Sanntis (#121)

* Create sanntis.xml * Add BGC0001472.fna.prodigal.faa.gb * Add test files * Create .shed.yml * Update tools/marine_omics/sanntis.xml Co-authored-by: Björn Grüning <[email protected]> * fix typo * fix single quotes * Update tools/marine_omics/sanntis.xml Co-authored-by: Björn Grüning <[email protected]> * Update tools/marine_omics/sanntis.xml Co-authored-by: Björn Grüning <[email protected]> * Update .shed.yml --------- Co-authored-by: Björn Grüning <[email protected]>
galaxyecology · Jul 26, 2024 · 3b5d66e · 3b5d66e
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diff --git a/tools/marine_omics/.shed.yml b/tools/marine_omics/.shed.yml
@@ -0,0 +1,15 @@
+categories:
+    - Ecology
+owner: ecology
+remote_repository_url: https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics
+homepage_url: https://github.com/Finn-Lab/SanntiS
+long_description: |
+  The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data
+type: unrestricted
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: "Wrapper for Sanntis tool: {{ tool_name }}."
+suite:
+  name: "marine_omics_suite"
+  description: "A suite of tools for marine omics data"
+  type: unrestricted
diff --git a/tools/marine_omics/sanntis.xml b/tools/marine_omics/sanntis.xml
@@ -0,0 +1,53 @@
+<tool id="sanntis_marine" name="Sanntis biosynthetic gene clusters" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
+    <description>in genomic and metagenomic data</description>
+    <macros>
+        <token name="@TOOL_VERSION@">0.9.3.5</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <edam_topics>
+        <edam_topic>topic_3387</edam_topic>
+    </edam_topics>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">sanntis</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        sanntis --ip-file '$input_interpro' --outfile 'output_sanntis.gff' '$input_genbank'
+    ]]></command>
+    <inputs>
+        <param name="input_interpro" type="data" format="tabular" label="Input the TSV file from InterProScan" help="Before using this tool you need to retrieve the right data by using the InterProScan tool"/>
+        <param name="input_genbank" type="data" format="genbank" label="Input a Genbank .gb file" help="It needs to have the right structure and fit the protein fasta file used in InterProScan"/>
+    </inputs>
+    <outputs>
+        <data name="output_sanntis" from_work_dir="output_sanntis.gff" format="gff3" label="Sanntis output data"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_interpro" value="BGC0001472.fna.prodigal.faa.ip.tsv"/>
+            <param name="input_genbank" value="BGC0001472.fna.prodigal.faa.gb"/>
+            <output name="output_sanntis" value="Sanntis_output_data.gff3"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What it does**
+
+SMBGC Annotation using Neural Networks Trained on Interpro Signatures
+Tool for identifying biosynthetic gene clusters (BGCs) in genomic & metagenomic data
+
+.....
+
+
+**Input**
+- A tsv file coming from InterProScan tool from which you can retrieve the right data.
+- The right Genbank file with the right structure that fits the protein fasta file used to run InterProScan tool
+
+**Output**
+- A Gff3 file
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1101/2023.05.23.540769</citation>
+    </citations>
+</tool>
diff --git a/tools/marine_omics/test-data/BGC0001472.fna.prodigal.faa.gb b/tools/marine_omics/test-data/BGC0001472.fna.prodigal.faa.gb
@@ -0,0 +1,155 @@
+LOCUS       BGC0001472                32 bp    DNA              UNK 01-JAN-1980
+DEFINITION  BGC0001472.
+ACCESSION   BGC0001472
+VERSION     BGC0001472
+KEYWORDS    .
+SOURCE      .
+  ORGANISM  .
+            .
+FEATURES             Location/Qualifiers
+     CDS             312..683
+                     /translation="MPTIQQLVRKGRQDKVEKNKTPALEGSPQRRGVCTRVFTTTPKKP
+                     NSALRKVARVRLTSGIEVTAYIPGEGHNLQEHSIVLVRGGRVKDLPGVRYKIIRGSLDT
+                     QGVKNRKQARSRYGAKKEK"
+                     /protein_id="BGC0001472_1"
+     CDS             686..1156
+                     /translation="MPRKGPAPKRPVIIDPVYSSPLVTSLINKILLDGKRSTAERIVYG
+                     AMEGLREKTGADPVITLKRALENVKPSLEVKSRRVGGATYQVPIEVKPGRAATLALRWV
+                     VGYSRARREKTMTERLMNELLDASNGLGAAVKKREDTHKMAESNKAFAHYRW"
+                     /protein_id="BGC0001472_2"
+     CDS             1195..3324
+                     /translation="MATTSLDLAKVRNIGIMAHIDAGKTTTTERILFYTGVSYKIGEVH
+                     DGAATMDWMEQEQERGITITSAATTCHWPLNDVDHTINIIDTPGHVDFTVEVERSLRVL
+                     DGAVTVFDGVAGVEPQSETVWRQADRYGVPRICFVNKLDRTGADFLRCVDMIVQRLGAV
+                     PIVMQLPIGAEADFRGVVDLVSMKAFVYPEEAVKGEMYDTVEIPDNLKEAAEEWRGKLL
+                     EAVSENDDQMMELYLEGEEPTEEQLHEAIRRITLASKGSADSVTVTPVFCGTAFKNKGV
+                     QPLLDAVVRYLPSPLDVEAIEGHDVKDPEKVVQRKPSDDEPFSGLAFKIASDPHLGKLT
+                     FVRIYSGRLEAGTAVLNSVKGKKERIGKIYRMHANKREEIPSVGAGDIVAVMGLKQTTT
+                     GETLCDDKNPVILESMDFPAPVIQVAIEPKSKGDQEKLGVAIQRLSEEDPSFQVHSDEE
+                     TGQTIIGGMGELHLEVLVDRMKREFRVEANVGKPQVAYRETIRKAVERIDYTHKKQTGG
+                     TGQFAKVQIAIEPIEGGDASYEFVNKVTGGRIPREYIPSVDAGAQEAMQFGILAGYEMV
+                     GVRVTLLDGGYHEVDSSELAFKIAGSQAFKEGARKASPVLLEPMMAVEVTTPEDYMGEV
+                     VGDINSRRGQIQAMEERHGARVVKGLVPLSEMFGYVGDLRSKTSGRASYSMQFDSYAEV
+                     PRNVAEEIIAKAKGE"
+                     /protein_id="BGC0001472_3"
+     CDS             3472..4665
+                     /translation="MAKAKFERTKPHVNIGTIGHIDHGKTTLTAAITKVLHDAYPDLNE
+                     ASAFDQIDKAPEERQRGITISIAHVEYQTESRHYAHVDCPGHADYIKNMITGAAQMDGA
+                     ILVVAATDGPMPQTKEHVLLARQVGVPYIVVALNKADMVDDEEILELVELEVRELLSEY
+                     EFPGDDLPVVKVSALKALEGDAEWGQTVLDLMKAVDESIPQPERDVEKPFLMPIEDVFT
+                     ITGRGTVVTGRIERGVLKVNETVDIVGIKTEKTTTTVTGIEMFRKLLDEGQAGENVGLL
+                     LRGIKREDVERGQVIIKPGSVTPHTEFQAQAYILSKDEGGRHTPFFNNYRPQFYFRTTD
+                     VTGVVTLPEGTEMVMPGDNTLMDVALIQPVAMEEGLKFAIREGGRTVGAGQVTKITK"
+                     /protein_id="BGC0001472_4"
+     CDS             4869..5570
+                     /translation="MRNDVTSMTAVLEGFTSRTPTSDGLAAERRPVPFADSVPVEPQPS
+                     AEDLRPVHDLRGTLERRRSSLHYAPLPVRTDVILSLLRDVLRRDRDDWGLDASAGALEG
+                     FVFAFRSEGAEPGLYRVTAEETCYLAGLDEIGPAENLGVQREFSTGAGIVALYASLDRA
+                     DTWAGSHGYRISALRASMATYDLNLRCQALGLVGTLFGGFVPSSVHHLVHSDGATRHSL
+                     LATTYARPPES"
+                     /protein_id="BGC0001472_5"
+     CDS             5567..7195
+                     /translation="MVAEMKAEQIGRAARTDMQLTVPARPVLRRGVRLRRAGESVVLDG
+                     ADRAQVFSGAFAREGLVPLTEACDGTRDHTELALKTGFDEATVYKCLALLSTAGAVEEA
+                     MSGEEPDVTPEWAVFLSRLGNSTGSNPSWADAAARLVSRSVRLEGDAALVAGARRSLRE
+                     VCPVVTEPAGPPGPGDELTVFFETPASAPLLAATEERCRQDGRPLLRVRADARTITIGP
+                     YADLSITPCLDCGRHGEADLSGEPPEYLHDLVVGLASHHVTALLARATISHLPGDFTVI
+                     DTATLSTVYRPVAVRPGCPRCSYARGPVAPQAPAGAVYEASVAMPPRAFLAPKDHQAHY
+                     YASNLRLQSQFKDWPSRPHTPLPALDISVLAGSERHDPSHGDTPLTLSSLGLLLKVAFG
+                     VKEDETTPERVKRWTAASGNIGSTTAYAVVRDDRIMPPGVYAYAQGSHTLVTVSGEVPP
+                     GDSPCDIIITGDLKKVMTKYGTFGFRLVFLDAGCNLASLRELAQHLGLGFTPRSDWDDD
+                     ALARLLGTSPADEPVAAFASLGGTA"
+                     /protein_id="BGC0001472_6"
+     CDS             7210..7821
+                     /translation="MSHDPRPQCLYLVGDTFSRRLTEHRGVPPELQVSFEDFLNDTAPH
+                     ADVVVPVHAGGDPGLRDETDRICAERSTPSVGLQLLPTKVLCGPVVVPGRTACYACYRK
+                     RAAQHAGTARPYDMDAALSGLPEGFGRQHLSVASGLLDLALTEIATGVTGIGGTVRTFN
+                     LVSGAVSSAVTVSVNRCPRCGGRFSQARADSAMPVPELLR"
+                     /protein_id="BGC0001472_7"
+     CDS             7845..9191
+                     /translation="MHLNRPQEHISAELRGLEELVSPYGLVSRTAPLPVREGEPPFAVQ
+                     LAYLGVPSRALPNLRTWAHDEDTGNSDGAGTGLTPERAKLVSIAEALERYSTCAWDDDE
+                     MVVAAENDLTEEFVSPSRWPSCSPTELARDDCSLSAYDPSVPIRWVRAWSLTRRIPVLV
+                     PAISVYLHMPYQSKSEEFIRGITTGAAVHSDVRSAVLGGLLEVVERDAIALVWLQQLRL
+                     PELVVDPARLDAGVRELHRVGTSTDLRVRLFDATTDFGVPVIYAVQLSDADPALAQIVA
+                     ATCDVHPEQALGKIYRELASLRVALRGYLSAYAGREPDPAKVSVVGGAVHNATRDRRDV
+                     FGFLLDGERPAYGLEGMPGLPAGADPLDTVVARLAARGAEVLVTDITTDEARQVGMRAV
+                     KVLVPEAMPVSFVHGERYLGTPRLYDAPRAMGHTSHAEDAVNPVQQPFA"
+                     /protein_id="BGC0001472_8"
+     CDS             9238..10437
+                     /translation="MTQITLEPGFLLLISLSYGRLQDHVTARLAPAEISGVSFVHLFAT
+                     IPQPVGSKYNDTFAPLIRELFAPERVGGAGGHGPYYFVRTQDAQLGTDTLQISIEGVSD
+                     EDSTRADLHRTAERYGCAAQVDATPLDSVPSPLWNAGFTGTGFSASSKRLFQEAAPTLV
+                     SFLNRAAETPQSPPPALGAIRLMAAHTRATLLRSPQREIDGYEFRELLSLRLLSYRSHF
+                     EAIYLRTKDPQSFDAACARFYEQVGAGVREFITACGDPDDDPADEMVRLWTKSITSESS
+                     HLAENFSDGSVVNAGHTLEDLVRKRGAPVEPTRFHTPPSPELDRLMHRDADFLAFRLQT
+                     SLLYSCLYTLGFSLAERYVFCYVVARANEDVCGKSMKELQDELDGLARSMASGSTKTAE
+                     "
+                     /protein_id="BGC0001472_9"
+     CDS             10511..10654
+                     /translation="MEQQIELDVLEISDLIAGAGENDDLAQVMAASCTTTSVSTSSSSS
+                     SS"
+                     /protein_id="BGC0001472_10"
+     CDS             10977..13634
+                     /translation="MGVNISPYVVYRRSRLPLGELGGMSFTTAWSRIDELHALRDEIGK
+                     NAVGLADRLGELVPTLGDDVRADLIRLRRDVHNLRHDRAVARLEPLRPHLGREVVDEVE
+                     TWCALGVRAEQCERAGREELESEKARAADGFGALFEHDAMARSIQLSGDRLYRGLRDLV
+                     AGDEASALKPSKARLRESSLVNFAYRASLKPSPFGRFTEIGAFPPDDPRPADPGGRHGG
+                     TQESVTTLNRLLVNWGPPGLPLVPGGMEPGHLVLNSTLRAGTEYVEYVGVAPGSREDGR
+                     MATERVLRVRREGLFDALLAAMPEGSAPAATVLRDLTAVTGKAETSRKVVQGLIRAGIL
+                     FFRPEIDDHDPDYSMKLDRVLAAGGTPETAALRGHFSELRRLETDFSEAAADERQKLLD
+                     SAYAAIGGIAELCKVSPPPEEVLKSPVFEDTPASTAPQAWNLPTVEGSIPALTGLWRLA
+                     SMMDNGQVKRLGLYSFATRVLGDRSTMPFLEFFQAFSSLTDQEQVDVFMGRDVEEAERY
+                     TRQRAEALRTIRQRLVPGDGTVHLDPSVIEKACEGVEDLLDTESVTFRAQFAQGVLPDR
+                     DRTLVVNGLLTGYGVYFSRFGSFVEGTDEWSLPAAQREHLARRFPGQVDLNSVLGFNFN
+                     LHPSVTRRVVNYPGAVSLGAERTVYGLARLEVRADQATRSLRLWDPEAQETLDLVPMNF
+                     MTPIGVPLLYRLLEALSPSNRYLWKPLDDIRDAGGPTVYGETAPRLVVGDVVADRRSWN
+                     VAAAEIPMLQDLSRDVPEALVAFDAWRLTRGLPRHAFVLCQTPEERDVMAGRSRKVTRQ
+                     WADYAHLRRASVHKPMYVDFRNPFLVRSFAKSALSRGDVVASIRECLPSVDDYGPDTGW
+                     TAAEEFFVELCTDN"
+                     /protein_id="BGC0001472_11"
+     CDS             13612..14571
+                     /translation="MNCVPTTSGQTGTREWRTVHIHVPHSLHTPFLCDVVEPLLRSEGL
+                     QDHFFFLRYWQGGPHLRLRMLCGPGAGSAEAAERVVAGLARAMPEFGAQAREEYALGLT
+                     LQDELARLEKETSEEGRPIGALDRVAYEPEYRKYGGTEGLQIAETVFRKSSVAVLGLLG
+                     GQPRAWVDERRAPIGEAARIMAMFLHGAGLDPRAAGLFLREYEDWWRTYAPDDMQRAWP
+                     KLFGGVSAQMTNLCAAVWRDGATDVFHDISAEAAARARSVCGAEPGGDVRDLRLDGTPY
+                     PGCLSNYVHTTNNRLGLVPAAEGLVAYLVRRGLEAMDG"
+                     /protein_id="BGC0001472_12"
+     CDS             14692..15894
+                     /translation="MTDRQDSAYPYPRTCPLHPPKEYASLRAEQPITKVTLASGRTAWL
+                     LTRHEHIRQLLADPHVSSNLAHPGYPLHFDAPPEVMEQMRPVLLAMDPPVHTAQRKMVI
+                     PEFTVKRVLQLRPRVEEIVDECISSMLAGEGPADLVEALALPVPSLVICELLGVPRSDR
+                     AFFQDRTNKLVSVDADPQERNSAHQELHAYFSELVTAQEADPGDDLLGRLVVKNRETGT
+                     FDHGELVGMANVLLVGGHETTANMISLGVVGLLENPDQLAKLRADPGLAPQAVDELLRY
+                     FSIADQVTSRVATADLEIGGVLIRAGEGVIGLSASGNHDEAVFPDPDRLDIERGGRHHL
+                     AFGHGIHQCIGQNLAKLELEVVFNALLARIPGLKLATPVAELPFKDSMGVYGLHKLPVS
+                     W"
+                     /protein_id="BGC0001472_13"
+     CDS             16220..16564
+                     /translation="MYLSIVMWDLKKSEATVESLREYLRDYAVDAYSALDGMRLKAWFS
+                     DSARQLWGAVYLWDSPEQMPGLYKVSRVIDLIGYPPTSVGGFTLEATAEGKSVHETLAG
+                     LGIALEGGTQ"
+                     /protein_id="BGC0001472_14"
+     CDS             17019..17729
+                     /translation="MLIEDIEPLLQSIRAGVEFIEIYGLDTVPVPDSLLAECERRRIPV
+                     RLLAASVANQVFKTEKKPKVFGIAKVPRPRRLSDLSDMTGDLILLDGVKIVGNIGAIVR
+                     TSFALGASGIVLVDSDLGSIADRRLIRASRGYVFSLPIVLASRAEALQYFQDNAMRPVV
+                     FEADGDLGVADLDGMDERLVLMFGSERIGPSGEFSDIAAKSVSIPMNPAAESLNVSVSA
+                     GIALHARARRNLSR"
+                     /protein_id="BGC0001472_15"
+     CDS             17815..19485
+                     /translation="ALLGLRPFTPWEVSVAELGPDHRAEVNVLAADGRRVELIFLNTAM
+                     HTGRHRLGLPSLWQDRRLVLRTVVADGSPLRRAGSYTYDGLVGVLTGLMESYRPTVVHT
+                     LDPDPDIQHSTEAVRRRDSEQPGYSDHADHTAAACFAWAAMIRWVARATADGGRIPGFV
+                     TVAYRGYYNRHWPKNLPQGVLARKAAHLVPYGGSPDWDCGNPSGCGDYNVGGDRPLTNR
+                     KGWVRSTHHRYPGTRTVLTAEPDGRLAAYAVLGLRVVRWQETGPGSGAWGPPHDLGGGP
+                     LAPALGSATTRDGRLLLFGLRFAALGGHGADNEREIVVLEQSAPGRGFRPWRGLGSPSP
+                     GRDEVRRTGVPVAVAAPDGQIHLFVRDAEKGVSTRVRDGAGRWSAWRDMGGGEVQDGLH
+                     TAVDEGGRVHVFGAGHHAVHHWTQDTPSAGLTARTQLTAAPVPAHAPAALPAPDGSVSL
+                     YYRAAAGSGLTTARAGTAVPGARFDGYXXVDAAPSPRGPVLLGRTAEGLVQLLMGGGLH
+                     VRTDGPAALDGASLRLGPDGRPSVAGLGPDAAPWMWRPR"
+                     /protein_id="BGC0001472_16"
+ORIGIN
+        1 gatcgatcga tcgatcgatc gatcgatcga tc
+//