Mercurial > repos > bgruening > uniprot_rest_interface

changeset 2:4a416eb3bfcf draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 074fed99c6df6bad17341bbfa57645f222907ad4
author bgruening
date Mon, 10 Apr 2017 13:19:09 -0400
parents 357dc1f016f5
children 61de5acfdd33
files test-data/test1_retrieve.fasta test-data/test2_retrieve.gff tool_dependencies.xml tool_dependencies.xml.orig uniprot.xml
diffstat 5 files changed, 135 insertions(+), 134 deletions(-) [+]
line wrap: on
line diff
--- a/test-data/test1_retrieve.fasta	Fri Oct 14 15:42:50 2016 -0400
+++ b/test-data/test1_retrieve.fasta	Mon Apr 10 13:19:09 2017 -0400
@@ -1,36 +1,12 @@
->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
-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=4 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
+>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
 >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
 MGGLAMLARQLGHEVTGSDANVYPPMSTLLEKQGIELIQGYDASQLDPQPDLVIIGNAMT
 RGNPCVEAVLEKNIPYMSGPQWLHDFVLRDRWVLAVAGTHGKTTTAGMATWILEQCGYKP
@@ -49,6 +25,69 @@
 ENGEIQYPVSEITIAVSSLVFSSASFAADLEDNMETLNDNLKVVEKADNAAQVKDALTKM
 RAAALDAQKATPPKLEGKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQ
 LKTTRNAYHQKYR
+>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|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
+>sp|S0DS17|APF8_GIBF5 Cytochrome P450 monooxygenase apf8 OS=Gibberella fujikuroi (strain CBS 195.34 / IMI 58289 / NRRL A-6831) GN=apf8 PE=1 SV=1
+MSYQSILLRQVNSLCDNLEEVARDENGGLIDMAMQSDYFTFDVMSEVIFGMAYNALKDTS
+YRFVTGALGSSNIRIGTLVQSPLPAMCRIDKYLFPESIQGRNKFLGFIGSLLRDRSKASF
+AGNGNVFSFLETAKDPDGGNQLSKSEIRAECATLVAAGTDTSSSTLAATLFYLSRNSKCY
+SRVSEEVRNAFSSHQDIKIGPELNSCVYLRACIEETLRMSPPVGAALWREIGPGGMNIGP
+LTLPAGVDVGTGIYSLHHNAAYHPEPFKYLPERWLVGEGSSTSESVELARSAFAPFSRGP
+RSCVGKGFAYHELTLTIAHILHRFDFSATEEDFALRHGSEGPGGINEFLLHDHVTGARSG
+PLLQFSMRR
+>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
+MKPLDPRLLRHSASARTMLAVGAVVSVVQTAALVAFCWSLTQLVVRAIGGADQAALAPVL
+ALAVGSAVVRGAAAWLLDVTGARGAARVTAELRRRALRAIADLGPAWTAARSRGRLATIV
+GPGLDALDPYFARYVPQLILTALATPIVVAVLLLSDPLTGVTVLVTLPVIPVFMVLVGWA
+TQEVQRRQWSRLTELASSFLEVVDGLSTLLVFRRARRQTARIRRVTEEYRVETMRVLRIS
+FLSGFVLELAASLSVALVAVSVGVRLIGGQLDLEVGLFVLLLAPEAFLPIRQVGVQFHAA
+AEGVAAADDVLGILEEERAARATRPVPGPATATPPAGDALVIRDLAVARGDRAVLSGVSA
+RFPRGRVTAVTGPSGVGKSSLLGAMLGHLPAGGAAGWIDDDASSLRPPVPTEIAWAGQRP
+GLVAGTVRENVALGVADPDDALVRRALALAAADGIDPDLVLGVGGQGLSGGQAQRVAVAR
+AVHRALALDCPLVLLDEPSSALDAATEERLAAGIRALADQGRAVVVVTHRGALVRAADAE
+LRLGGASGEDDAPAAVGSSVGAGRVAPARIAPEPAWRAQVAP
+>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
+MNRDGVLRLAQPPTRRTLPGLLAGLASAVGAVALLATSAWLITRASEQPPILFLGMAIVG
+VRAFALGRAAFRYLERITSHDAAFRALATLRVGVFERLLPFAPAGLRDTRRGDLLARLVG
+DVDRLQDLPLRVVQPLAVSVVVQAASVAVVGAVLPAAGIALAVVLGVALVVGIGATTALA
+GRAETRIAPLRARLQDLVLDFVGGLDVLTSFGAVDDRLAAIDRAATELRRAELRSAAAAG
+VTTGVVLAGTGAVAGWTVLQGVPGLASGTLDPAWLALAALVPLALVEQATAVPLAVQAWR
+RVRTSAERVAGVVPETVPDEIPREPDDAADAQPVTADASPAGTTLEVRDLVTRWPGADED
+ALAPVSLVVRPGETVVVRGPSGSGKSSLAAALARFLESRGAYELDGRDARSMPPSAVRRI
+VGLCEQAPHLFDASIRQNLLFARDDATDDELVAVLARVGLADWTAGRGGLDARVGDRGGL
+VSGGQAQRIALARALLADFPVLVLDEPTADVDAERARAVLRDVLTAARDRGPGVLLLTHT
+DVPHDLVDRTVELRVAGDRVRTE
+>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
+MRKVFVTLLLSVVSLFAYGSERMGQDTQIWDFHRITNIPNYDTFGKLWTTLQGEYIATIA
+LIAVIAVLSAFALHYMVIGPKQFSHDGKKIYAFTLFERLFHFIAAISWVILVPTGFVMMF
+GEVFGGGVFVRVCKNLHAFATILFIISIIPMFLCWIKRMLPASYDIRWMMIVGGYLSKIK
+RPVPAGKFNFGQKSWYYIAVFGGFLMIITGGFMYFLDFNSTAIQGLFGLTQIELLRISAI
+VHNFLGIVCAVFFGVHIYMAVFAIKGSIHSMISGYKEEEEVYILHSYWYKELSNKKQIEP
+SFSYDPNVKI
 >sp|O14639|ABLM1_HUMAN Actin-binding LIM protein 1 OS=Homo sapiens GN=ABLIM1 PE=1 SV=3
 MPAFLGLKCLGKLCSSEKSKVTSSERTSARGSNRKRLIVEDRRVSGTSFTAHRRATITHL
 LYLCPKDYCPRGRVCNSVDPFVAHPQDPHHPSEKPVIHCHKCGEPCKGEVLRVQTKHFHI
@@ -63,42 +102,3 @@
 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=4 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 ATCC 700819 / 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
--- a/test-data/test2_retrieve.gff	Fri Oct 14 15:42:50 2016 -0400
+++ b/test-data/test2_retrieve.gff	Mon Apr 10 13:19:09 2017 -0400
@@ -1,16 +1,7 @@
 ##gff-version 3
 ##sequence-region S0DS17 1 369
-S0DS17	UniProtKB	Chain	1	369	.	.	.	ID=PRO_0000437163;Note=Cytochrome P450 momooxygenase apf8	
+S0DS17	UniProtKB	Chain	1	369	.	.	.	ID=PRO_0000437163;Note=Cytochrome P450 monooxygenase apf8	
 S0DS17	UniProtKB	Metal binding	303	303	.	.	.	Note=Iron (heme axial ligand);Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P04798	
-##sequence-region M5BAG7 1 563
-M5BAG7	UniProtKB	Transmembrane	21	43	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
-M5BAG7	UniProtKB	Transmembrane	49	71	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
-M5BAG7	UniProtKB	Transmembrane	132	153	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
-M5BAG7	UniProtKB	Transmembrane	159	181	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
-M5BAG7	UniProtKB	Transmembrane	236	259	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
-M5BAG7	UniProtKB	Transmembrane	274	296	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
-M5BAG7	UniProtKB	Domain	20	301	.	.	.	Note=ABC transmembrane type-1;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50929	
-M5BAG7	UniProtKB	Domain	345	559	.	.	.	Note=ABC transporter;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50893	
 ##sequence-region A0A077Z587 1 772
 A0A077Z587	UniProtKB	Transmembrane	593	617	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
 A0A077Z587	UniProtKB	Transmembrane	637	656	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
@@ -23,6 +14,54 @@
 A0A077ZFY8	UniProtKB	Domain	1	89	.	.	.	Note=Mur_ligase;Ontology_term=ECO:0000259;evidence=ECO:0000259|Pfam:PF01225	
 A0A077ZFY8	UniProtKB	Domain	96	279	.	.	.	Note=Mur_ligase_M;Ontology_term=ECO:0000259;evidence=ECO:0000259|Pfam:PF08245	
 A0A077ZFY8	UniProtKB	Domain	300	349	.	.	.	Note=Mur_ligase_C;Ontology_term=ECO:0000259;evidence=ECO:0000259|Pfam:PF02875	
+##sequence-region Q0P8A9 1 310
+Q0P8A9	UniProtKB	Transmembrane	55	78	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
+Q0P8A9	UniProtKB	Transmembrane	99	124	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
+Q0P8A9	UniProtKB	Transmembrane	136	156	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
+Q0P8A9	UniProtKB	Transmembrane	195	216	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
+Q0P8A9	UniProtKB	Transmembrane	244	264	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
+Q0P8A9	UniProtKB	Domain	93	274	.	.	.	Note=Ni_hydr_CYTB;Ontology_term=ECO:0000259;evidence=ECO:0000259|Pfam:PF01292	
+##sequence-region A0A077ZHN8 1 634
+A0A077ZHN8	UniProtKB	Transmembrane	14	36	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
+A0A077ZHN8	UniProtKB	Transmembrane	56	80	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
+A0A077ZHN8	UniProtKB	Transmembrane	113	132	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
+A0A077ZHN8	UniProtKB	Transmembrane	290	310	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
+A0A077ZHN8	UniProtKB	Domain	312	364	.	.	.	Note=HAMP;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50885	
+A0A077ZHN8	UniProtKB	Domain	369	598	.	.	.	Note=Methyl-accepting transducer;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50111	
+A0A077ZHN8	UniProtKB	Coiled coil	170	204	.	.	.	Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Coils	
+A0A077ZHN8	UniProtKB	Coiled coil	569	607	.	.	.	Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Coils	
+##sequence-region M5BAG7 1 563
+M5BAG7	UniProtKB	Transmembrane	21	43	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
+M5BAG7	UniProtKB	Transmembrane	49	71	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
+M5BAG7	UniProtKB	Transmembrane	132	153	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
+M5BAG7	UniProtKB	Transmembrane	159	181	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
+M5BAG7	UniProtKB	Transmembrane	236	259	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
+M5BAG7	UniProtKB	Transmembrane	274	296	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
+M5BAG7	UniProtKB	Domain	20	301	.	.	.	Note=ABC transmembrane type-1;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50929	
+M5BAG7	UniProtKB	Domain	345	559	.	.	.	Note=ABC transporter;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50893	
+M5BAG7	UniProtKB	Nucleotide binding	379	386	.	.	.	Note=ATP;Ontology_term=ECO:0000256;evidence=ECO:0000256|PROSITE-ProRule:PRU00434	
+##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;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24275569;Dbxref=PMID:24275569	
+Q13685	UniProtKB	Natural variant	250	250	.	.	.	ID=VAR_037061;Note=I->V;Dbxref=dbSNP:rs2305835	
+##sequence-region M5B8V9 1 582
+M5B8V9	UniProtKB	Transmembrane	20	43	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
+M5B8V9	UniProtKB	Transmembrane	55	77	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
+M5B8V9	UniProtKB	Transmembrane	134	154	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
+M5B8V9	UniProtKB	Transmembrane	161	180	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
+M5B8V9	UniProtKB	Transmembrane	236	260	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
+M5B8V9	UniProtKB	Domain	20	302	.	.	.	Note=ABC transmembrane type-1;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50929	
+M5B8V9	UniProtKB	Domain	340	570	.	.	.	Note=ABC transporter;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50893	
+M5B8V9	UniProtKB	Nucleotide binding	372	379	.	.	.	Note=ATP;Ontology_term=ECO:0000256;evidence=ECO:0000256|PROSITE-ProRule:PRU00434	
 ##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;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00125	
@@ -62,40 +101,3 @@
 O14639	UniProtKB	Sequence conflict	532	532	.	.	.	Note=A->R;Ontology_term=ECO:0000305;evidence=ECO:0000305	
 O14639	UniProtKB	Sequence conflict	563	563	.	.	.	Note=K->E;Ontology_term=ECO:0000305;evidence=ECO:0000305	
 O14639	UniProtKB	Sequence conflict	578	578	.	.	.	Note=V->I;Ontology_term=ECO:0000305;evidence=ECO:0000305	
-##sequence-region M5B8V9 1 582
-M5B8V9	UniProtKB	Transmembrane	20	43	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
-M5B8V9	UniProtKB	Transmembrane	55	77	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
-M5B8V9	UniProtKB	Transmembrane	134	154	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
-M5B8V9	UniProtKB	Transmembrane	161	180	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
-M5B8V9	UniProtKB	Transmembrane	236	260	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
-M5B8V9	UniProtKB	Domain	20	302	.	.	.	Note=ABC transmembrane type-1;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50929	
-M5B8V9	UniProtKB	Domain	340	570	.	.	.	Note=ABC transporter;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50893	
-##sequence-region A0A077ZHN8 1 634
-A0A077ZHN8	UniProtKB	Transmembrane	14	36	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
-A0A077ZHN8	UniProtKB	Transmembrane	56	80	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
-A0A077ZHN8	UniProtKB	Transmembrane	113	132	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
-A0A077ZHN8	UniProtKB	Transmembrane	290	310	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
-A0A077ZHN8	UniProtKB	Domain	312	364	.	.	.	Note=HAMP;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50885	
-A0A077ZHN8	UniProtKB	Domain	369	598	.	.	.	Note=Methyl-accepting transducer;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50111	
-A0A077ZHN8	UniProtKB	Coiled coil	170	204	.	.	.	Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Coils	
-A0A077ZHN8	UniProtKB	Coiled coil	569	607	.	.	.	Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Coils	
-##sequence-region Q0P8A9 1 310
-Q0P8A9	UniProtKB	Transmembrane	55	78	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
-Q0P8A9	UniProtKB	Transmembrane	99	124	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
-Q0P8A9	UniProtKB	Transmembrane	136	156	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
-Q0P8A9	UniProtKB	Transmembrane	195	216	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
-Q0P8A9	UniProtKB	Transmembrane	244	264	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
-Q0P8A9	UniProtKB	Domain	93	274	.	.	.	Note=Ni_hydr_CYTB;Ontology_term=ECO:0000259;evidence=ECO:0000259|Pfam:PF01292	
-##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;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24275569;Dbxref=PMID:24275569	
-Q13685	UniProtKB	Natural variant	250	250	.	.	.	ID=VAR_037061;Note=I->V;Dbxref=dbSNP:rs2305835	
--- a/tool_dependencies.xml	Fri Oct 14 15:42:50 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="requests" version="2.7">
-        <repository changeset_revision="3b91ce908441" name="package_python_2_7_requests_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/tool_dependencies.xml.orig	Mon Apr 10 13:19:09 2017 -0400
@@ -0,0 +1,11 @@
+<?xml version="1.0"?>
+<tool_dependency>
+<<<<<<< HEAD:tools/uniprot_id_mapping/tool_dependencies.xml
+    <package name="requests" version="2.7">
+        <repository name="package_requests_2_7" owner="iuc" />
+=======
+    <package name="request" version="2.7">
+        <repository name="package_python_2_7_request_2_7" owner="iuc" />
+>>>>>>> dc07b37de57cdd358da4ecabd9558736d5b80f97:tools/uniprot_rest_interface/tool_dependencies.xml
+    </package>
+</tool_dependency>
--- a/uniprot.xml	Fri Oct 14 15:42:50 2016 -0400
+++ b/uniprot.xml	Mon Apr 10 13:19:09 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"/>