| Previous changeset 1:cd2a41c65447 (2016-10-14) Next changeset 3:df4c547b2533 (2017-04-10) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 074fed99c6df6bad17341bbfa57645f222907ad4 |
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modified:
test-data/test1_retrieve.fasta test-data/test2_retrieve.gff uniprot.xml |
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removed:
tool_dependencies.xml |
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| diff -r cd2a41c65447 -r fe94765e8814 test-data/test1_retrieve.fasta --- a/test-data/test1_retrieve.fasta Fri Oct 14 17:59:02 2016 -0400 +++ b/test-data/test1_retrieve.fasta Mon Apr 10 13:19:36 2017 -0400 |
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| b'@@ -1,36 +1,12 @@\n->sp|S0DS17|APF8_GIBF5 Cytochrome P450 momooxygenase apf8 OS=Gibberella fujikuroi (strain CBS 195.34 / IMI 58289 / NRRL A-6831) GN=apf8 PE=1 SV=1\n-MSYQSILLRQVNSLCDNLEEVARDENGGLIDMAMQSDYFTFDVMSEVIFGMAYNALKDTS\n-YRFVTGALGSSNIRIGTLVQSPLPAMCRIDKYLFPESIQGRNKFLGFIGSLLRDRSKASF\n-AGNGNVFSFLETAKDPDGGNQLSKSEIRAECATLVAAGTDTSSSTLAATLFYLSRNSKCY\n-SRVSEEVRNAFSSHQDIKIGPELNSCVYLRACIEETLRMSPPVGAALWREIGPGGMNIGP\n-LTLPAGVDVGTGIYSLHHNAAYHPEPFKYLPERWLVGEGSSTSESVELARSAFAPFSRGP\n-RSCVGKGFAYHELTLTIAHILHRFDFSATEEDFALRHGSEGPGGINEFLLHDHVTGARSG\n-PLLQFSMRR\n->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=4 SV=1\n-MNRDGVLRLAQPPTRRTLPGLLAGLASAVGAVALLATSAWLITRASEQPPILFLGMAIVG\n-VRAFALGRAAFRYLERITSHDAAFRALATLRVGVFERLLPFAPAGLRDTRRGDLLARLVG\n-DVDRLQDLPLRVVQPLAVSVVVQAASVAVVGAVLPAAGIALAVVLGVALVVGIGATTALA\n-GRAETRIAPLRARLQDLVLDFVGGLDVLTSFGAVDDRLAAIDRAATELRRAELRSAAAAG\n-VTTGVVLAGTGAVAGWTVLQGVPGLASGTLDPAWLALAALVPLALVEQATAVPLAVQAWR\n-RVRTSAERVAGVVPETVPDEIPREPDDAADAQPVTADASPAGTTLEVRDLVTRWPGADED\n-ALAPVSLVVRPGETVVVRGPSGSGKSSLAAALARFLESRGAYELDGRDARSMPPSAVRRI\n-VGLCEQAPHLFDASIRQNLLFARDDATDDELVAVLARVGLADWTAGRGGLDARVGDRGGL\n-VSGGQAQRIALARALLADFPVLVLDEPTADVDAERARAVLRDVLTAARDRGPGVLLLTHT\n-DVPHDLVDRTVELRVAGDRVRTE\n->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\n-MGSQQAADETQKVVERIILNINVRKDKRSFGLGIKIKKGNVFVSSIRPGSIAEDHFKLYD\n-VIKDVNGSRIDSRELCRDLIRTHKVLTVTVERELSKNIEQPGQGDRKSSTECPYLETAQP\n-FSEMEKNQWSKLPADVREILKKQFATASQYGLQAPARTEQPTQTEHRKVSVLENIVRFEI\n-TSDVPRDKSLRKPSDGQQLYKIVASYQCISLLADQMIIYLWLRIGWLILTFNLFVTQAVS\n-LHWKRVAEYGKNPRPQARKHAAFGYDMLRHYVVLFGGQGERDENYNDTWIFDVLAGRWYA\n-VHRNVAPPAMHGAAFGLNDGKFYLVGGCDQTQCFDDVWVFLTSTFEWHKLAPKGELRPTG\n-RLGAIGGFYATGSHIIYGLGTTINDQFLEDIFFFDIPMQRWYKIIERLFVYSPFTPHPRR\n-HMSSLMVSPSEVLLFGGCSKHGQCPTGDAWLFNVQSHVWQSLPFCPSPRMEASAVTLLSS\n-DDVEPKPAAVLIYGGRRYTSQHLLGSPMLEPDEVVIYDLVGKSWSIRSSKYEDSSGLPEQ\n-RSAASTASTLTEVYMFGGEAYDGRLLDDFWMLAGDWRESATNQKCQQVNFNLLALHGLLM\n-SASFALILPAGALWALYKSARVTKQKKSGGWTMTHTIAQTCGMVIVAAGAVCSIQAKRDN\n-GKHFGSVHGVLGIIVIALLCVQVALGFSKSLIRTEAQRRTINRVHFWLAIVLLPLAFLNI\n-ILGLQLIAVPVGLLLGFFVHIFCLLAALGLILPILRFRKANRSVAFPPPNDD\n+>sp|Q13685|AAMP_HUMAN Angio-associated migratory cell protein OS=Homo sapiens GN=AAMP PE=1 SV=2\n+MESESESGAAADTPPLETLSFHGDEEIIEVVELDPGPPDPDDLAQEMEDVDFEEEEEEEG\n+NEEGWVLEPQEGVVGSMEGPDDSEVTFALHSASVFCVSLDPKTNTLAVTGGEDDKAFVWR\n+LSDGELLFECAGHKDSVTCAGFSHDSTLVATGDMSGLLKVWQVDTKEEVWSFEAGDLEWM\n+EWHPRAPVLLAGTADGNTWMWKVPNGDCKTFQGPNCPATCGRVLPDGKRAVVGYEDGTIR\n+IWDLKQGSPIHVLKGTEGHQGPLTCVAANQDGSLILTGSVDCQAKLVSATTGKVVGVFRP\n+ETVASQPSLGEGEESESNSVESLGFCSVMPLAAVGYLDGTLAIYDLATQTLRHQCQHQSG\n+IVQLLWEAGTAVVYTCSLDGIVRLWDARTGRLLTDYRGHTAEILDFALSKDASLVVTTSG\n+DHKAKVFCVQRPDR\n >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=3 SV=1\n MGGLAMLARQLGHEVTGSDANVYPPMSTLLEKQGIELIQGYDASQLDPQPDLVIIGNAMT\n RGNPCVEAVLEKNIPYMSGPQWLHDFVLRDRWVLAVAGTHGKTTTAGMATWILEQCGYKP\n@@ -49,6 +25,69 @@\n ENGEIQYPVSEITIAVSSLVFSSASFAADLEDNMETLNDNLKVVEKADNAAQVKDALTKM\n RAAALDAQKATPPKLEGKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQ\n LKTTRNAYHQKYR\n+>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\n+MEFRGFFPRSDRPLINMVHVSCGISILVLMVVRLLLRLKYPTPPIIPKPKPMMTGLAHLG\n+HLVIYLLFIALPVIGLVMMYNRGNPWFAFGLTMPYASEANFERVDSLKSWHETLANLGYF\n+VIGSALAGYFLWQADRDQRDVTAEIEIRTGLANSSDFLRSARINMIQAGAASRIAEMEAM\n+KRNIAQAESEIKQSQQGYRAYQNRPVKTPADEALDTELNQRFQAYITGMQPMLKYAKNGM\n+FEAIINHESEQIRPLDNAYTDILNKAVKIRSTRANQLAELAHQRTRLGGMFMIGAFVLAL\n+VMTLITFMVLRRIVIRPLQHAAQRIEKIASGDLTMNDEPAGRNEIGRLSRHLQQMQHSLG\n+MTVGTVRQGAEEIYRGTSEISAGNADLSSRTEEQAAAIEQTAASMEQLTATVKQNADNAH\n+HASKLAQEASIKASDGGQTVSGVVKTMGAISTSSKKISEITAVINSIAFQTNILALNAAV\n+EAARAGEQGRGFAVV'..b'ALVVGIGATTALA\n+GRAETRIAPLRARLQDLVLDFVGGLDVLTSFGAVDDRLAAIDRAATELRRAELRSAAAAG\n+VTTGVVLAGTGAVAGWTVLQGVPGLASGTLDPAWLALAALVPLALVEQATAVPLAVQAWR\n+RVRTSAERVAGVVPETVPDEIPREPDDAADAQPVTADASPAGTTLEVRDLVTRWPGADED\n+ALAPVSLVVRPGETVVVRGPSGSGKSSLAAALARFLESRGAYELDGRDARSMPPSAVRRI\n+VGLCEQAPHLFDASIRQNLLFARDDATDDELVAVLARVGLADWTAGRGGLDARVGDRGGL\n+VSGGQAQRIALARALLADFPVLVLDEPTADVDAERARAVLRDVLTAARDRGPGVLLLTHT\n+DVPHDLVDRTVELRVAGDRVRTE\n+>tr|Q0P8A9|Q0P8A9_CAMJE Putative formate dehydrogenase, cytochrom B subunit OS=Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) GN=fdhC PE=4 SV=1\n+MRKVFVTLLLSVVSLFAYGSERMGQDTQIWDFHRITNIPNYDTFGKLWTTLQGEYIATIA\n+LIAVIAVLSAFALHYMVIGPKQFSHDGKKIYAFTLFERLFHFIAAISWVILVPTGFVMMF\n+GEVFGGGVFVRVCKNLHAFATILFIISIIPMFLCWIKRMLPASYDIRWMMIVGGYLSKIK\n+RPVPAGKFNFGQKSWYYIAVFGGFLMIITGGFMYFLDFNSTAIQGLFGLTQIELLRISAI\n+VHNFLGIVCAVFFGVHIYMAVFAIKGSIHSMISGYKEEEEVYILHSYWYKELSNKKQIEP\n+SFSYDPNVKI\n >sp|O14639|ABLM1_HUMAN Actin-binding LIM protein 1 OS=Homo sapiens GN=ABLIM1 PE=1 SV=3\n MPAFLGLKCLGKLCSSEKSKVTSSERTSARGSNRKRLIVEDRRVSGTSFTAHRRATITHL\n LYLCPKDYCPRGRVCNSVDPFVAHPQDPHHPSEKPVIHCHKCGEPCKGEVLRVQTKHFHI\n@@ -63,42 +102,3 @@\n QLQEEQLMKLNSGLGQLILKEEMEKESRERSSLLASRYDSPINSASHIPSSKTASLPGYG\n RNGLHRPVSTDFAQYNSYGDVSGGVRDYQTLPDGHMPAMRMDRGVSMPNMLEPKIFPYEM\n LMVTNRGRNKILREVDRTRLERHLAPEVFREIFGMSIQEFDRLPLWRRNDMKKKAKLF\n->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=4 SV=1\n-MKPLDPRLLRHSASARTMLAVGAVVSVVQTAALVAFCWSLTQLVVRAIGGADQAALAPVL\n-ALAVGSAVVRGAAAWLLDVTGARGAARVTAELRRRALRAIADLGPAWTAARSRGRLATIV\n-GPGLDALDPYFARYVPQLILTALATPIVVAVLLLSDPLTGVTVLVTLPVIPVFMVLVGWA\n-TQEVQRRQWSRLTELASSFLEVVDGLSTLLVFRRARRQTARIRRVTEEYRVETMRVLRIS\n-FLSGFVLELAASLSVALVAVSVGVRLIGGQLDLEVGLFVLLLAPEAFLPIRQVGVQFHAA\n-AEGVAAADDVLGILEEERAARATRPVPGPATATPPAGDALVIRDLAVARGDRAVLSGVSA\n-RFPRGRVTAVTGPSGVGKSSLLGAMLGHLPAGGAAGWIDDDASSLRPPVPTEIAWAGQRP\n-GLVAGTVRENVALGVADPDDALVRRALALAAADGIDPDLVLGVGGQGLSGGQAQRVAVAR\n-AVHRALALDCPLVLLDEPSSALDAATEERLAAGIRALADQGRAVVVVTHRGALVRAADAE\n-LRLGGASGEDDAPAAVGSSVGAGRVAPARIAPEPAWRAQVAP\n->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\n-MEFRGFFPRSDRPLINMVHVSCGISILVLMVVRLLLRLKYPTPPIIPKPKPMMTGLAHLG\n-HLVIYLLFIALPVIGLVMMYNRGNPWFAFGLTMPYASEANFERVDSLKSWHETLANLGYF\n-VIGSALAGYFLWQADRDQRDVTAEIEIRTGLANSSDFLRSARINMIQAGAASRIAEMEAM\n-KRNIAQAESEIKQSQQGYRAYQNRPVKTPADEALDTELNQRFQAYITGMQPMLKYAKNGM\n-FEAIINHESEQIRPLDNAYTDILNKAVKIRSTRANQLAELAHQRTRLGGMFMIGAFVLAL\n-VMTLITFMVLRRIVIRPLQHAAQRIEKIASGDLTMNDEPAGRNEIGRLSRHLQQMQHSLG\n-MTVGTVRQGAEEIYRGTSEISAGNADLSSRTEEQAAAIEQTAASMEQLTATVKQNADNAH\n-HASKLAQEASIKASDGGQTVSGVVKTMGAISTSSKKISEITAVINSIAFQTNILALNAAV\n-EAARAGEQGRGFAVVASEVRTLASRSAQAAKEIEGLISESVRLIDLGSDEVATAGKTMST\n-IVDAVASVTHIMQEIAAASDEQSRGITQVSQAISEMDKVTQQNASLVEEASAAAVSLEEQ\n-AARLTEAVDVFRLHKHSVSAEPRGAGEPVSFATV\n->tr|Q0P8A9|Q0P8A9_CAMJE Putative formate dehydrogenase, cytochrom B subunit OS=Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) GN=fdhC PE=4 SV=1\n-MRKVFVTLLLSVVSLFAYGSERMGQDTQIWDFHRITNIPNYDTFGKLWTTLQGEYIATIA\n-LIAVIAVLSAFALHYMVIGPKQFSHDGKKIYAFTLFERLFHFIAAISWVILVPTGFVMMF\n-GEVFGGGVFVRVCKNLHAFATILFIISIIPMFLCWIKRMLPASYDIRWMMIVGGYLSKIK\n-RPVPAGKFNFGQKSWYYIAVFGGFLMIITGGFMYFLDFNSTAIQGLFGLTQIELLRISAI\n-VHNFLGIVCAVFFGVHIYMAVFAIKGSIHSMISGYKEEEEVYILHSYWYKELSNKKQIEP\n-SFSYDPNVKI\n->sp|Q13685|AAMP_HUMAN Angio-associated migratory cell protein OS=Homo sapiens GN=AAMP PE=1 SV=2\n-MESESESGAAADTPPLETLSFHGDEEIIEVVELDPGPPDPDDLAQEMEDVDFEEEEEEEG\n-NEEGWVLEPQEGVVGSMEGPDDSEVTFALHSASVFCVSLDPKTNTLAVTGGEDDKAFVWR\n-LSDGELLFECAGHKDSVTCAGFSHDSTLVATGDMSGLLKVWQVDTKEEVWSFEAGDLEWM\n-EWHPRAPVLLAGTADGNTWMWKVPNGDCKTFQGPNCPATCGRVLPDGKRAVVGYEDGTIR\n-IWDLKQGSPIHVLKGTEGHQGPLTCVAANQDGSLILTGSVDCQAKLVSATTGKVVGVFRP\n-ETVASQPSLGEGEESESNSVESLGFCSVMPLAAVGYLDGTLAIYDLATQTLRHQCQHQSG\n-IVQLLWEAGTAVVYTCSLDGIVRLWDARTGRLLTDYRGHTAEILDFALSKDASLVVTTSG\n-DHKAKVFCVQRPDR\n' |
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| diff -r cd2a41c65447 -r fe94765e8814 test-data/test2_retrieve.gff --- a/test-data/test2_retrieve.gff Fri Oct 14 17:59:02 2016 -0400 +++ b/test-data/test2_retrieve.gff Mon Apr 10 13:19:36 2017 -0400 |
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| b'@@ -1,16 +1,7 @@\n ##gff-version 3\n ##sequence-region S0DS17 1 369\n-S0DS17\tUniProtKB\tChain\t1\t369\t.\t.\t.\tID=PRO_0000437163;Note=Cytochrome P450 momooxygenase apf8\t\n+S0DS17\tUniProtKB\tChain\t1\t369\t.\t.\t.\tID=PRO_0000437163;Note=Cytochrome P450 monooxygenase apf8\t\n S0DS17\tUniProtKB\tMetal binding\t303\t303\t.\t.\t.\tNote=Iron (heme axial ligand);Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P04798\t\n-##sequence-region M5BAG7 1 563\n-M5BAG7\tUniProtKB\tTransmembrane\t21\t43\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n-M5BAG7\tUniProtKB\tTransmembrane\t49\t71\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n-M5BAG7\tUniProtKB\tTransmembrane\t132\t153\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n-M5BAG7\tUniProtKB\tTransmembrane\t159\t181\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n-M5BAG7\tUniProtKB\tTransmembrane\t236\t259\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n-M5BAG7\tUniProtKB\tTransmembrane\t274\t296\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n-M5BAG7\tUniProtKB\tDomain\t20\t301\t.\t.\t.\tNote=ABC transmembrane type-1;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50929\t\n-M5BAG7\tUniProtKB\tDomain\t345\t559\t.\t.\t.\tNote=ABC transporter;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50893\t\n ##sequence-region A0A077Z587 1 772\n A0A077Z587\tUniProtKB\tTransmembrane\t593\t617\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n A0A077Z587\tUniProtKB\tTransmembrane\t637\t656\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n@@ -23,6 +14,54 @@\n A0A077ZFY8\tUniProtKB\tDomain\t1\t89\t.\t.\t.\tNote=Mur_ligase;Ontology_term=ECO:0000259;evidence=ECO:0000259|Pfam:PF01225\t\n A0A077ZFY8\tUniProtKB\tDomain\t96\t279\t.\t.\t.\tNote=Mur_ligase_M;Ontology_term=ECO:0000259;evidence=ECO:0000259|Pfam:PF08245\t\n A0A077ZFY8\tUniProtKB\tDomain\t300\t349\t.\t.\t.\tNote=Mur_ligase_C;Ontology_term=ECO:0000259;evidence=ECO:0000259|Pfam:PF02875\t\n+##sequence-region Q0P8A9 1 310\n+Q0P8A9\tUniProtKB\tTransmembrane\t55\t78\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+Q0P8A9\tUniProtKB\tTransmembrane\t99\t124\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+Q0P8A9\tUniProtKB\tTransmembrane\t136\t156\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+Q0P8A9\tUniProtKB\tTransmembrane\t195\t216\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+Q0P8A9\tUniProtKB\tTransmembrane\t244\t264\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+Q0P8A9\tUniProtKB\tDomain\t93\t274\t.\t.\t.\tNote=Ni_hydr_CYTB;Ontology_term=ECO:0000259;evidence=ECO:0000259|Pfam:PF01292\t\n+##sequence-region A0A077ZHN8 1 634\n+A0A077ZHN8\tUniProtKB\tTransmembrane\t14\t36\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+A0A077ZHN8\tUniProtKB\tTransmembrane\t56\t80\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+A0A077ZHN8\tUniProtKB\tTransmembrane\t113\t132\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+A0A077ZHN8\tUniProtKB\tTransmembrane\t290\t310\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+A0A077ZHN8\tUniProtKB\tDomain\t312\t364\t.\t.\t.\tNote=HAMP;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50885\t\n+A0A077ZHN8\tUniProtKB\tDomain\t369\t598\t.\t.\t.\tNote=Methyl-accepting transducer;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50111\t\n+A0A077ZHN8\tUniProtKB\tCoiled coil\t170\t204\t.\t.\t.\tOntology_term=ECO:0000256;evidence=ECO:0000256|SAM:Coils\t\n+A0A077ZHN8\tUniProtKB\tCoiled coil\t569\t607\t.\t.\t.\tOntology_term=ECO:0000256;evidence=ECO:0000256|SAM:Coils\t\n+##sequence-region M5BAG7 1 563\n+M5BAG7\tUniProtKB\tTransmembrane\t21\t43\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+M5BAG7\tUniProtKB\tTransmembrane\t49\t71\t.\t.\t.\tNote=Helical;Ont'..b'\t1\t778\t.\t.\t.\tID=PRO_0000075697;Note=Actin-binding LIM protein 1\t\n O14639\tUniProtKB\tDomain\t97\t156\t.\t.\t.\tNote=LIM zinc-binding 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00125\t\n@@ -62,40 +101,3 @@\n O14639\tUniProtKB\tSequence conflict\t532\t532\t.\t.\t.\tNote=A->R;Ontology_term=ECO:0000305;evidence=ECO:0000305\t\n O14639\tUniProtKB\tSequence conflict\t563\t563\t.\t.\t.\tNote=K->E;Ontology_term=ECO:0000305;evidence=ECO:0000305\t\n O14639\tUniProtKB\tSequence conflict\t578\t578\t.\t.\t.\tNote=V->I;Ontology_term=ECO:0000305;evidence=ECO:0000305\t\n-##sequence-region M5B8V9 1 582\n-M5B8V9\tUniProtKB\tTransmembrane\t20\t43\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n-M5B8V9\tUniProtKB\tTransmembrane\t55\t77\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n-M5B8V9\tUniProtKB\tTransmembrane\t134\t154\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n-M5B8V9\tUniProtKB\tTransmembrane\t161\t180\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n-M5B8V9\tUniProtKB\tTransmembrane\t236\t260\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n-M5B8V9\tUniProtKB\tDomain\t20\t302\t.\t.\t.\tNote=ABC transmembrane type-1;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50929\t\n-M5B8V9\tUniProtKB\tDomain\t340\t570\t.\t.\t.\tNote=ABC transporter;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50893\t\n-##sequence-region A0A077ZHN8 1 634\n-A0A077ZHN8\tUniProtKB\tTransmembrane\t14\t36\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n-A0A077ZHN8\tUniProtKB\tTransmembrane\t56\t80\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n-A0A077ZHN8\tUniProtKB\tTransmembrane\t113\t132\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n-A0A077ZHN8\tUniProtKB\tTransmembrane\t290\t310\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n-A0A077ZHN8\tUniProtKB\tDomain\t312\t364\t.\t.\t.\tNote=HAMP;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50885\t\n-A0A077ZHN8\tUniProtKB\tDomain\t369\t598\t.\t.\t.\tNote=Methyl-accepting transducer;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50111\t\n-A0A077ZHN8\tUniProtKB\tCoiled coil\t170\t204\t.\t.\t.\tOntology_term=ECO:0000256;evidence=ECO:0000256|SAM:Coils\t\n-A0A077ZHN8\tUniProtKB\tCoiled coil\t569\t607\t.\t.\t.\tOntology_term=ECO:0000256;evidence=ECO:0000256|SAM:Coils\t\n-##sequence-region Q0P8A9 1 310\n-Q0P8A9\tUniProtKB\tTransmembrane\t55\t78\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n-Q0P8A9\tUniProtKB\tTransmembrane\t99\t124\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n-Q0P8A9\tUniProtKB\tTransmembrane\t136\t156\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n-Q0P8A9\tUniProtKB\tTransmembrane\t195\t216\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n-Q0P8A9\tUniProtKB\tTransmembrane\t244\t264\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n-Q0P8A9\tUniProtKB\tDomain\t93\t274\t.\t.\t.\tNote=Ni_hydr_CYTB;Ontology_term=ECO:0000259;evidence=ECO:0000259|Pfam:PF01292\t\n-##sequence-region Q13685 1 434\n-Q13685\tUniProtKB\tChain\t1\t434\t.\t.\t.\tID=PRO_0000050832;Note=Angio-associated migratory cell protein\t\n-Q13685\tUniProtKB\tRepeat\t89\t129\t.\t.\t.\tNote=WD 1\t\n-Q13685\tUniProtKB\tRepeat\t132\t171\t.\t.\t.\tNote=WD 2\t\n-Q13685\tUniProtKB\tRepeat\t173\t212\t.\t.\t.\tNote=WD 3\t\n-Q13685\tUniProtKB\tRepeat\t214\t254\t.\t.\t.\tNote=WD 4\t\n-Q13685\tUniProtKB\tRepeat\t258\t299\t.\t.\t.\tNote=WD 5\t\n-Q13685\tUniProtKB\tRepeat\t315\t354\t.\t.\t.\tNote=WD 6\t\n-Q13685\tUniProtKB\tRepeat\t356\t395\t.\t.\t.\tNote=WD 7\t\n-Q13685\tUniProtKB\tRepeat\t398\t433\t.\t.\t.\tNote=WD 8\t\n-Q13685\tUniProtKB\tCompositional bias\t53\t59\t.\t.\t.\tNote=Poly-Glu\t\n-Q13685\tUniProtKB\tModified residue\t20\t20\t.\t.\t.\tNote=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24275569;Dbxref=PMID:24275569\t\n-Q13685\tUniProtKB\tNatural variant\t250\t250\t.\t.\t.\tID=VAR_037061;Note=I->V;Dbxref=dbSNP:rs2305835\t\n' |
| b |
| diff -r cd2a41c65447 -r fe94765e8814 tool_dependencies.xml --- a/tool_dependencies.xml Fri Oct 14 17:59:02 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="requests" version="2.7"> - <repository changeset_revision="7e330b122c8c" name="package_python_2_7_requests_2_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |
| b |
| diff -r cd2a41c65447 -r fe94765e8814 uniprot.xml --- a/uniprot.xml Fri Oct 14 17:59:02 2016 -0400 +++ b/uniprot.xml Mon Apr 10 13:19:36 2017 -0400 |
| [ |
| @@ -6,14 +6,8 @@ <requirements> <requirement type="package" version="2.7">requests</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[ + <command detect_errors="aggressive"><![CDATA[ cut -f ${id_column} $infile > id_file.tabular && @@ -237,14 +231,14 @@ <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"/> + <output name="outfile_retrieve_fasta" file="test1_retrieve.fasta" ftype="fasta" compare="sim_size" /> </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"/> + <output name="outfile_retrieve_gff" file="test2_retrieve.gff" ftype="gff" compare="sim_size" /> </test> <test> <param name="infile" value="id_uniprot.tab" ftype="tabular"/> |