changeset 0:48522382b6a4 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 2b8ad1bbfe098129ae32cd8311a755dff58ae97b-dirty
author bgruening
date Fri, 09 Oct 2015 16:42:22 -0400
parents
children cd2a41c65447
files 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 tool_dependencies.xml.orig uniprot.py uniprot.xml
diffstat 11 files changed, 907 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Oct 09 16:42:22 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	Fri Oct 09 16:42:22 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	Fri Oct 09 16:42:22 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	Fri Oct 09 16:42:22 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	Fri Oct 09 16:42:22 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	Fri Oct 09 16:42:22 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	Fri Oct 09 16:42:22 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	Fri Oct 09 16:42:22 2015 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="requests" version="2.7">
+        <repository changeset_revision="ad6b0c21d92b" name="package_python_2_7_requests_2_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml.orig	Fri Oct 09 16:42:22 2015 -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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/uniprot.py	Fri Oct 09 16:42:22 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	Fri Oct 09 16:42:22 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">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[
+
+        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>