consensus         6 ~~v~~~GiGLHsG~~v~l~l~PA~~~tGIvF~R~dl~~~~~IpA~~~~V   54 (277)
+T CAX58257.1|CE1    6 RSVSLTGVGLHSGKKVTLTLRPAPANTGIVFRRTDLDGPPEIPADADNV   54 (277)
+Confidence            456778888773      44688888999998875     555554443
+
+
+No 4
+>APK54672.1|GT103
+Probab=2.06  E-value=18  Score=24.88  Aligned_cols=168  Identities=24%  Similarity=0.353  Sum_probs=95.1  Template_Neff=2.800
+
+Q 6VYB_A          629 FAQVKQIYKTPPIKDFGGFNFSQILPDPSKSKRSFIEDLLFNKVTFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFG  708 (966)
+Q Consensus       629 faqvkqiyktppikdfggfnfsqilpdpskskrsfiedllfnkvtfngltvlpplltdemiaqytsallagtitsgwtfg  708 (966)
+                      |.|-|.|+.-+.+.+-..--+.--||..-..++.|-.+.-.+---|.||--                      ..||.  
+T Consensus         1 ~~~~~~~~s~~~~~~~d~~~i~LsLPET~~RR~~f~~~~~~G~q~FdGlR~----------------------~~GWI--   56 (232)
+T APK54672.1|GT1    1 FSQYKSIFSQCEISPQDVDFICLSLPETIERRRDFEQDNPYGIQLFDGLRH----------------------RPGWI--   56 (232)
+Confidence            456667776666666555445555777666666666555544444555432                      34663  
+
+
+Q 6VYB_A          709 AGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTAS------AL-------GKLQDVVNQNA  775 (966)
+Q Consensus       709 agaalqipfamqmayrfngigvtqnvlyenqklianqfnsaigkiqdslsstas------al-------gklqdvvnqna  775 (966)
+                       |+++..-+..+-|-   --+..+-.+-|..-+....|.+.+..+++-|...-+      .|       -|+..|-....
+T Consensus        57 -GCglSyk~l~r~al---~~~~~~lti~EDDV~fp~df~~~~~~v~~yL~~~~~~WDvFsGliAdlH~dtkIl~ve~~~g  132 (232)
+T APK54672.1|GT1   57 -GCGLSYKFLARKAL---ENGIPQLTICEDDVLFPPDFESKYSQVKDYLDTRRNDWDVFSGLIADLHPDTKILKVERFDG  132 (232)
+Confidence             33333333222222   234455567788888888888888888887753221      11       23444444444
+
+
+Q 6VYB_A          776 QALNTLVKQLSSNFGAISSVLNDILSRLDPPEAE---VQIDRLITGRLQSLQT  825 (966)
+Q Consensus       776 qalntlvkqlssnfgaissvlndilsrldppeae---vqidrlitgrlqslqt  825 (966)
+                      ...-++=|-.|--|..-+.-.-++|+..||....   ..|||.+.. .+.|..
+T Consensus       133 ~~yv~iDkMtSmV~NIYs~~al~~L~~Wd~~~~d~~TNTIDRylE~-~~~LrV  184 (232)
+T APK54672.1|GT1  133 IEYVTIDKMTSMVFNIYSESALEKLAQWDEKNHDAETNTIDRYLEN-QEGLRV  184 (232)
+Confidence            4555555555555555555555788888876544   468998753 334433
+
+
+No 5
+>AAD04130.1|GT13|24-440|6.3e-183
+Probab=1.69  E-value=23  Score=25.58  Aligned_cols=47  Identities=28%  Similarity=0.384  Sum_probs=24.8  Template_Neff=3.500
+
+Q 6VYB_A          302 ADSFVIRGDEVRQIAPGQTGKIADYNYKLP-DDFTGCVIAWNSNNLDNY  349 (966)
+Q Consensus       302 adsfvirgdevrqiapgqtgkiadynyklp-ddftgcviawnsnnldny  349 (966)
+                      +++++|-.|. -.|||.--.-...--+-|. |+---||-|||.|.....
+T Consensus       156 ~~~VII~EdD-m~iapDFf~yf~~~~~lL~~D~sl~cvSaWNDNG~~~~  203 (390)
+T AAD04130.1|GT1  156 FSRVIIVEDD-LEIAPDFFSYFSATYPLLDRDPSLWCVSAWNDNGKEQF  203 (390)
+Confidence            3344444433 3566653322222222233 444579999999987654
+
+
+No 6
+>ACR10769.1|PL1|79-276|1.4e-54
+Probab=1.28  E-value=33  Score=21.64  Aligned_cols=53  Identities=25%  Similarity=0.395  Sum_probs=33.8  Template_Neff=5.700
+
+Q 6VYB_A           59 KSN-IIRGWIFGTTLD--SKSLLIVNNATNVVIKVCEFQFCNDPFLGVCTF-EYVSF  111 (966)
+Q Consensus        59 ksn-iirgwifgttld--sksllivnnatnvvikvcefqfcndpflgvctf-eyvsf  111 (966)
+                      .+| |||-.-|-...+  ...-+-++++.+|.|--|+|.-..|-.+.+..- .||.+
+T Consensus        59 ~~NVIIRnl~~~~~~~~~~~Dai~i~~s~nVWIDHcsfs~~~Dg~ldv~~~s~~VTi  115 (196)
+T ACR10769.1|PL1   59 ASNVIIRNLRIRDGNDGFDGDAISIDGSSNVWIDHCSFSWGGDGLIDIKKGSDNVTI  115 (196)
+Confidence            344 566666655553  223333578899999999999998887755432 34443
+
+
+No 7
+>AAR43340.1|GT19|17-374|6.8e-144
+Probab=1.27  E-value=33  Score=23.45  Aligned_cols=14  Identities=36%  Similarity=0.700  Sum_probs=11.3  Template_Neff=5.700
+
+Q 6VYB_A          254 SVYAWNRKRISNCV  267 (966)
+Q Consensus       254 svyawnrkrisncv  267 (966)
+                      +|+||..+|+..-.
+T Consensus       116 qvWAWr~~R~k~i~  129 (357)
+T AAR43340.1|GT1  116 QVWAWRPGRIKKIK  129 (357)
+Confidence            79999999987643
+
+
+No 8
+>BAD47100.1|GH125|74-473|3.2e-189
+Probab=1.27  E-value=32  Score=24.58  Aligned_cols=41  Identities=32%  Similarity=0.588  Sum_probs=32.3  Template_Neff=3.500
+
+Q 6VYB_A           98 DPFLGVCTFEYVSFKNLREFVFKNIDGYF-------KIYSKHTPINLV  138 (966)
+Q Consensus        98 dpflgvctfeyvsfknlrefvfknidgyf-------kiyskhtpinlv  138 (966)
+                      -|+||-|.-+---+.|-|+|+...-.-||       -|=|.|++.+-+
+T Consensus       291 lPylG~~~~~DpiYqnTR~~iLS~~NPYy~~G~~~~GIGsPHtg~~~i  338 (402)
+T BAD47100.1|GH1  291 LPYLGYCSKDDPIYQNTRRFILSKENPYFYEGKAAEGIGSPHTGPRYI  338 (402)
+Confidence            48899999888889999999988766665       266778876655
+
+
+No 9
+>ACY95489.1|CBM14|33-88|9.4e-16
+Probab=1.13  E-value=38  Score=18.15  Aligned_cols=36  Identities=31%  Similarity=0.470  Sum_probs=23.4  Template_Neff=6.300
+
+Q 6VYB_A          238 TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSA  277 (966)
+Q Consensus       238 tnlcpfgevfnatrfasvyawnrkrisncvadysvlynsa  277 (966)
+                      ...||.|.+|+...-.=++.++-+   .|--| |+-|||.
+T Consensus        39 ~~~Cp~g~~FD~~~~~C~~~~~v~---~C~~~-~~~~~~~   74 (81)
+T ACY95489.1|CBM   39 EFSCPPGLVFDPETQTCDWPENVD---DCSNC-SIRYNSG   74 (81)
+Confidence            458999999998876666644431   24433 5666664
+
+
+No 10
+>AAK92730.1|PL1_1.hmm|3.6e-111|138-336
+Probab=0.87  E-value=49  Score=21.39  Aligned_cols=50  Identities=28%  Similarity=0.484  Sum_probs=43.2  Template_Neff=2.500
+
+Q 6VYB_A          277 ASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADY  326 (966)
+Q Consensus       277 asfstfkcygvsptklndlcftnvyadsfvirgdevrqiapgqtgkiady  326 (966)
+                      .|+.|..--|++-.--+.-|+|--|+....|.|=.+..+.|+..|-|.|-
+T Consensus        18 ~S~KTIDGRGa~V~I~~g~citiq~v~nVIIHgi~IH~c~p~~~g~ir~s   67 (199)
+T AAK92730.1|PL1   18 NSFKTIDGRGANVHIANGACITIQYVSNVIIHGIHIHDCKPGGNGMVRDS   67 (199)
+Confidence            46777777888888888899999999999999999999999998888764
+
+
Binary file test-data/dbCAN-fam-V8/dbCAN-fam-V8_cs219.ffdata has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dbCAN-fam-V8/dbCAN-fam-V8_cs219.ffindex	Mon Jul 27 04:37:03 2020 -0400
@@ -0,0 +1,641 @@
+AA1	130000	614
+AA10	98449	182
+AA11	89861	198
+AA12	161477	401
+AA13	205723	233
+AA14	84523	269
+AA15	202053	196
+AA16	2537	168
+AA1_1	72683	316
+AA1_2	163839	340
+AA1_3	13117	316
+AA2	50468	260
+AA3	175231	645
+AA3_1	132900	776
+AA3_2	109017	591
+AA3_3	152711	592
+AA3_4	117354	551
+AA4	29900	535
+AA5	101197	751
+AA5_1	127310	826
+AA5_2	56821	607
+AA6	51847	197
+AA7	83849	457
+AA8	137667	816
+AA9	65399	217
+CBM1	143663	30
+CBM10	587	29
+CBM11	31337	166
+CBM12	7963	35
+CBM13	202249	200
+CBM14	6549	82
+CBM15	187832	146
+CBM16	181198	132
+CBM17	173997	204
+CBM18	77912	41
+CBM19	126554	45
+CBM2	53796	105
+CBM20	139439	91
+CBM21	7998	107
+CBM22	179903	157
+CBM23	134513	161
+CBM24	106005	77
+CBM25	60676	79
+CBM26	70634	78
+CBM27	163083	167
+CBM28	77953	209
+CBM29	154838	145
+CBM3	142429	87
+CBM30	62778	92
+CBM31	116063	93
+CBM32	616	120
+CBM34	16724	117
+CBM35	0	117
+CBM36	81639	125
+CBM37	156062	63
+CBM38	49755	133
+CBM39	78942	95
+CBM4	24839	132
+CBM40	71507	177
+CBM41	128335	107
+CBM42	17609	137
+CBM43	116609	85
+CBM44	82069	65
+CBM45	35210	83
+CBM46	59324	90
+CBM47	8105	129
+CBM48	125686	98
+CBM49	193665	79
+CBM5	177402	44
+CBM50	178810	47
+CBM51	64368	135
+CBM52	189940	52
+CBM53	76078	89
+CBM54	168537	117
+CBM55	182270	47
+CBM56	80372	182
+CBM57	156125	143
+CBM58	176573	117
+CBM59	50728	146
+CBM6	169738	133
+CBM60	165499	111
+CBM61	1500	143
+CBM62	103830	132
+CBM63	203091	79
+CBM64	39709	84
+CBM65	20745	120
+CBM66	139530	158
+CBM67	62100	183
+CBM68	186041	95
+CBM69	52322	130
+CBM70	123217	165
+CBM71	147133	204
+CBM72	5128	130
+CBM73	100024	51
+CBM74	187978	309
+CBM75	49888	283
+CBM76	154983	160
+CBM77	148424	104
+CBM78	145774	133
+CBM79	126599	111
+CBM8	9993	144
+CBM80	69465	89
+CBM81	59414	98
+CBM82	106082	130
+CBM83	164179	110
+CBM84	78162	138
+CBM85	26881	167
+CBM9	13433	193
+CE1	116156	210
+CE10	172669	335
+CE11	52044	278
+CE12	97509	211
+CE13	36921	354
+CE14	106403	125
+CE15	62870	346
+CE16	79037	267
+CE2	97071	210
+CE3	92750	196
+CE4	4980	148
+CE5	57610	190
+CE6	161252	98
+CE7	183858	317
+CE8	171685	291
+CE9	77362	372
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Binary file test-data/dbCAN-fam-V8/dbCAN-fam-V8_hhm.ffdata has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dbCAN-fam-V8/dbCAN-fam-V8_hhm.ffindex	Mon Jul 27 04:37:03 2020 -0400
@@ -0,0 +1,641 @@
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