Mercurial > repos > bgruening > uniprot_id_mapping
changeset 0:58b259f51c44 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_id_mapping commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
| author | bgruening |
|---|---|
| date | Sat, 26 Sep 2015 18:36:17 -0400 |
| parents | |
| children | |
| files | foo macros.xml test-data/id_map_refseq.txt test-data/id_uniprot.tab test-data/test1_map.tab test-data/test1_retrieve.fasta test-data/test2_map.tab test-data/test2_retrieve.gff tool_dependencies.xml uniprot.py uniprot.xml |
| diffstat | 11 files changed, 1000 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/foo Sat Sep 26 18:36:17 2015 -0400 @@ -0,0 +1,104 @@ +>tr|S0DS17|S0DS17_GIBF5 Related to cytochrom P450 OS=Gibberella fujikuroi (strain CBS 195.34 / IMI 58289 / NRRL A-6831) GN=FFUJ_00006 PE=3 SV=1 +MSYQSILLRQVNSLCDNLEEVARDENGGLIDMAMQSDYFTFDVMSEVIFGMAYNALKDTS +YRFVTGALGSSNIRIGTLVQSPLPAMCRIDKYLFPESIQGRNKFLGFIGSLLRDRSKASF +AGNGNVFSFLETAKDPDGGNQLSKSEIRAECATLVAAGTDTSSSTLAATLFYLSRNSKCY +SRVSEEVRNAFSSHQDIKIGPELNSCVYLRACIEETLRMSPPVGAALWREIGPGGMNIGP +LTLPAGVDVGTGIYSLHHNAAYHPEPFKYLPERWLVGEGSSTSESVELARSAFAPFSRGP +RSCVGKGFAYHELTLTIAHILHRFDFSATEEDFALRHGSEGPGGINEFLLHDHVTGARSG +PLLQFSMRR +>tr|M5BAG7|M5BAG7_9MICO ABC transporter, fused permease/ABC transporter involved in the biosynthesis of cytochrom bd, fused permease/ATP-binding protein OS=Clavibacter michiganensis subsp. nebraskensis NCPPB 2581 GN=cydC PE=3 SV=1 +MNRDGVLRLAQPPTRRTLPGLLAGLASAVGAVALLATSAWLITRASEQPPILFLGMAIVG +VRAFALGRAAFRYLERITSHDAAFRALATLRVGVFERLLPFAPAGLRDTRRGDLLARLVG +DVDRLQDLPLRVVQPLAVSVVVQAASVAVVGAVLPAAGIALAVVLGVALVVGIGATTALA +GRAETRIAPLRARLQDLVLDFVGGLDVLTSFGAVDDRLAAIDRAATELRRAELRSAAAAG +VTTGVVLAGTGAVAGWTVLQGVPGLASGTLDPAWLALAALVPLALVEQATAVPLAVQAWR +RVRTSAERVAGVVPETVPDEIPREPDDAADAQPVTADASPAGTTLEVRDLVTRWPGADED +ALAPVSLVVRPGETVVVRGPSGSGKSSLAAALARFLESRGAYELDGRDARSMPPSAVRRI +VGLCEQAPHLFDASIRQNLLFARDDATDDELVAVLARVGLADWTAGRGGLDARVGDRGGL +VSGGQAQRIALARALLADFPVLVLDEPTADVDAERARAVLRDVLTAARDRGPGVLLLTHT +DVPHDLVDRTVELRVAGDRVRTE +>tr|A0A077Z587|A0A077Z587_TRITR Kelch 3 and Kelch 4 and Cytochrom B561 domain con taining protein OS=Trichuris trichiura GN=TTRE_0000309301 PE=4 SV=1 +MGSQQAADETQKVVERIILNINVRKDKRSFGLGIKIKKGNVFVSSIRPGSIAEDHFKLYD +VIKDVNGSRIDSRELCRDLIRTHKVLTVTVERELSKNIEQPGQGDRKSSTECPYLETAQP +FSEMEKNQWSKLPADVREILKKQFATASQYGLQAPARTEQPTQTEHRKVSVLENIVRFEI +TSDVPRDKSLRKPSDGQQLYKIVASYQCISLLADQMIIYLWLRIGWLILTFNLFVTQAVS +LHWKRVAEYGKNPRPQARKHAAFGYDMLRHYVVLFGGQGERDENYNDTWIFDVLAGRWYA +VHRNVAPPAMHGAAFGLNDGKFYLVGGCDQTQCFDDVWVFLTSTFEWHKLAPKGELRPTG +RLGAIGGFYATGSHIIYGLGTTINDQFLEDIFFFDIPMQRWYKIIERLFVYSPFTPHPRR +HMSSLMVSPSEVLLFGGCSKHGQCPTGDAWLFNVQSHVWQSLPFCPSPRMEASAVTLLSS +DDVEPKPAAVLIYGGRRYTSQHLLGSPMLEPDEVVIYDLVGKSWSIRSSKYEDSSGLPEQ +RSAASTASTLTEVYMFGGEAYDGRLLDDFWMLAGDWRESATNQKCQQVNFNLLALHGLLM +SASFALILPAGALWALYKSARVTKQKKSGGWTMTHTIAQTCGMVIVAAGAVCSIQAKRDN +GKHFGSVHGVLGIIVIALLCVQVALGFSKSLIRTEAQRRTINRVHFWLAIVLLPLAFLNI +ILGLQLIAVPVGLLLGFFVHIFCLLAALGLILPILRFRKANRSVAFPPPNDD +>tr|A0A077ZFY8|A0A077ZFY8_TRITR PmbA TldD and Mur ligase M and Mur ligase and Mur ligase C and Cytochrom B562 domain containing protein OS=Trichuris trichiura GN=TTRE_0000758701 PE=4 SV=1 +MGGLAMLARQLGHEVTGSDANVYPPMSTLLEKQGIELIQGYDASQLDPQPDLVIIGNAMT +RGNPCVEAVLEKNIPYMSGPQWLHDFVLRDRWVLAVAGTHGKTTTAGMATWILEQCGYKP +GFVIGGVPGNFEVSARLGESNFFVIEADEYDCAFFDKRSKFVHYCPRTLILNNLEFDHAD +IFDDLKAIQKQFHHLVRIVPGQGRIIWPENDINLKQTMAMGCWSEQELVGEQGHWQAKKL +TTDASEWEVLLDGEKVGEVKWSLVGEHNMHNGLMAIAAARHVGVAPADAANALGSFINAR +RRLELRGEANGVTVYDDFAHHPTAILATLAALRGKVGGTARIIAVLEPRSNTMKMGICKD +DLAPSLGRADEVFLLQPAHIPWQVAEVAEACVQPAHWSGDVDTLADMVVKTAQPGDHILV +MSNGGFGGIHQKLLDDFRETLYIMALAMKVISQVEAQRKILEEAVSTALELASGKSDGAE +VAVSKTTGISVSTRYGEVENVEFNSDGALGITVYHQNRKGSASSTDLSPQAIARTVQAAL +DIARYTSPDPCAGVADKELLAFDAPDLDLFHPAEVSPDEAIELAARAEQAALQADKRITN +TEGGSFNSHYGVKVFGNSHGMLQGYCSTRHSLSSCVIAEENGDMERDYAYTIGRAMSDLQ +TPEWVGADCARRTLSRLSPRKLSTMKAPVIFANEVATGLFGHLVGAIAGGSVYRKSTFLL +DSLGKQILPDWLTIEEHPHLLKGLASTPFDSEGVRTERRDIIKDGILTQWLLTSYSARKL +GLKSTGHAGGIHNWRIAGQGLSFEQMLKEMGTGLVVTELMGQGVSAITGDYSRGAAGFWV +ENGEIQYPVSEITIAVSSLVFSSASFAADLEDNMETLNDNLKVVEKADNAAQVKDALTKM +RAAALDAQKATPPKLEGKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQ +LKTTRNAYHQKYR +>sp|O14639|ABLM1_HUMAN Actin-binding LIM protein 1 OS=Homo sapiens GN=ABLIM1 PE=1 SV=3 +MPAFLGLKCLGKLCSSEKSKVTSSERTSARGSNRKRLIVEDRRVSGTSFTAHRRATITHL +LYLCPKDYCPRGRVCNSVDPFVAHPQDPHHPSEKPVIHCHKCGEPCKGEVLRVQTKHFHI +KCFTCKVCGCDLAQGGFFIKNGEYLCTLDYQRMYGTRCHGCGEFVEGEVVTALGKTYHPN +CFACTICKRPFPPGDRVTFNGRDCLCQLCAQPMSSSPKETTFSSNCAGCGRDIKNGQALL +ALDKQWHLGCFKCKSCGKVLTGEYISKDGAPYCEKDYQGLFGVKCEACHQFITGKVLEAG +DKHYHPSCARCSRCNQMFTEGEEMYLQGSTVWHPDCKQSTKTEEKLRPTRTSSESIYSRP +GSSIPGSPGHTIYAKVDNEILDYKDLAAIPKVKAIYDIERPDLITYEPFYTSGYDDKQER +QSLGESPRTLSPTPSAEGYQDVRDRMIHRSTSQGSINSPVYSRHSYTPTTSRSPQHFHRP +GNEPSSGRNSPLPYRPDSRPLTPTYAQAPKHFHVPDQGINIYRKPPIYKQHAALAAQSKS +SEDIIKFSKFPAAQAPDPSETPKIETDHWPGPPSFAVVGPDMKRRSSGREEDDEELLRRR +QLQEEQLMKLNSGLGQLILKEEMEKESRERSSLLASRYDSPINSASHIPSSKTASLPGYG +RNGLHRPVSTDFAQYNSYGDVSGGVRDYQTLPDGHMPAMRMDRGVSMPNMLEPKIFPYEM +LMVTNRGRNKILREVDRTRLERHLAPEVFREIFGMSIQEFDRLPLWRRNDMKKKAKLF +>tr|M5B8V9|M5B8V9_9MICO ABC transporter involved in the biosynthesis of cytochrom bd, fused permease/ATP-binding protein OS=Clavibacter michiganensis subsp. nebraskensis NCPPB 2581 GN=CMN_01519 PE=3 SV=1 +MKPLDPRLLRHSASARTMLAVGAVVSVVQTAALVAFCWSLTQLVVRAIGGADQAALAPVL +ALAVGSAVVRGAAAWLLDVTGARGAARVTAELRRRALRAIADLGPAWTAARSRGRLATIV +GPGLDALDPYFARYVPQLILTALATPIVVAVLLLSDPLTGVTVLVTLPVIPVFMVLVGWA +TQEVQRRQWSRLTELASSFLEVVDGLSTLLVFRRARRQTARIRRVTEEYRVETMRVLRIS +FLSGFVLELAASLSVALVAVSVGVRLIGGQLDLEVGLFVLLLAPEAFLPIRQVGVQFHAA +AEGVAAADDVLGILEEERAARATRPVPGPATATPPAGDALVIRDLAVARGDRAVLSGVSA +RFPRGRVTAVTGPSGVGKSSLLGAMLGHLPAGGAAGWIDDDASSLRPPVPTEIAWAGQRP +GLVAGTVRENVALGVADPDDALVRRALALAAADGIDPDLVLGVGGQGLSGGQAQRVAVAR +AVHRALALDCPLVLLDEPSSALDAATEERLAAGIRALADQGRAVVVVTHRGALVRAADAE +LRLGGASGEDDAPAAVGSSVGAGRVAPARIAPEPAWRAQVAP +>tr|A0A077ZHN8|A0A077ZHN8_TRITR HAMP and MCPsignal and TarH and Cytochrom B N dom ain containing protein OS=Trichuris trichiura GN=TTRE_0000819801 PE=4 SV=1 +MEFRGFFPRSDRPLINMVHVSCGISILVLMVVRLLLRLKYPTPPIIPKPKPMMTGLAHLG +HLVIYLLFIALPVIGLVMMYNRGNPWFAFGLTMPYASEANFERVDSLKSWHETLANLGYF +VIGSALAGYFLWQADRDQRDVTAEIEIRTGLANSSDFLRSARINMIQAGAASRIAEMEAM +KRNIAQAESEIKQSQQGYRAYQNRPVKTPADEALDTELNQRFQAYITGMQPMLKYAKNGM +FEAIINHESEQIRPLDNAYTDILNKAVKIRSTRANQLAELAHQRTRLGGMFMIGAFVLAL +VMTLITFMVLRRIVIRPLQHAAQRIEKIASGDLTMNDEPAGRNEIGRLSRHLQQMQHSLG +MTVGTVRQGAEEIYRGTSEISAGNADLSSRTEEQAAAIEQTAASMEQLTATVKQNADNAH +HASKLAQEASIKASDGGQTVSGVVKTMGAISTSSKKISEITAVINSIAFQTNILALNAAV +EAARAGEQGRGFAVVASEVRTLASRSAQAAKEIEGLISESVRLIDLGSDEVATAGKTMST +IVDAVASVTHIMQEIAAASDEQSRGITQVSQAISEMDKVTQQNASLVEEASAAAVSLEEQ +AARLTEAVDVFRLHKHSVSAEPRGAGEPVSFATV +>tr|Q0P8A9|Q0P8A9_CAMJE Putative formate dehydrogenase, cytochrom B subunit OS=Campylobacter jejuni subsp. jejuni serotype O:2 (strain NCTC 11168) GN=fdhC PE=4 SV=1 +MRKVFVTLLLSVVSLFAYGSERMGQDTQIWDFHRITNIPNYDTFGKLWTTLQGEYIATIA +LIAVIAVLSAFALHYMVIGPKQFSHDGKKIYAFTLFERLFHFIAAISWVILVPTGFVMMF +GEVFGGGVFVRVCKNLHAFATILFIISIIPMFLCWIKRMLPASYDIRWMMIVGGYLSKIK +RPVPAGKFNFGQKSWYYIAVFGGFLMIITGGFMYFLDFNSTAIQGLFGLTQIELLRISAI +VHNFLGIVCAVFFGVHIYMAVFAIKGSIHSMISGYKEEEEVYILHSYWYKELSNKKQIEP +SFSYDPNVKI +>sp|Q13685|AAMP_HUMAN Angio-associated migratory cell protein OS=Homo sapiens GN=AAMP PE=1 SV=2 +MESESESGAAADTPPLETLSFHGDEEIIEVVELDPGPPDPDDLAQEMEDVDFEEEEEEEG +NEEGWVLEPQEGVVGSMEGPDDSEVTFALHSASVFCVSLDPKTNTLAVTGGEDDKAFVWR +LSDGELLFECAGHKDSVTCAGFSHDSTLVATGDMSGLLKVWQVDTKEEVWSFEAGDLEWM +EWHPRAPVLLAGTADGNTWMWKVPNGDCKTFQGPNCPATCGRVLPDGKRAVVGYEDGTIR +IWDLKQGSPIHVLKGTEGHQGPLTCVAANQDGSLILTGSVDCQAKLVSATTGKVVGVFRP +ETVASQPSLGEGEESESNSVESLGFCSVMPLAAVGYLDGTLAIYDLATQTLRHQCQHQSG +IVQLLWEAGTAVVYTCSLDGIVRLWDARTGRLLTDYRGHTAEILDFALSKDASLVVTTSG +DHKAKVFCVQRPDR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sat Sep 26 18:36:17 2015 -0400 @@ -0,0 +1,228 @@ +<macros> +<token name="@EXECUTABLE@">1.0</token> + <macro name="macro-category_FROM"> + <param name="category_FROM" type="select" label="Choose your database category (FROM):" + help="Select a databse from which your ids are coming from"> + <option value="uniprot">UniProt</option> + <option value="oseqdb">Other sequence databases</option> + <option value="3Dstrdb">3D structure databases</option> + <option value="ppidb">Protein-protein interaction databases</option> + <option value="chemistry">Chemistry</option> + <option value="protfgdb">Protein family/group databases</option> + <option value="polymorphismANDmutation">Polymorphism and mutation databases</option> + <option value="2DgelDB">2D gel databases</option> + <option value="ProtocolsMaterialsDB">Protocols and materials databases</option> + <option value="GenomeAnnotationDB">Genome annotation databases</option> + <option value="OrganismSpecificGeneDB">Organism-specific gene databases</option> + <option value="phylogenomic">Phylogenomic databases</option> + <option value="EnzymePathwayDB">Enzyme and pathway databases</option> + <option value="GeneExpression">Gene expression databases</option> + <option value="other">Other</option> + </param> + </macro> + <macro name="macro-category_TO"> + <param name="category_TO" type="select" label="Choose your database category (TO):" + help="Select a database which will be used for mapping"> + <option value="uniprot">UniProt</option> + <option value="oseqdb">Other sequence databases</option> + <option value="3Dstrdb">3D structure databases</option> + <option value="ppidb">Protein-protein interaction databases</option> + <option value="chemistry">Chemistry</option> + <option value="protfgdb">Protein family/group databases</option> + <option value="polymorphismANDmutation">Polymorphism and mutation databases</option> + <option value="2DgelDB">2D gel databases</option> + <option value="ProtocolsMaterialsDB">Protocols and materials databases</option> + <option value="GenomeAnnotationDB">Genome annotation databases</option> + <option value="OrganismSpecificGeneDB">Organism-specific gene databases</option> + <option value="phylogenomic">Phylogenomic databases</option> + <option value="EnzymePathwayDB">Enzyme and pathway databases</option> + <option value="GeneExpression">Gene expression databases</option> + <option value="other">Other</option> + </param> + </macro> + <macro name="macro-db_uniprot_FROM"> + <param name="db_uniprot_FROM" type="select" label="Choose a database:" + help=""> + <option value="ACC+ID">UniProtKB AC/ID</option> + <option value="ACC">UniProtKB AC</option> + <option value="ID">UniProtKB ID</option> + <option value="ACC">UniProtKB AC</option> + <option value="UPARC">UniParc</option> + <option value="NF50">UniRef50</option> + <option value="NF90">UniRef90</option> + <option value="NF100">UniRef100</option> + <option value="GENENAME">Gene name</option> + </param> + </macro> + <macro name="macro-db_uniprot_TO"> + <param name="db_uniprot_TO" type="select" label="Choose a database:" + help=""> + <option value="ACC">UniProtKB AC</option> + <option value="ID">UniProtKB ID</option> + <option value="ACC">UniProtKB AC</option> + <option value="UPARC">UniParc</option> + <option value="NF50">UniRef50</option> + <option value="NF90">UniRef90</option> + <option value="NF100">UniRef100</option> + <option value="GENENAME">Gene name</option> + </param> + </macro> + <macro name="macro-db_oseqdb"> + <param name="db_oseqdb" type="select" label="Choose a database:" + help=""> + <option value="EMBL_ID">EMBL/GenBank/DDBJ</option> + <option value="EMBL">EMBL/GenBank/DDBJ CDS</option> + <option value="PIR">PIR</option> + + <option value="UNIGENE_ID">UniParc</option> + <option value="P_ENTREZGENEID">Entrez Gene (GeneID)</option> + <option value="P_GI">GI number</option> + <option value="P_REFSEQ_AC">RefSeq Protein</option> + <option value="REFSEQ_NT_ID">RefSeq Nucleotide</option> + </param> + </macro> + <macro name="macro-db_3Dstrdb"> + <param name="db_3Dstrdb" type="select" label="Choose a database:" + help=""> + <option value="PDB_ID">PDB</option> + <option value="DISPROT_ID">DisProt</option> + </param> + </macro> + <macro name="macro-db_ppidb"> + <param name="db_ppidb" type="select" label="Choose a database:" + help=""> + <option value="BIOGRID_ID">BioGrid</option> + <option value="DIP_ID">DIP</option> + <option value="MINT_ID">MINT</option> + <option value="STRING_ID">STRING</option> + </param> + </macro> + <macro name="macro-db_chemistry"> + <param name="db_chemistry" type="select" label="Choose a database:" + help=""> + <option value="CHEMBL_ID">ChEMBL</option> + <option value="DrugBank_ID">DrugBank</option> + <option value="GUIDETOPHARMACOLOGY_ID">GuidetoPHARMACOLOGY</option> + </param> + </macro> + <macro name="macro-db_protfgdb"> + <param name="db_protfgdb" type="select" label="Choose a database:" + help=""> + <option value="ALLERGOME_ID">Allergome</option> + <option value="MEROPS_ID">MEROPS</option> + <option value="MYCOCLAP_ID">mycoCLAP</option> + <option value="PEROXIBASE_ID">PeroxiBase</option> + <option value="REBASE_ID">REBASE</option> + <option value="TCDB_ID">TCDB</option> + </param> + </macro> + <macro name="macro-db_polymorphismANDmutation"> + <param name="db_polymorphismANDmutation" type="select" label="Choose a database:" + help=""> + <option value="DMDM_ID">DMDM</option> + </param> + </macro> + <macro name="macro-db_2DgelDB"> + <param name="db_2DgelDB" type="select" label="Choose a database:" + help=""> + <option value="WORLD_2DPAGE_ID">World-2DPAGE</option> + </param> + </macro> + <macro name="macro-db_ProtocolsMaterialsDB"> + <param name="db_ProtocolsMaterialsDB" type="select" label="Choose a database:" + help=""> + <option value="DNASU_ID">DNASU</option> + </param> + </macro> + <macro name="macro-db_GenomeAnnotationDB"> + <param name="db_GenomeAnnotationDB" type="select" label="Choose a database:" + help=""> + <option value="ENSEMBL_ID">Ensembl</option> + <option value="ENSEMBL_PRO_ID">Ensembl Protein</option> + <option value="ENSEMBL_TRS_ID">Ensembl Transcript</option> + <option value="ENSEMBLGENOME_ID">Ensembl Genomes</option> + <option value="ENSEMBLGENOME_PRO_ID">Ensembl Genomes Protein</option> + <option value="ENSEMBLGENOME_TRS_ID">Ensembl Genomes Transcript</option> + <option value="P_ENTREZGENEID">GeneID</option> + <option value="KEGG_ID">KEGG</option> + <option value="PATRIC_ID">PATRIC</option> + <option value="UCSC_ID">UCSC</option> + <option value="VECTORBASE_ID">VectorBase</option> + </param> + </macro> + <macro name="macro-db_OrganismSpecificGeneDB"> + <param name="db_OrganismSpecificGeneDB" type="select" label="Choose a database:" + help=""> + <option value="ARACHNOSERVER_ID">ArachnoServer</option> + <option value="CGD">CGD</option> + <option value="CONOSERVER_ID">ConoServer</option> + <option value="DICTYBASE_ID">dictyBase</option> + <option value="ECHOBASE_ID">EchoBASE</option> + <option value="ECOGENE_ID">EcoGene</option> + <option value="EUHCVDB_ID">euHCVdb</option> + <option value="EUPATHDB_ID">EuPathDB</option> + <option value="FLYBASE_ID">FlyBase</option> + <option value="GENECARDS_ID">GeneCards</option> + <option value="GENEFARM_ID">GeneFarm</option> + <option value="GENOLIST_ID">GenoList</option> + <option value="H_INVDB_ID">H-InvDB</option> + <option value="HGNC_ID">HGNC</option> + <option value="HPA_ID">HPA</option> + <option value="LEGIOLIST_ID">LegioList</option> + <option value="MAIZEGDB_ID">MaizeGDB</option> + <option value="MIM_ID">MIM</option> + <option value="MGI_ID">MGI</option> + <option value="NEXTPROT_ID">neXtProt</option> + <option value="ORPHANET_ID">Orphanet</option> + <option value="PHARMGKB_ID">PharmGKB</option> + <option value="POMBASE_ID">PomBase</option> + <option value="PSEUDOCAP_ID">PseudoCAP</option> + <option value="RGD_ID">RGD</option> + <option value="SGD_ID">SGD</option> + <option value="TAIR_ID">TAIR</option> + <option value="TUBERCULIST_ID">TubercuList</option> + <option value="WORMBASE_ID">WormBase</option> + <option value="WORMBASE_TRS_ID">WormBase Transcript</option> + <option value="WORMBASE_PRO_ID">WormBase Protein</option> + <option value="XENBASE_ID">Xenbase</option> + <option value="ZFIN_ID">ZFIN</option> + </param> + </macro> + <macro name="macro-db_phylogenomic"> + <param name="db_phylogenomic" type="select" label="Choose a database:" + help=""> + <option value="EGGNOG_ID">eggNOG</option> + <option value="GENETREE_ID">GeneTree</option> + <option value="HOGENOM_ID">HOGENOM</option> + <option value="HOVERGEN_ID">HOVERGEN</option> + <option value="KO_ID">KO</option> + <option value="OMA_ID">OMA</option> + <option value="ORTHODB_ID">OrthoDB</option> + <option value="PROTCLUSTDB_ID">ProtClustDB</option> + <option value="TREEFAM_ID">TreeFam</option> + </param> + </macro> + <macro name="macro-db_EnzymePathwayDB"> + <param name="db_EnzymePathwayDB" type="select" label="Choose a database:" + help=""> + <option value="BIOCYC_ID">BioCyc</option> + <option value="REACTOME_ID">Reactome</option> + <option value="UNIPATHWAY_ID">UniPathWay</option> + </param> + </macro> + <macro name="macro-db_GeneExpression"> + <param name="db_GeneExpression" type="select" label="Choose a database:" + help=""> + <option value="CLEANEX_ID">CleanEx</option> + </param> + </macro> + <macro name="macro-db_other"> + <param name="db_other" type="select" label="Choose a database:" + help=""> + <option value="CHITARS_ID">ChiTaRS</option> + <option value="GENOMERNAI_ID">GenomeRNAi</option> + <option value="GENEWIKI_ID">GeneWiki</option> + <option value="NEXTBIO_ID">NextBio</option> + </param> + </macro> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/id_map_refseq.txt Sat Sep 26 18:36:17 2015 -0400 @@ -0,0 +1,7 @@ +LN734406.1 +CAD29848.1 +CAD29848.1 +CAB85965.1 +NM_130786 +P04217 +NM_001087
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/id_uniprot.tab Sat Sep 26 18:36:17 2015 -0400 @@ -0,0 +1,9 @@ +Q0P8A9 +A0A077ZHN8 +A0A077ZFY8 +M5B8V9 +M5BAG7 +S0DS17 +A0A077Z587 +Q13685 +O14639
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1_map.tab Sat Sep 26 18:36:17 2015 -0400 @@ -0,0 +1,10 @@ +From To +Q0P8A9 fdhC +A0A077ZHN8 TTRE_0000819801 +A0A077ZFY8 TTRE_0000758701 +M5B8V9 CMN_01519 +M5BAG7 cydC +S0DS17 FFUJ_00006 +A0A077Z587 TTRE_0000309301 +Q13685 AAMP +O14639 ABLIM1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1_retrieve.fasta Sat Sep 26 18:36:17 2015 -0400 @@ -0,0 +1,104 @@ +>tr|S0DS17|S0DS17_GIBF5 Related to cytochrom P450 OS=Gibberella fujikuroi (strain CBS 195.34 / IMI 58289 / NRRL A-6831) GN=FFUJ_00006 PE=3 SV=1 +MSYQSILLRQVNSLCDNLEEVARDENGGLIDMAMQSDYFTFDVMSEVIFGMAYNALKDTS +YRFVTGALGSSNIRIGTLVQSPLPAMCRIDKYLFPESIQGRNKFLGFIGSLLRDRSKASF +AGNGNVFSFLETAKDPDGGNQLSKSEIRAECATLVAAGTDTSSSTLAATLFYLSRNSKCY +SRVSEEVRNAFSSHQDIKIGPELNSCVYLRACIEETLRMSPPVGAALWREIGPGGMNIGP +LTLPAGVDVGTGIYSLHHNAAYHPEPFKYLPERWLVGEGSSTSESVELARSAFAPFSRGP +RSCVGKGFAYHELTLTIAHILHRFDFSATEEDFALRHGSEGPGGINEFLLHDHVTGARSG +PLLQFSMRR +>tr|M5BAG7|M5BAG7_9MICO ABC transporter, fused permease/ABC transporter involved in the biosynthesis of cytochrom bd, fused permease/ATP-binding protein OS=Clavibacter michiganensis subsp. nebraskensis NCPPB 2581 GN=cydC PE=3 SV=1 +MNRDGVLRLAQPPTRRTLPGLLAGLASAVGAVALLATSAWLITRASEQPPILFLGMAIVG +VRAFALGRAAFRYLERITSHDAAFRALATLRVGVFERLLPFAPAGLRDTRRGDLLARLVG +DVDRLQDLPLRVVQPLAVSVVVQAASVAVVGAVLPAAGIALAVVLGVALVVGIGATTALA +GRAETRIAPLRARLQDLVLDFVGGLDVLTSFGAVDDRLAAIDRAATELRRAELRSAAAAG +VTTGVVLAGTGAVAGWTVLQGVPGLASGTLDPAWLALAALVPLALVEQATAVPLAVQAWR +RVRTSAERVAGVVPETVPDEIPREPDDAADAQPVTADASPAGTTLEVRDLVTRWPGADED +ALAPVSLVVRPGETVVVRGPSGSGKSSLAAALARFLESRGAYELDGRDARSMPPSAVRRI +VGLCEQAPHLFDASIRQNLLFARDDATDDELVAVLARVGLADWTAGRGGLDARVGDRGGL +VSGGQAQRIALARALLADFPVLVLDEPTADVDAERARAVLRDVLTAARDRGPGVLLLTHT +DVPHDLVDRTVELRVAGDRVRTE +>tr|A0A077Z587|A0A077Z587_TRITR Kelch 3 and Kelch 4 and Cytochrom B561 domain con taining protein OS=Trichuris trichiura GN=TTRE_0000309301 PE=4 SV=1 +MGSQQAADETQKVVERIILNINVRKDKRSFGLGIKIKKGNVFVSSIRPGSIAEDHFKLYD +VIKDVNGSRIDSRELCRDLIRTHKVLTVTVERELSKNIEQPGQGDRKSSTECPYLETAQP +FSEMEKNQWSKLPADVREILKKQFATASQYGLQAPARTEQPTQTEHRKVSVLENIVRFEI +TSDVPRDKSLRKPSDGQQLYKIVASYQCISLLADQMIIYLWLRIGWLILTFNLFVTQAVS +LHWKRVAEYGKNPRPQARKHAAFGYDMLRHYVVLFGGQGERDENYNDTWIFDVLAGRWYA +VHRNVAPPAMHGAAFGLNDGKFYLVGGCDQTQCFDDVWVFLTSTFEWHKLAPKGELRPTG +RLGAIGGFYATGSHIIYGLGTTINDQFLEDIFFFDIPMQRWYKIIERLFVYSPFTPHPRR +HMSSLMVSPSEVLLFGGCSKHGQCPTGDAWLFNVQSHVWQSLPFCPSPRMEASAVTLLSS +DDVEPKPAAVLIYGGRRYTSQHLLGSPMLEPDEVVIYDLVGKSWSIRSSKYEDSSGLPEQ +RSAASTASTLTEVYMFGGEAYDGRLLDDFWMLAGDWRESATNQKCQQVNFNLLALHGLLM +SASFALILPAGALWALYKSARVTKQKKSGGWTMTHTIAQTCGMVIVAAGAVCSIQAKRDN +GKHFGSVHGVLGIIVIALLCVQVALGFSKSLIRTEAQRRTINRVHFWLAIVLLPLAFLNI +ILGLQLIAVPVGLLLGFFVHIFCLLAALGLILPILRFRKANRSVAFPPPNDD +>tr|A0A077ZFY8|A0A077ZFY8_TRITR PmbA TldD and Mur ligase M and Mur ligase and Mur ligase C and Cytochrom B562 domain containing protein OS=Trichuris trichiura GN=TTRE_0000758701 PE=4 SV=1 +MGGLAMLARQLGHEVTGSDANVYPPMSTLLEKQGIELIQGYDASQLDPQPDLVIIGNAMT +RGNPCVEAVLEKNIPYMSGPQWLHDFVLRDRWVLAVAGTHGKTTTAGMATWILEQCGYKP +GFVIGGVPGNFEVSARLGESNFFVIEADEYDCAFFDKRSKFVHYCPRTLILNNLEFDHAD +IFDDLKAIQKQFHHLVRIVPGQGRIIWPENDINLKQTMAMGCWSEQELVGEQGHWQAKKL +TTDASEWEVLLDGEKVGEVKWSLVGEHNMHNGLMAIAAARHVGVAPADAANALGSFINAR +RRLELRGEANGVTVYDDFAHHPTAILATLAALRGKVGGTARIIAVLEPRSNTMKMGICKD +DLAPSLGRADEVFLLQPAHIPWQVAEVAEACVQPAHWSGDVDTLADMVVKTAQPGDHILV +MSNGGFGGIHQKLLDDFRETLYIMALAMKVISQVEAQRKILEEAVSTALELASGKSDGAE +VAVSKTTGISVSTRYGEVENVEFNSDGALGITVYHQNRKGSASSTDLSPQAIARTVQAAL +DIARYTSPDPCAGVADKELLAFDAPDLDLFHPAEVSPDEAIELAARAEQAALQADKRITN +TEGGSFNSHYGVKVFGNSHGMLQGYCSTRHSLSSCVIAEENGDMERDYAYTIGRAMSDLQ +TPEWVGADCARRTLSRLSPRKLSTMKAPVIFANEVATGLFGHLVGAIAGGSVYRKSTFLL +DSLGKQILPDWLTIEEHPHLLKGLASTPFDSEGVRTERRDIIKDGILTQWLLTSYSARKL +GLKSTGHAGGIHNWRIAGQGLSFEQMLKEMGTGLVVTELMGQGVSAITGDYSRGAAGFWV +ENGEIQYPVSEITIAVSSLVFSSASFAADLEDNMETLNDNLKVVEKADNAAQVKDALTKM +RAAALDAQKATPPKLEGKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQ +LKTTRNAYHQKYR +>sp|O14639|ABLM1_HUMAN Actin-binding LIM protein 1 OS=Homo sapiens GN=ABLIM1 PE=1 SV=3 +MPAFLGLKCLGKLCSSEKSKVTSSERTSARGSNRKRLIVEDRRVSGTSFTAHRRATITHL +LYLCPKDYCPRGRVCNSVDPFVAHPQDPHHPSEKPVIHCHKCGEPCKGEVLRVQTKHFHI +KCFTCKVCGCDLAQGGFFIKNGEYLCTLDYQRMYGTRCHGCGEFVEGEVVTALGKTYHPN +CFACTICKRPFPPGDRVTFNGRDCLCQLCAQPMSSSPKETTFSSNCAGCGRDIKNGQALL +ALDKQWHLGCFKCKSCGKVLTGEYISKDGAPYCEKDYQGLFGVKCEACHQFITGKVLEAG +DKHYHPSCARCSRCNQMFTEGEEMYLQGSTVWHPDCKQSTKTEEKLRPTRTSSESIYSRP +GSSIPGSPGHTIYAKVDNEILDYKDLAAIPKVKAIYDIERPDLITYEPFYTSGYDDKQER +QSLGESPRTLSPTPSAEGYQDVRDRMIHRSTSQGSINSPVYSRHSYTPTTSRSPQHFHRP +GNEPSSGRNSPLPYRPDSRPLTPTYAQAPKHFHVPDQGINIYRKPPIYKQHAALAAQSKS +SEDIIKFSKFPAAQAPDPSETPKIETDHWPGPPSFAVVGPDMKRRSSGREEDDEELLRRR +QLQEEQLMKLNSGLGQLILKEEMEKESRERSSLLASRYDSPINSASHIPSSKTASLPGYG +RNGLHRPVSTDFAQYNSYGDVSGGVRDYQTLPDGHMPAMRMDRGVSMPNMLEPKIFPYEM +LMVTNRGRNKILREVDRTRLERHLAPEVFREIFGMSIQEFDRLPLWRRNDMKKKAKLF +>tr|M5B8V9|M5B8V9_9MICO ABC transporter involved in the biosynthesis of cytochrom bd, fused permease/ATP-binding protein OS=Clavibacter michiganensis subsp. nebraskensis NCPPB 2581 GN=CMN_01519 PE=3 SV=1 +MKPLDPRLLRHSASARTMLAVGAVVSVVQTAALVAFCWSLTQLVVRAIGGADQAALAPVL +ALAVGSAVVRGAAAWLLDVTGARGAARVTAELRRRALRAIADLGPAWTAARSRGRLATIV +GPGLDALDPYFARYVPQLILTALATPIVVAVLLLSDPLTGVTVLVTLPVIPVFMVLVGWA +TQEVQRRQWSRLTELASSFLEVVDGLSTLLVFRRARRQTARIRRVTEEYRVETMRVLRIS +FLSGFVLELAASLSVALVAVSVGVRLIGGQLDLEVGLFVLLLAPEAFLPIRQVGVQFHAA +AEGVAAADDVLGILEEERAARATRPVPGPATATPPAGDALVIRDLAVARGDRAVLSGVSA +RFPRGRVTAVTGPSGVGKSSLLGAMLGHLPAGGAAGWIDDDASSLRPPVPTEIAWAGQRP +GLVAGTVRENVALGVADPDDALVRRALALAAADGIDPDLVLGVGGQGLSGGQAQRVAVAR +AVHRALALDCPLVLLDEPSSALDAATEERLAAGIRALADQGRAVVVVTHRGALVRAADAE +LRLGGASGEDDAPAAVGSSVGAGRVAPARIAPEPAWRAQVAP +>tr|A0A077ZHN8|A0A077ZHN8_TRITR HAMP and MCPsignal and TarH and Cytochrom B N dom ain containing protein OS=Trichuris trichiura GN=TTRE_0000819801 PE=4 SV=1 +MEFRGFFPRSDRPLINMVHVSCGISILVLMVVRLLLRLKYPTPPIIPKPKPMMTGLAHLG +HLVIYLLFIALPVIGLVMMYNRGNPWFAFGLTMPYASEANFERVDSLKSWHETLANLGYF +VIGSALAGYFLWQADRDQRDVTAEIEIRTGLANSSDFLRSARINMIQAGAASRIAEMEAM +KRNIAQAESEIKQSQQGYRAYQNRPVKTPADEALDTELNQRFQAYITGMQPMLKYAKNGM +FEAIINHESEQIRPLDNAYTDILNKAVKIRSTRANQLAELAHQRTRLGGMFMIGAFVLAL +VMTLITFMVLRRIVIRPLQHAAQRIEKIASGDLTMNDEPAGRNEIGRLSRHLQQMQHSLG +MTVGTVRQGAEEIYRGTSEISAGNADLSSRTEEQAAAIEQTAASMEQLTATVKQNADNAH +HASKLAQEASIKASDGGQTVSGVVKTMGAISTSSKKISEITAVINSIAFQTNILALNAAV +EAARAGEQGRGFAVVASEVRTLASRSAQAAKEIEGLISESVRLIDLGSDEVATAGKTMST +IVDAVASVTHIMQEIAAASDEQSRGITQVSQAISEMDKVTQQNASLVEEASAAAVSLEEQ +AARLTEAVDVFRLHKHSVSAEPRGAGEPVSFATV +>tr|Q0P8A9|Q0P8A9_CAMJE Putative formate dehydrogenase, cytochrom B subunit OS=Campylobacter jejuni subsp. jejuni serotype O:2 (strain NCTC 11168) GN=fdhC PE=4 SV=1 +MRKVFVTLLLSVVSLFAYGSERMGQDTQIWDFHRITNIPNYDTFGKLWTTLQGEYIATIA +LIAVIAVLSAFALHYMVIGPKQFSHDGKKIYAFTLFERLFHFIAAISWVILVPTGFVMMF +GEVFGGGVFVRVCKNLHAFATILFIISIIPMFLCWIKRMLPASYDIRWMMIVGGYLSKIK +RPVPAGKFNFGQKSWYYIAVFGGFLMIITGGFMYFLDFNSTAIQGLFGLTQIELLRISAI +VHNFLGIVCAVFFGVHIYMAVFAIKGSIHSMISGYKEEEEVYILHSYWYKELSNKKQIEP +SFSYDPNVKI +>sp|Q13685|AAMP_HUMAN Angio-associated migratory cell protein OS=Homo sapiens GN=AAMP PE=1 SV=2 +MESESESGAAADTPPLETLSFHGDEEIIEVVELDPGPPDPDDLAQEMEDVDFEEEEEEEG +NEEGWVLEPQEGVVGSMEGPDDSEVTFALHSASVFCVSLDPKTNTLAVTGGEDDKAFVWR +LSDGELLFECAGHKDSVTCAGFSHDSTLVATGDMSGLLKVWQVDTKEEVWSFEAGDLEWM +EWHPRAPVLLAGTADGNTWMWKVPNGDCKTFQGPNCPATCGRVLPDGKRAVVGYEDGTIR +IWDLKQGSPIHVLKGTEGHQGPLTCVAANQDGSLILTGSVDCQAKLVSATTGKVVGVFRP +ETVASQPSLGEGEESESNSVESLGFCSVMPLAAVGYLDGTLAIYDLATQTLRHQCQHQSG +IVQLLWEAGTAVVYTCSLDGIVRLWDARTGRLLTDYRGHTAEILDFALSKDASLVVTTSG +DHKAKVFCVQRPDR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test2_map.tab Sat Sep 26 18:36:17 2015 -0400 @@ -0,0 +1,5 @@ +From To +NM_130786 A1BG_HUMAN +NM_130786 V9HWD8_HUMAN +NM_001087 A0A024R410_HUMAN +NM_001087 AAMP_HUMAN
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test2_retrieve.gff Sat Sep 26 18:36:17 2015 -0400 @@ -0,0 +1,55 @@ +##gff-version 3 +##sequence-region S0DS17 1 369 +##sequence-region M5BAG7 1 563 +##sequence-region A0A077Z587 1 772 +##sequence-region A0A077ZFY8 1 973 +##sequence-region O14639 1 778 +O14639 UniProtKB Chain 1 778 . . . ID=PRO_0000075697;Note=Actin-binding LIM protein 1 +O14639 UniProtKB Domain 97 156 . . . Note=LIM zinc-binding 1;evidence=ECO:0000255|PROSITE-ProRule:PRU00125 +O14639 UniProtKB Domain 156 216 . . . Note=LIM zinc-binding 2;evidence=ECO:0000255|PROSITE-ProRule:PRU00125 +O14639 UniProtKB Domain 224 283 . . . Note=LIM zinc-binding 3;evidence=ECO:0000255|PROSITE-ProRule:PRU00125 +O14639 UniProtKB Domain 283 343 . . . Note=LIM zinc-binding 4;evidence=ECO:0000255|PROSITE-ProRule:PRU00125 +O14639 UniProtKB Domain 710 778 . . . Note=HP;evidence=ECO:0000255|PROSITE-ProRule:PRU00595 +O14639 UniProtKB Coiled coil 590 614 . . . evidence=ECO:0000255 +O14639 UniProtKB Modified residue 367 367 . . . Note=Phosphoserine;evidence=ECO:0000244|PubMed:19690332 +O14639 UniProtKB Modified residue 373 373 . . . Note=Phosphotyrosine;evidence=ECO:0000244|PubMed:19690332 +O14639 UniProtKB Modified residue 396 396 . . . Note=Phosphotyrosine;evidence=ECO:0000244|PubMed:15592455 +O14639 UniProtKB Modified residue 426 426 . . . Note=Phosphoserine;evidence=ECO:0000244|PubMed:19690332,ECO:0000244|PubMed:24275569 +O14639 UniProtKB Modified residue 431 431 . . . Note=Phosphoserine;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:19690332 +O14639 UniProtKB Modified residue 433 433 . . . Note=Phosphothreonine;evidence=ECO:0000244|PubMed:19690332 +O14639 UniProtKB Modified residue 435 435 . . . Note=Phosphoserine;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:19690332,ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:21406692,ECO:0000244|PubMed:24275569 +O14639 UniProtKB Modified residue 439 439 . . . Note=Phosphotyrosine;evidence=ECO:0000244|PubMed:15144186 +O14639 UniProtKB Modified residue 455 455 . . . Note=Phosphoserine;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:24275569 +O14639 UniProtKB Modified residue 458 458 . . . Note=Phosphoserine;evidence=ECO:0000244|PubMed:18669648 +O14639 UniProtKB Modified residue 587 587 . . . Note=Phosphoserine;evidence=ECO:0000244|PubMed:18669648 +O14639 UniProtKB Modified residue 640 640 . . . Note=Phosphoserine;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231 +O14639 UniProtKB Modified residue 655 655 . . . Note=Phosphoserine;evidence=ECO:0000244|PubMed:18669648 +O14639 UniProtKB Modified residue 706 706 . . . Note=Phosphoserine;evidence=ECO:0000244|PubMed:24275569 +O14639 UniProtKB Alternative sequence 1 316 . . . ID=VSP_012099;Note=In isoform 3%2C isoform 4 and isoform 5.;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:17974005 +O14639 UniProtKB Alternative sequence 1 81 . . . ID=VSP_012100;Note=In isoform 2 and isoform 6.;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:7584044 +O14639 UniProtKB Alternative sequence 347 347 . . . ID=VSP_041185;Note=In isoform 5 and isoform 6.;evidence=ECO:0000303|PubMed:14702039 +O14639 UniProtKB Alternative sequence 348 373 . . . ID=VSP_012101;Note=In isoform 4.;evidence=ECO:0000303|PubMed:15489334 +O14639 UniProtKB Alternative sequence 480 514 . . . ID=VSP_012102;Note=In isoform 3%2C isoform 4 and isoform 5.;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:17974005 +O14639 UniProtKB Alternative sequence 531 531 . . . ID=VSP_057209;Note=In isoform 6.;evidence=ECO:0000303|PubMed:14702039 +O14639 UniProtKB Natural variant 434 434 . . . ID=VAR_050141;Dbxref=dbSNP:rs11593544 +O14639 UniProtKB Natural variant 637 637 . . . ID=VAR_050142;Dbxref=dbSNP:rs7091419 +O14639 UniProtKB Sequence conflict 499 499 . . . evidence=ECO:0000305 +O14639 UniProtKB Sequence conflict 532 532 . . . evidence=ECO:0000305 +O14639 UniProtKB Sequence conflict 563 563 . . . evidence=ECO:0000305 +O14639 UniProtKB Sequence conflict 578 578 . . . evidence=ECO:0000305 +##sequence-region M5B8V9 1 582 +##sequence-region A0A077ZHN8 1 634 +##sequence-region Q0P8A9 1 310 +##sequence-region Q13685 1 434 +Q13685 UniProtKB Chain 1 434 . . . ID=PRO_0000050832;Note=Angio-associated migratory cell protein +Q13685 UniProtKB Repeat 89 129 . . . Note=WD 1 +Q13685 UniProtKB Repeat 132 171 . . . Note=WD 2 +Q13685 UniProtKB Repeat 173 212 . . . Note=WD 3 +Q13685 UniProtKB Repeat 214 254 . . . Note=WD 4 +Q13685 UniProtKB Repeat 258 299 . . . Note=WD 5 +Q13685 UniProtKB Repeat 315 354 . . . Note=WD 6 +Q13685 UniProtKB Repeat 356 395 . . . Note=WD 7 +Q13685 UniProtKB Repeat 398 433 . . . Note=WD 8 +Q13685 UniProtKB Compositional bias 53 59 . . . Note=Poly-Glu +Q13685 UniProtKB Modified residue 20 20 . . . Note=Phosphoserine;evidence=ECO:0000244|PubMed:24275569 +Q13685 UniProtKB Natural variant 250 250 . . . ID=VAR_037061;Dbxref=dbSNP:rs2305835
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sat Sep 26 18:36:17 2015 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="request" version="2.7"> + <repository changeset_revision="5eb0bfde4f2f" name="package_request_2_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/uniprot.py Sat Sep 26 18:36:17 2015 -0400 @@ -0,0 +1,117 @@ +#!/usr/bin/env python +""" +uniprot python interface +to access the uniprot database + +Based on work from Jan Rudolph: https://github.com/jdrudolph/uniprot +available services: + map + retrieve +""" + +import requests +import sys, argparse + +url = 'http://www.uniprot.org/' + +def _retrieve(query, format='txt'): + """_retrieve is not meant for use with the python interface, use `retrieve` + instead""" + tool = 'batch/' + + query = list(set(query.split('\n'))) + queries = [query[i:i+100] for i in range(0, len(query), 100)] + + data = {'format':format} + + responses = [requests.post(url + tool, data=data, files={'file':' '.join(query)}) for query in queries] + page = ''.join([response.text for response in responses]) + return page + +def retrieve(ids, format='txt'): + """ request entries by uniprot acc using batch retrieval + + Args: + query: list of ids to retrieve + format: txt by default + + Help: + possible formats: + txt, xml, rdf, fasta, gff""" + if type(ids) is not list: + ids = [ids] + return _retrieve(' '.join(ids), format) + +def _map(query, f, t, format='tab'): + """ _map is not meant for use with the python interface, use `map` instead + """ + tool = 'mapping/' + + data = { + 'from':f, + 'to':t, + 'format':format, + 'query': query + } + response = requests.post(url + tool, data=data) + page = response.text + return page + +def map(ids, f, t, format='tab'): + """ map a list of ids from one format onto another using uniprots mapping api + + Args: + query: id or list of ids to be mapped + f: from ACC | P_ENTREZGENEID | ... + t: to ... + format: tab by default + + Help: + for a list of all possible mappings visit + 'http://www.uniprot.org/faq/28' + """ + if type(ids) is not list: + ids = [ids] + page = _map(' '.join(ids), f, t, format) + result = dict() + for row in page.splitlines()[1:]: + key, value = row.split('\t') + if key in result: + result[key].add(value) + else: + result[key] = set([value]) + return result + +if __name__ == '__main__': + import argparse + import sys + + parser = argparse.ArgumentParser(description='retrieve uniprot mapping') + subparsers = parser.add_subparsers(dest='tool') + + mapping = subparsers.add_parser('map') + mapping.add_argument('f', help='from') + mapping.add_argument('t', help='to') + mapping.add_argument('inp', nargs='?', type=argparse.FileType('r'), + default=sys.stdin, help='input file (default: stdin)') + mapping.add_argument('out', nargs='?', type=argparse.FileType('w'), + default=sys.stdout, help='output file (default: stdout)') + mapping.add_argument('--format', default='tab', help='output format') + + retrieve = subparsers.add_parser('retrieve') + retrieve.add_argument('inp', metavar = 'in', nargs='?', type=argparse.FileType('r'), + default=sys.stdin, help='input file (default: stdin)') + retrieve.add_argument('out', nargs='?', type=argparse.FileType('w'), + default=sys.stdout, help='output file (default: stdout)') + retrieve.add_argument('-f', '--format', help='specify output format', default='txt') + + args = parser.parse_args() + query = args.inp.read() + + if args.tool == 'map': + args.out.write(_map(query, args.f, args.t, args.format)) + + elif args.tool == 'retrieve': + args.out.write(_retrieve(query, format=args.format)) + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/uniprot.xml Sat Sep 26 18:36:17 2015 -0400 @@ -0,0 +1,355 @@ +<tool id="uniprot" name="UniProt" version="0.1"> + <description>ID mapping and retrieval</description> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="2.7">request</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <regex match="Error:" /> + <regex match="Exception:" /> + </stdio> + <version_command>echo "UniProt ID mapping for Galaxy in version 0.1"</version_command> + <command><![CDATA[ + + cut -f ${id_column} $infile > id_file.tabular && + + $__tool_directory__/uniprot.py + + #if $tool.tool_choice == "retrieve": + retrieve -f $tool.format $infile ./output + #elif $tool.tool_choice == "map": + map + + #if $tool.from.category_FROM == "uniprot": + $tool.from.db_uniprot_FROM + #elif $tool.from.category_FROM == "oseqdb": + $tool.from.db_oseqdb + #elif $tool.from.category_FROM == "3Dstrdb": + $tool.from.db_3Dstrdb + #elif $tool.from.category_FROM == "ppidb": + $tool.from.db_ppidb + #elif $tool.from.category_FROM == "chemistry": + $tool.from.db_chemistry + #elif $tool.from.category_FROM == "protfgdb": + $tool.from.db_protfgdb + #elif $tool.from.category_FROM == "polymorphismANDmutation": + $tool.from.db_polymorphismANDmutation + #elif $tool.from.category_FROM == "db_2DgelDB": + $tool.from.db_2DgelDB + #elif $tool.from.category_FROM == "ProtocolsMaterialsDB": + $tool.from.ProtocolsMaterialsDB + #elif $tool.from.category_FROM == "db_GenomeAnnotationDB": + $tool.from.db_GenomeAnnotationDB + #elif $tool.from.category_FROM == "db_OrganismSpecificGeneDB": + $tool.from.db_OrganismSpecificGeneDB + #elif $tool.from.category_FROM == "db_phylogenomic": + $tool.from.db_phylogenomic + #elif $tool.from.category_FROM == "db_EnzymePathwayDB": + $tool.from.db_EnzymePathwayDB + #elif $tool.from.category_FROM == "db_GeneExpression": + $tool.from.db_GeneExpression + #elif $tool.from.category_FROM == "db_other": + $tool.from.db_other + #end if + + #if $tool.to.category_TO == "uniprot": + $tool.to.db_uniprot_TO + #elif $tool.to.category_TO == "oseqdb": + $tool.to.db_oseqdb + #elif $tool.to.category_TO == "3Dstrdb": + $tool.to.db_3Dstrdb + #elif $tool.to.category_TO == "ppidb": + $tool.to.db_ppidb + #elif $tool.to.category_TO == "chemistry": + $tool.to.db_chemistry + #elif $tool.to.category_TO == "protfgdb": + $tool.to.db_protfgdb + #elif $tool.to.category_TO == "polymorphismANDmutation": + $tool.to.db_polymorphismANDmutation + #elif $tool.to.category_TO == "db_2DgelDB": + $tool.to.db_2DgelDB + #elif $tool.to.category_TO == "ProtocolsMaterialsDB": + $tool.to.ProtocolsMaterialsDB + #elif $tool.to.category_TO == "db_GenomeAnnotationDB": + $tool.to.db_GenomeAnnotationDB + #elif $tool.frtoom.category_TO == "db_OrganismSpecificGeneDB": + $tool.to.db_OrganismSpecificGeneDB + #elif $tool.to.category_TO == "db_phylogenomic": + $tool.to.db_phylogenomic + #elif $tool.to.category_TO == "db_EnzymePathwayDB": + $tool.to.db_EnzymePathwayDB + #elif $tool.to.category_TO == "db_GeneExpression": + $tool.to.db_GeneExpression + #elif $tool.to.category_TO == "db_other": + $tool.to.db_other + #end if + + id_file.tabular + ./output + #end if + + ]]></command> + <inputs> + <param name="infile" type="data" format="tabular" label="Input file with IDs" + help="One ID in each line."/> + <param name="id_column" label="ID column" type="data_column" data_ref="infile" help=""/> + + <conditional name="tool"> + <param name="tool_choice" type="select" label="Do you want to map IDs or retrieve data from UniProt" help=""> + <option value="retrieve">Retrieve: request entries by uniprot accession using batch retrieval</option> + <option value="map" selected="True">Map: map a list of ids from one format onto another using uniprots mapping API</option> + </param> + <when value="map"> + <conditional name="from"> + <expand macro="macro-category_FROM"/> + <when value="uniprot"> + <expand macro="macro-db_uniprot_FROM"/> + </when> + <when value="oseqdb"> + <expand macro="macro-db_oseqdb"/> + </when> + <when value="3Dstrdb"> + <expand macro="macro-db_3Dstrdb"/> + </when> + <when value="ppidb"> + <expand macro="macro-db_ppidb"/> + </when> + <when value="chemistry"> + <expand macro="macro-db_chemistry"/> + </when> + <when value="protfgdb"> + <expand macro="macro-db_protfgdb"/> + </when> + <when value="polymorphismANDmutation"> + <expand macro="macro-db_polymorphismANDmutation"/> + </when> + <when value="2DgelDB"> + <expand macro="macro-db_2DgelDB"/> + </when> + <when value="ProtocolsMaterialsDB"> + <expand macro="macro-db_ProtocolsMaterialsDB"/> + </when> + <when value="GenomeAnnotationDB"> + <expand macro="macro-db_GenomeAnnotationDB"/> + </when> + <when value="OrganismSpecificGeneDB"> + <expand macro="macro-db_OrganismSpecificGeneDB"/> + </when> + <when value="phylogenomic"> + <expand macro="macro-db_phylogenomic"/> + </when> + <when value="EnzymePathwayDB"> + <expand macro="macro-db_EnzymePathwayDB"/> + </when> + <when value="GeneExpression"> + <expand macro="macro-db_GeneExpression"/> + </when> + <when value="other"> + <expand macro="macro-db_other"/> + </when> + </conditional> + <conditional name="to"> + <expand macro="macro-category_TO"/> + <when value="uniprot"> + <expand macro="macro-db_uniprot_TO"/> + </when> + <when value="oseqdb"> + <expand macro="macro-db_oseqdb"/> + </when> + <when value="3Dstrdb"> + <expand macro="macro-db_3Dstrdb"/> + </when> + <when value="ppidb"> + <expand macro="macro-db_ppidb"/> + </when> + <when value="chemistry"> + <expand macro="macro-db_chemistry"/> + </when> + <when value="protfgdb"> + <expand macro="macro-db_protfgdb"/> + </when> + <when value="polymorphismANDmutation"> + <expand macro="macro-db_polymorphismANDmutation"/> + </when> + <when value="2DgelDB"> + <expand macro="macro-db_2DgelDB"/> + </when> + <when value="ProtocolsMaterialsDB"> + <expand macro="macro-db_ProtocolsMaterialsDB"/> + </when> + <when value="GenomeAnnotationDB"> + <expand macro="macro-db_GenomeAnnotationDB"/> + </when> + <when value="OrganismSpecificGeneDB"> + <expand macro="macro-db_OrganismSpecificGeneDB"/> + </when> + <when value="phylogenomic"> + <expand macro="macro-db_phylogenomic"/> + </when> + <when value="EnzymePathwayDB"> + <expand macro="macro-db_EnzymePathwayDB"/> + </when> + <when value="GeneExpression"> + <expand macro="macro-db_GeneExpression"/> + </when> + <when value="other"> + <expand macro="macro-db_other"/> + </when> + </conditional> + </when> + <when value="retrieve"> + <param name="format" type="select" label="Choose format of output file" help=""> + <option value="fasta">fasta</option> + <option value="gff">gff</option> + </param> + </when> + </conditional> + + </inputs> + <outputs> + <data name="outfile_retrieve_fasta" format="fasta" from_work_dir="./output" + label="${tool.name} on ${on_string} (retrieve output)"> + <filter>tool['tool_choice'] == 'retrieve'</filter> + <filter>tool['format'] == 'fasta'</filter> + </data> + <data name="outfile_retrieve_gff" format="gff" from_work_dir="./output" + label="${tool.name} on ${on_string} (retrieve output)"> + <filter>tool['tool_choice'] == 'retrieve'</filter> + <filter>tool['format'] == 'gff'</filter> + </data> + <data name="outfile_map" format="tabular" from_work_dir="./output" + label="${tool.name} on ${on_string} (map output)"> + <filter>tool['tool_choice'] == 'map'</filter> + </data> + </outputs> + <tests> + <test> + <param name="infile" value="id_uniprot.tab" ftype="tabular"/> + <param name="id_column" value="c1"/> + <param name="format" value="fasta"/> + <param name="tool_choice" value="retrieve"/> + <output name="outfile_retrieve" file="test1_retrieve.fasta" ftype="fasta"/> + </test> + <test> + <param name="infile" value="id_uniprot.tab" ftype="tabular"/> + <param name="id_column" value="c1"/> + <param name="format" value="gff"/> + <param name="tool_choice" value="retrieve"/> + <output name="outfile_retrieve" file="test2_retrieve.gff" ftype="gff"/> + </test> + <test> + <param name="infile" value="id_uniprot.tab" ftype="tabular"/> + <param name="id_column" value="c1"/> + <param name="tool_choice" value="map"/> + <param name="category_FROM" value="uniprot"/> + <param name="db_uniprot_FROM" value="ID"/> + <param name="category_TO" value="uniprot"/> + <param name="db_uniprot_TO" value="GENENAME"/> + <output name="outfile_map" file="test1_map.tab" ftype="tabular"/> + </test> + <test> + <param name="infile" value="id_map_refseq.txt" ftype="tabular"/> + <param name="id_column" value="c1"/> + <param name="tool_choice" value="map"/> + <param name="category_FROM" value="oseqdb"/> + <param name="db_oseqdb" value="REFSEQ_NT_ID"/> + <param name="category_TO" value="uniprot"/> + <param name="db_uniprot_TO" value="ID"/> + <output name="outfile_map" file="test2_map.tab" ftype="tabular"/> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +**What it does** + +This tool provides access to the UniProt API. You can retrieve sequence informations given a list of sequence identifiers or map +identifiers between different databases. +Hence, this tool offers you two modes: *map* and *retrieve*. + +----- + +**INPUT** + +The input is a list of IDs. + +*example*: + +Q0P8A9 +A0A077ZHN8 +A0A077ZFY8 +M5B8V9 +M5BAG7 +S0DS17 +.... + +----- + +**MAP OUTPUT EXAMPLES** + +FROM refseq TO embl:: + + From To + NM_130786 A1BG_HUMAN + NM_130786 V9HWD8_HUMAN + NM_001087 A0A024R410_HUMAN + NM_001087 AAMP_HUMAN + +FROM uniprot TO genename:: + + From To + Q0P8A9 fdhC + A0A077ZHN8 TTRE_0000819801 + A0A077ZFY8 TTRE_0000758701 + M5B8V9 CMN_01519 + M5BAG7 cydC + S0DS17 FFUJ_00006 + A0A077Z587 TTRE_0000309301 + Q13685 AAMP + O14639 ABLIM1 + +----- + +**RETRIEVE OUTPUT EXAMPLES** + +retrieve gff:: + + #gff-version 3 + #sequence-region S0DS17 1 369 + #sequence-region M5BAG7 1 563 + #sequence-region A0A077Z587 1 772 + #sequence-region A0A077ZFY8 1 973 + #sequence-region O14639 1 778 + O14639 UniProtKB Chain 1 778 . . . ID=PRO_0000075697;Note=Actin-binding LIM protein 1 + O14639 UniProtKB Domain 97 156 . . . Note=LIM zinc-binding 1;evidence=ECO:0000255|PROSITE-ProRule:PRU00125 + O14639 UniProtKB Domain 156 216 . . . Note=LIM zinc-binding 2;evidence=ECO:0000255|PROSITE-ProRule:PRU00125 + O14639 Un... + +retrieve fasta:: + + >tr|S0DS17|S0DS17_GIBF5 Related to cytochrom P450 OS=Gibberella fujikuroi (strain CBS 195.34 / IMI 58289 / NRRL A-6831) GN=FFUJ_00006 PE=3 SV=1 + MSYQSILLRQVNSLCDNLEEVARDENGGLIDMAMQSDYFTFDVMSEVIFGMAYNALKDTS + YRFVTGALGSSNIRIGTLVQSPLPAMCRIDKY... + >tr|M5BAG7|M5BAG7_9MICO ABC transporter, fused permease/ABC transporter involved in the biosynthesis of cytochrom bd, fused permease/ATP-binding protein OS=Clavibacter michiganensis subsp. nebraskensis NCPPB 2581 GN=cydC PE=3 SV=1 + MNRDGVLRLAQPPTRRTLPGLLAGLASAVGAVALLATSAWLITRASEQPPILFLGMAIVG + VRAFALGRAAFRYLERITSHDAAFRALATLRV... + >tr|A0A077Z587|A0A077Z587_TRITR Kelch 3 and Kelch 4 and Cytochrom B561 domain con taining protein OS=Trichuris trichiura GN=TTRE_0000309301 PE=4 SV=1 + MGSQQAADETQKVVERIILNINVRKDKRSFGLGIKIKKGNVFVSSIRPGSIAEDHFKLYD + VIKDVNGSRIDSRELCRDLIRTHKVLTV... + +----- + +This tool is based on the work `Jan Rudolph`_ and the UniProt API. + +.. _Jan Rudolph: https://github.com/jdrudolph/uniprot + + ]]></help> + <citations> + <citation type="doi">10.1093/nar/gku989</citation> + </citations> +</tool>