# HG changeset patch # User greg # Date 1509371626 14400 # Node ID a7867769a70617d1a2437810b771d98ae8047b4c # Parent 34ca28db0a5d55515012958fc31c7f78c1603d44 Uploaded diff -r 34ca28db0a5d -r a7867769a706 gene_family_phylogeny_builder.xml --- a/gene_family_phylogeny_builder.xml Wed Aug 30 13:11:48 2017 -0400 +++ b/gene_family_phylogeny_builder.xml Mon Oct 30 09:53:46 2017 -0400 @@ -1,13 +1,17 @@ - + builds phylogenetic trees of aligned orthologous gene family clusters macros.xml - + + plant_tribes_gene_family_phylogeny_builder + proc.log ]]> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + @@ -137,10 +81,17 @@ - This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary @@ -152,17 +103,17 @@ **Required options** * **Orthogroup alignments** - orthogroup alignment fasta files produced by the GeneFamilyAligner tool selected from your history. Depending on how the GeneFamilyAligner tool was executed, these could either be pre-processed alignments, trimmed alignments or both trimmed and filtered alignments. - * **Gene family scaffold** - one of the PlantTribes gene family scaffolds installed into Galaxy by the PlantTribes Scaffold Download Data Manager tool. - * **Protein clustering method** - gene family scaffold protein clustering method as described in the AssemblyPostProcessor tool. * **Phylogenetic inference method** - method for estimating orthogroup maximum likelihood (ML) phylogenetic trees. PlantTribes estimates ML phylogenetic trees using either RAxML or FastTree algorithms. + - **Gene family scaffold** - one of the PlantTribes gene family scaffolds installed into Galaxy by the PlantTribes Scaffold Download Data Manager tool. This is used only if RAxML is selected as the phylogenetic inference method. + - **Protein clustering method** - gene family scaffold protein clustering method as described in the AssemblyPostProcessor tool. This is used only if RAxML is selected as the phylogenetic inference method. + **Other options** * **Rooting order configuration** - select 'Yes' to enable selection of a rooting order configuration file for RAxML. Scaffold configuration templates (.rootingOrder.config) of how to customize the RAxML ML tree rooting order can be found in the scaffold data installed into Galaxy via the PlantTribes Scaffolds Download Data Manager tool, and is also available at the PlantTribes GitHub `repository`_. Phylogenetic tree rooting order settings shown in these templates are used as defaults if 'No' is selected. * **Bootstrap replicates** - number of bootstrap replicates for RAxML to conduct a rapid bootstrap analysis and search for the best-scoring ML tree (default = 100). * **Maximum orthogroup size** - maximum number of sequences allowed in orthogroup alignments (default = 100). * **Minimum orthogroup size** - minimum number of sequences allowed in orthogroup alignments (default = 4). - * **Output additional directory of phylogenetic tree files** - selecting 'Yes' will produce an additional output that has an associated directory of files that are copies of the elements of the phylogenetic trees output dataset collection (this output will be used for future downstream tools). .. _repository: https://github.com/dePamphilis/PlantTribes/tree/master/config diff -r 34ca28db0a5d -r a7867769a706 macros.xml --- a/macros.xml Wed Aug 30 13:11:48 2017 -0400 +++ b/macros.xml Mon Oct 30 09:53:46 2017 -0400 @@ -1,47 +1,6 @@ 1.0 - - - plant_tribes_assembly_post_processor - - - - - plant_tribes_gene_family_aligner - - - - - plant_tribes_gene_family_classifier - - - - - plant_tribes_gene_family_integrator - - - - - plant_tribes_kaks_analysis - - - - - r-optparse - - - - - plant_tribes_gene_family_phylogeny_builder - - - - - - - - @@ -49,74 +8,12 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @misc{None, diff -r 34ca28db0a5d -r a7867769a706 plant_tribes_scaffolds.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plant_tribes_scaffolds.loc Mon Oct 30 09:53:46 2017 -0400 @@ -0,0 +1,3 @@ +## Plant Tribes scaffolds +#Value Name Path Description +22Gv1.1 22Gv1.1 ${__HERE__}/test-data/tool-data/plant_tribes/scaffolds/22Gv1.1 22 plant genomes (Angiosperms clusters, version 1.1; 22Gv1.1) diff -r 34ca28db0a5d -r a7867769a706 test-data/3722.faa.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3722.faa.aln Mon Oct 30 09:53:46 2017 -0400 @@ -0,0 +1,312 @@ +>gnl_Glyma1.01_PACid_16266208 +---MANE-------------------------------------------------GKKS +NNFYSILGLSKECTELELKNAYRKLAKKWHPDRCSATG---NLELVEEAKKKFQEIREAY +S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSHTKSNENG +--EESFEELQ------QLFEDMFQADI--GL----------DGGPSL------------- +----ASSDSSTSSA------------------YMTYSESSS---------SNKRNSS-EM +NFGK---AENSSVFDASY------QNFCFG-VN--QLQDIKKGK---GGILGGGGRSRHR +SGRKQKMFY-GHDV-------------------------- +>gnl_Glyma1.01_PACid_16266209 +---MANE-------------------------------------------------GKKS +NNFYSILGLSKECTELELKNAYRKLAKKWHPDRCSATG---NLELVEEAKKKFQEIREAY +S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSHTKSNENG +--EESFEELQ------QLFEDMFQADI--GL----------DGGPSL------------- +----ASSDSSTSSA------------------YMTYSESSS---------SNKRNSS-EM +NFGK---AENSSVFDASY------QNFCFG-TG--EPTPRYKEG--------KGGNSRRR +R--------------------------------------- +>gnl_Glyma1.01_PACid_16266210 +---MANE-------------------------------------------------GKKS +NNFYSILGLSKECTELELKNAYRKLAKKWHPDRCSATG---NLELVEEAKKKFQEIREAY +S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSHTKSNENG +--EESFEELQ------QLFEDMFQADI--GL----------DGGPSL------------- +----ASSDSSTSSA------------------YMTYSESSS---------SNKRNSS-EM +NFGK---AENSSVFDASY------QNFCFG-VG--HVNYHYQ------------------ +---------------------------------------- +>gnl_Glyma1.01_PACid_16301083 +---MADE-------------------------------------------------GNKS +NNFYSILGLKKECTELELKNAYRKLAKKWHPDRCSATG---NSELVEEAKKKFQEIREAY +S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSQTKSNENG +--EESFEELQ------QLFEDMFEADI--GL----------DGGPSL------------- +----ASSDCSTSSA------------------YMTYSESSS---------SNKHNSS-EM +NFGK---AENSSVFDAGY------QNFCFG-VN--QLQDIKKKK---GGIL-GGGRSRHR +NGRKQNMSY-GHDVSSNDYPGISTK--------------- +>gnl_Glyma1.01_PACid_16301085 +---MADE-------------------------------------------------GNKS +NNFYSILGLKKECTELELKNAYRKLAKKWHPDRCSATG---NSELVEEAKKKFQEIREAY +S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSQTKSNENG +--EESFEELQ------QLFEDMFEADI--GL----------DGGPSL------------- +----ASSDCSTSSA------------------YMTYSESSS---------SNKHNSS-EM +NFGK---AENSSVFDAGY------QNFCFG-VG--HVNYHYQ------------------ +---------------------------------------- +>gnl_Glyma1.01_PACid_16301084 +---MADE-------------------------------------------------GNKS +NNFYSILGLKKECTELELKNAYRKLAKKWHPDRCSATG---NSELVEEAKKKFQEIREAY +S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSQTKSNENG +--EESFEELQ------QLFEDMFEADI--GL----------DGGPSL------------- +----ASSDCSTSSA------------------YMTYSESSS---------SNKHNSS-EM +NFGK---AENSSVFDAGY------QNFCFG-TG--EPTPRYKEE--------KGGNSRRR +---------------------------------------- +>gnl_Medtr3.5_Medtr8g022310.1 +---MANE-------------------------------------------------GNKS +NDFYAVLGLNKECSDSELRNAYKKLALKWHPDRCSASG---NVKFVEEAKKKFQAIQEAY +S------VLSDSNKRLMYDVGVYDS--------DDDENGMGDFLNEMVTMMSQTKSNENG +--EESFEELQ------QLFDDMFQADI--GL----------NGSTSL------------- +----NASGCSTSST------------------FMTFSESSN---------SNKRNST-QM +NFGK---AEDSSSFGANY------QNFCFG-MK--HLQEDVEKE--KGGILEGGGSKKQR +KGRKQKISC-GH-VSSNDHPGISAN--------------- +>gnl_Medtr3.5_Medtr8g022310.2 +---MANE-------------------------------------------------GNKS +NDFYAVLGLNKECSDSELRNAYKKLALKWHPDRCSASG---NVKFVEEAKKKFQAIQEAY +S------VLSDSNKRLMYDVGVYDS--------DDDENGMGDFLNEMVTMMSQTKSNENG +--EESFEELQ------QLFDDMFQADI--GL----------NGSTSL------------- +----NASGCSTSST------------------FMTFSESSN---------SNKRNST-QM +NFGK---AEDSSSFGANY------QNFCFG-VN--LVNYHYQ------------------ +---------------------------------------- +>gnl_Musac1.0_GSMUA_Achr6T31040_001 +---MAAE-------------------------------------------------EDKS +GDFYAVLGLRKECSETELRNAYKKLAMRWHPDKCLASG---NAQIVGEAKEKFQEIQKAY +S------VLSDSNKRFLYDVGVYDND------DDNDENGMGDFIGEMLEMMSQTKPNENS +--QDSFQELQ------ELFVEMFQDDL--DAG---------FGGSIFH-DCPWAQP---- +---TNGQDCWTSSG------------------LHFANGRSK--------CGNKRGNS-AV +NLGK----VNLEELEHGT------SDFYFG-LN--DAAQPSQGKGGS--------NNKRR +NGRKQKVSS-NHDVSS------------------------ +>gnl_Musac1.0_GSMUA_Achr9T18140_001 +---MAAG-------------------------------------------------EEKI +GDFYTVLGLRKECSEAELRIAYKKLAMRWHPDKCSASG---NHRRMEEAKEKFQEIQKAY +S------VLSDSSKRFLYDVGIYDNE------DDNDEKGMGDFIGEIAQMMSQTKSGENG +--HDSFEELQ------RMFLDMFQDDL--DAG---------FGDSSIH-SGPQARP---- +---TDGLNCSMPSG------------------LQFADGGNN--------GSNKRGNS-EK +--------AKLDGLENSS------TGFCFG-LN--DAGQSSKGKGSA--------NSKRR +NGRKQKVSS-KHDVSSSD-AEVSF---------------- +>gnl_Musac1.0_GSMUA_Achr8T23700_001 +---MASD-------------------------------------------------MDAS +GDFYSVLGLKKECSEAELRNAYKKLALKWHPDKCSASG---NEIRMKEAKQQFQEIQKAY +S------VLSDSNKRFLYDVGAYDKD------DDKDEEGMVEFLGEMAQMMRQTKCCGSG +--QESFEQLQ------QMFVEMFHDDL--DAG---------F------------------ +--------CGHSSA---------------------TSGAAS--------CGNKRDNS-AM +DSGK----RKPDELDPAA------IGFCLG-TK--DAGQSSKGRGS---------NSKRR +NRRKQKASS-KHDNSSHN-AKVSA---------------- +>gnl_Musac1.0_GSMUA_AchrUn_randomT02210_001 +---MEGD-------------------------------------------------EEKS +GDFYAVLGLKKEGSMAELKNAYKKLAMKWHPDKCPASG---NKIRMDKAKEKFQEIQKAY +S------VLSDSNKRFLYDVGVYDKD------DEEDEEGMGDFIGEIAQMMSQSKPSGSG +--HESLEELH------RQVVEMFLDEL--DAGD-------RFSSANQ------------- +----GASSCDGRDD----------------------------------GGGNKRGNW-AV +DWGK----EKLNELGPGT------GGFCFG-VS------------------------RRV +HSFDLMIDV-VHLIHSDL-------------------TLE +>gnl_Orysa6.0_PACid_16843526 +---MADGG-------------------------------------EKC-RDAAG-EGGGG +GDLYAVLGLKKECSDADLKLAYRKLAMRWHPDKCSSSS---SAKHMEEAKEKFQEIQGAY +S------VLSDSNKRFLYDVGVYDDDD----NDDDNLQGMGDFIGEMAQMMSQARPTR-- +--QESFKELQ------QLFVDMFQADL--DSG---------FCNGPSKCYHTQAQSQTRT +SSTSPSMSPSPPPP------------------VATEAESPS------CNGINKRGSS-AM +DSGK-PPRASEVGSGQSQ------SGFCFG-KS--DAKQAAKTRSGNT-------ASRRR +NGRKQKVSS-KHDVSSEDEMPGSQW-----------HGVA +>gnl_Orysa6.0_PACid_16843528 +---MADGG-------------------------------------EKC-RDAAG-EGGGG +GDLYAVLGLKKECSDADLKLAYRKLAMRWHPDKCSSSS---SAKHMEEAKEKFQEIQGAY +S------VLSDSNKRFLYDVGVYDDDD----NDDDNLQGMGDFIGEMAQMMSQARPTR-- +--QESFKELQ------QLFVDMFQADL--DSG---------FCNGPSKCYHTQAQSQTRT +SSTSPSMSPSPPPP------------------VATEAESPS------CNGINKRGSS-AM +DSGK-PPRASEVGSGQSQ------SGFCFGQKS--DAKQAAKTRSGNT-------ASRRR +NGRKQKVSS-KHDVSSEDEMPGSQW-----------HGVA +>gnl_Poptr2.2_PACid_18217800 +---MANGGE----------------------------------------------DKWKS +NDLYQVLGLNKECTDTELRSAYKKLALRWHPDRCSASG---NSKFVEEAKKKFQAIQQAY +S------VLSDTNKRFLYDVGVDDS--------DDDENGMGDFLNEMAVMMSQTKPSENM +--EESLEELQ------ELFDEMFQEDL--HS----------FGIDSQ------------- +----AAPSC--PPS------------------YVSYSESSN--------SNNKRVSA-DM +NLGK-TKVDDSSSFNSHF------EKFCLG-T-----------GGTAATFQEGEGGSKRR +NSRRSQRQT-KARQETKSFFGL------------------ +>gnl_Poptr2.2_PACid_18234651 +---MENGGE----------------------------------------------EKGKS +NDFYQVLGLNKDCTATELRNAYKKLALKWHPDRCSASE---NSRFVDEAKKKFQTIQQAY +S------VLSDTNKRFLYDVGVYDS--------EDDENGMGGFMNEMAAMMSQTKPHENV +--EESFEELQ------GLFEEMFQEDL--DS----------FGIACQ------------- +----ATT-------------------------CVSYSESSN--------SNDKRVSV-DM +NLKK-TKVDDSSGFNSHV------EKFCLG-V-----------SGTPAIFQEGE-GSKRR +SSRRNRR--------------------------------- +>gnl_Poptr2.2_PACid_18234649 +MLRMENGGE----------------------------------------------EKGKS +NDFYQVLGLNKDCTATELRNAYKKLALKWHPDRCSASE---NSRFVDEAKKKFQTIQQAY +S------VLSDTNKRFLYDVGVYDS--------EDDENGMGGFMNEMAAMMSQTKPHENV +--EESFEELQ------GLFEEMFQEDL--DS----------FGIACQ------------- +----ATT-------------------------CVSYSESSN--------SNDKRVSV-DM +NLKK-TKVDDSSGFNSHV------EKFCLG-VE--HQQSFKKGKGVRGGVQGGT-GGRER +KGRKQEVSS-GYDVSSHD-HGISAS--------------- +>gnl_Poptr2.2_PACid_18234650 +---MENGGE----------------------------------------------EKGKS +NDFYQVLGLNKDCTATELRNAYKKLALKWHPDRCSASE---NSRFVDEAKKKFQTIQQAY +S------VLSDTNKRFLYDVGVYDS--------EDDENGMGGFMNEMAAMMSQTKPHENV +--EESFEELQ------GLFEEMFQEDL--DS----------FGIACQ------------- +----ATT-------------------------CVSYSESSN--------SNDKRVSV-DM +NLKK-TKVDDSSGFNSHV------EKFCLG-VE--HQQSFKKGKGVRGGVQGGT-GGRER +KGRKQEVSS-GYDVSSHD-HGISAS--------------- +>gnl_Soltu3.4_PGSC0003DMP400016105 +---M-------------------------------------------------------G +NDYYAVLGLKKECTETELRNAYKKLALKWHPDRCSASG---NSKFVDEAKKKFQAIQEAY +S------VLSDANKRFLYDVGVYDSG------DDDDENGMGDFLNEMAAMMSQNKSNENQ +--EETFEELQ------DMFDEIFNSDN--GM------------SSSS------------- +----SSSSRTGTPS------------------MCSTTSSTSSSET-FFTFSNKRSSG-EM +KSGK--------GDSCQF------QGFCEG-T-----------GGASGKSNERE-RSRRK +NSKSGRKQ-------------------------------- +>gnl_Soltu3.4_PGSC0003DMP400016106 +---M-------------------------------------------------------G +NDYYAVLGLKKECTETELRNAYKKLALKWHPDRCSASG---NSKFVDEAKKKFQAIQEAY +S------VLSDANKRFLYDVGVYDSG------DDDDENGMGDFLNEMAAMMSQNKSNENQ +--EETFEELQ------DMFDEIFNSDN--GM------------SSSS------------- +----SSSSRTGTPS------------------MCSTTSSTSSSET-FFTFSNKRSSG-EM +KSGK--------GDSCQF------QGFCEG-VE--HLEKAMKENGVGGKIPRVD-GSNRM +DAKRQKVLS------------------------------- +>gnl_Ambtr1.0.27_AmTr_v1.0_scaffold00007.329 +---MAPR-------------------------------------------------GEKD +SDFYAILGLKKECSASDLRNAYKRLALRWHPDRCSASG---NTKFVEECKKKFQAIQQAY +S------VLSDANKRFLYDVGAYGS--------DDDDQGMGEFLGEMAVMMSQTKPSEKG +--PESFEDLQ------NLFQEMFERDL--DM----------FKSSTSH------------ +----NNNNDNNNNN------------------HRSSDNNNCSSVH-CFSNTNKRNCS-DM +NAGE-ASEVGRFAFSCYATEFLHKQTFSVG-AD------DVRSES----------SNKRR +NGRKQKSTS-SSRKS------------------------- +>gnl_Aquco1.0_PACid_18141277 +---MAS--------------------------------------------------EEEA +SDFYKVLGLKNNCSSLELRNAYKKLALKWHPDRCAASG---NSKFVEEAKKNFQAIQEAY +S------VLSDEQKRFMYDVGVYDKD------DDDENEDMGDFLGEMMSMMKQENTSADG +--QQSFEDLQ------NLFQEMVQNDK--EF----------YNPASQ------------- +----NSSIYNASNNMFSFSNNENLNNASNNTFSSFYNENLN--------SSNKKSCS-SM +SAEN--TKVDFNMESLDF------RSFSIG-LE--GGTSFQNSKGRG--------VTGRR +TGRKQKGSS-CNDMSSHD-SKILA---------------- +>gnl_Arath10_AT3G14200.1 +---MASSN-----------------------------------------------SEKIN +ENLYAVLGLKKECSKTELRSAYKKLALRWHPDRCSS------MEFVEEAKKKFQAIQEAY +S------VLSDSNKRFLYDVGAYNTD------DDDDQNGMGDFLNEMATMMNQSKPSDNN +-TGDSFEQLQ------DLFNEMFQGDA--AA----------FPSS--------------- +------SSCSTSNF------------------TSSRSFVFD--------TNSQRSSSFAT +SSMG--MNNDPFGYDPRA------HSFSLG-VD--HQQEFKKGKN----------NGGRR +NRRKNNVPSAGHETSSSNNYGVPTS--------------- +>gnl_Bradi1.2_Bradi3g60090.1 +---MATGG-------------------------------------DKCGGKPAA-AGVGG +GDLYSVLGVNKECSDADLKVAYRKLAMRWHPDRCSSSS---STKHMEEAKEKFQEIQGAY +S------VLSDANKRFLYDVGVYEEHEE---EDDDTLQGMGDFLGEMAHMMSQTQPAR-- +--QESFEELQ------QLFVDMFQSDI--ESG---------FCNGPAK-DHDPVQRQTRT +FSTPPSPSPSPPPP------------------LATVDEAAS------CNGINKRGSS-AM +GSGK-PPRAGEVSGGHGQ------SEFCFG-MS--DAKQAPKARGGN--------ASRRR +NGQKQKLSS-KHDVSSGDEMPRP-------------HAAV +>gnl_Carpa1.181_PACid_16420351 +---MADG------------------------------------------------EDKNN +SDLYAVLGLNKECTPAELRNAYKKLAMRWHPDRCSASG---NSMFVEEAKKKFQAIQEAY +S------VLSDANKRFLYDVGAYES--------DDDENGMGDFLNEMAAMMSQTKPNENG +NAQESFEELQ------ELFQEMFQGDMGFNT----------FGSSSQP------------ +----TTSSCSASSA------------------YATCSETSN-------PNNNKRNSS-EM +NYGK-KKVDDSSGFHAHF------QTFCLG-VE--QQQDFKKGKEARGGIRGKP-GGSRR +QGRKQKVSS-RHNVSSND-LGISAS--------------- +>gnl_Frave2.0_gene05408 +---MAGGKWVPPPLSQFHLHIKRFRRRQKVSGSSGNTEPSGYTDCKNISNR---RMEEKG +NDFYAVMGLKKECSDSELRNAYKKLALIWHPDRCSASG---NSKFVEEAKKKFQDIQQAY +S------VLSDANKRFLYDVGAYES--------DDDENGMGDFLNEMAVMMSQTKPNENG +--GESFEQLQ------ELFEEMFQGDI--EG----------FSSCSQP------------ +----PTSCSTSSSS------------------YALYCENST--------PSNKRNSS-AM +NYGN--ATLDSSGFDAHF------HNFCVG-T-----------GGKPAKDREGD-ARKRK +DSRRSNR--------------------------------- +>gnl_Mimgu1.0_PACid_17694730 +---MAAD-------------------------------------------------EEKS +SDFYGVLGLRKECTAAELRVAYKKLAMKWHPDRCSASG---NLKYVEEAKNKFQAVQQAY +S------VLSDANKRFLYDVGIYDSE------DDADENGMGDFLNEMVAMMGQSKPNENK +--NESFQELQ------DLFEEIFNNDA--EEV---------FKIPPPH------------ +--FPYQDSCSETRT-----------------------------------ASNKRNAR-EM +GSVN-----FSNIEATPF------EGFCIG-ENVIFGGERIQTRPG---------GGSRR +T--KPKIST-SID-----------------------GLIS +>gnl_Nelnu1.0_NNU_010544-RA +------------------------------------------------------------ +---------------------MNLLLQKWHPDRCSSSG---NSKFVEDSKKKFQAIQEAY +S------VLSDENKRFLYDVGVYDCDD-----DDDDENGMGEFLGEMATMMSQIKPSENG +--PESLEKLQ------ELFEEMFQRDM--DDG---------FFSPSPQCA---------- +---SFSSSCSSSSS---------------STTYFSYNNNKH---------DNKRNCS-DI +SSMD--DFYTFGTDSIQF------SNFCIG-VE--GGE-DSKVRGGK---------SRRK +SNRRQKVSSSKHDPSCR----------------------- +>gnl_Solly2.3_Solyc03g123560.2.1 +---M----------------------------------------------------EDKS +NDYYAVLGLKKECTDTELRNAYKKLALKWHPDRCSASG---NLKFVDEAKKQFQAIQEAY +S------VLSDANKKFLYDVGVYDSG------DDDDENGMGDFLNEMAAMMSQNKSNENQ +-GEETFEELQ------DMFNEMFNSDN--GT----------FSSSSS------------- +----SSSSWTGTPS------------------MCSTTSSTSSSET-FLTFPNKRSSG-EM +KSGS-----SVRGDSCQF------QGFCVG-A-----------GGTSGKCNERE-RSWRK +NSKSGRKH-------------------------------- +>gnl_Sorbi1.4_PACid_1968370 +---MDAGG-------------------------------------EKFSDAAAAEGGEGG +GDLYAVLGLKKECSDADLKVAYRKLAKKWHPDKCSSSS---SVKHMEEAKEKFQEIQGAY +S------VLSDANKRLLYDVGVYDDED-----DEDSMQGMGDFIGEMAQMMSQVRPTR-- +--QESFEELQ------QLFVDMFQSDI--DSG---------FCNGSAK-DQVQGQAKSRT +CSTSPSSSPSPPPP----------------PTIVKEAEVSS------CNGFNKRGSS-AM +DSGK-PPRP--VEGGAGQ------AGFCFG-VS--DTKQTPKPRGPN--------TSRRR +NGRKQKLSS-KHDVSSEDETAGS----------------- +>gnl_Thepa2.0_Tp3g12470 +---MASNN-----------------------------------------------SEKGN +DDLYGVLGLKKECTTTELRTAYKKLALRWHPDRCSSMG---TPEFVDEAKKKFQAIQEAY +S------VLSDSNKRFLYDVGAYNS-------DDEDQNGMGDFLNEMAAMMNQSKPSENN +-SGDSFEQLQ------DLFNEMFQGDA--AA----------FSSSSS------------- +------SSCSASTF------------------TSSCSFVFD--------TNSQRSPF-ET +SSMG---TNDLFGFDHSA------HTFSLG-VE--HQQDFKKGKN----------SGGRR +NRRKNNAQSAAHETASSNNYGVPTS--------------- +>gnl_Theca1.0_Tc06_g010450 +---MANG-------------------------------------------------EEKN +NDFYAVLGLNKECTPTELRTAYKKLALRWHPDRCSASG---NSKFVEEAKKKFQAIQQAY +S------VLSDSNKRFLYDVGAYDS--------DDDENGMGDFLNEMAGMMSQTKSNENG +--GESFEELQ------ELFEEMFQADI--DS----------FESTGQ------------- +----STPSCSASSS------------------FGSYGESSS---------SNKRNSS-EM +SSVE-TRLESSSSFDAQF------HSFCLG-VE--HRQDIKQHRGARGGMRGAAGGSRRR +NGRKQKVSS-GHDVTSND-CGISAS--------------- +>gnl_Vitvi12X_PACid_17827068 +---MAAG-------------------------------------------------EEKS +NDFYAVLGLKKECTASELRNAYKRLALMWHPDRCSSSG---NSKFVEEAKKKFQAIQEAY +S------VLSDANKRFLYDVGAYDS--------DDDENGMGDFLNEMAVMMSQTKSNENG +--KESFEELQ------ELFEDMFQRDV--DA----------FNSASHH------------ +----PMNSFPSSTS------------------TSSYCESSN--------ANNKRNSA-EM +GSGRMMSAGESSAFDAHF------QSFCFG-T-----------GGTPGRFQEGE-RSKRR +NSRRSQR--------------------------------- +>gnl_Selmo1.0_PACid_15401289 +---M----------------------------------------------------EKRK +EDPYTVLGVQKSSSSSEIRSAYRKLAMKWHPDK--------QHSLEDQAKAKFQGIQEAY +S------VLSDDKKRVLYDSGLYDEG------DDE------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------VS--------------------------- +---------------------------------------- +>gnl_Orysa6.0_PACid_16864430 +---MARGGG-----------------------------------G----------GGGAD +ADLYAVLGLSRECTDADLRLAYRKLAMIWHPDRCSVAGGSASAAGVDEAKERFQEIQGAY +S------VLSDSNKRFLYDVGVYDGNDGDDDDDEADLSGMGDFLGEMAQMMSQATP---- +--AESFEELQ------QLFVDMFQDDI--DAG---------LCQSTP------------- +----PPPSWPSPPA-------------------AANARSPAAAAT-SRKGVNKRCSP-AA +MDMD-----SGLSSLLGI------SGFCFE-AP--WTSQDASTAAGGG-------GGKRR +KQRPPPA---SHNV-------------------------- +>gnl_Sorbi1.4_PACid_1982925 +---MAATSH-----------------------------------CGNIQDQDEEASAPGA +ADLYAVLGLNRECTDAELRVAYRRLAMIWHPDRCSASG--SSPARMEEAKERFQEIQGAY +S------VLSDSNKRLLYDVGVYDSDD-----DEADLSGMGDFLGEMADMMSQATP---- +--TETFEELQ------QVFVDMFQDDLD-DAG---------FFGGLPT-TGRRAQA--PS +TSLPPSVSSSPLRP----------------TPAAGRSKGPQATPSSSFKGVERRGST-ST +AKRPRPNGSAGLESDLGL------SGFCFM-VS--KEMSKSKERQAV---WASD-DGDRS +TDGKQRLST-SRDVSGGG-MSRSLQGQSSKNLLQCMASKS +>gnl_Medtr3.5_Medtr8g022310.3 +---MANE-------------------------------------------------GNKS +NDFYAVLGLNKECSDSELRNAYKKLALKWHPDRCSASG---NVKFVEEAKKKFQAIQEAY +S------VLSDSNKRLMYDVGVYDS--------DDDENVRHLF----------------- +---HTIHELG------TLFCVMFCFFISLR------------GE---------------- +---------KRSNL------------------NLTFSLSH-------------------- +------------------------------------------------------------ +---------------------------------------- +>gnl_Nelnu1.0_NNU_000115-RA +---MEVD------------------------------------------------SHRSS +PSYYTILGVDQNSSASEIRNAYRKLAMQWHPDKWTKTP-----SLLEKAKSKFQQIQEAY +SGGLLVFMLSDQGKRTLYDVGLYDPDD-----ETNDEVGLRRF--HAGDDISHERC---- +--EETGEEIQLGGTTGDVSGNVTRAGV--EDGECWWCVVVRWSCSLKE------------ +----------------------------------------------------------EL +KEGQ--------------------MGIISE-SD--DA----------------------- +----------GHDTPSLPHLHGSEL-----ELLGRTGCCN +>contig_7 +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------ENEWSGAEFLNEMAAMMTQNKSNENG +--TGTFEELQ------QLFDEMFQSDI--ES----------FNGCSSS------------ +----SNETCS---------------------------------------NSNKRNSI-ES +SSAN----------------FRPENGNESG-----------------------E-ISGKK +NTRKGKGDX------------------------------- diff -r 34ca28db0a5d -r a7867769a706 test-data/3722.faa.aln.tree --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3722.faa.aln.tree Mon Oct 30 09:53:46 2017 -0400 @@ -0,0 +1,1 @@ +(((((gnl_Glyma1.01_PACid_16301085:0.016443402,gnl_Glyma1.01_PACid_16301084:0.053278093)0.803:0.023390563,gnl_Glyma1.01_PACid_16301083:0.030298601)0.901:0.027099626,((gnl_Glyma1.01_PACid_16266209:0.056847680,gnl_Glyma1.01_PACid_16266210:0.015624714)0.811:0.025333131,gnl_Glyma1.01_PACid_16266208:0.034488143)0.905:0.035494603)0.999:0.188079149,(gnl_Medtr3.5_Medtr8g022310.2:0.024981315,(gnl_Medtr3.5_Medtr8g022310.3:0.465525159,gnl_Medtr3.5_Medtr8g022310.1:0.036690818)0.074:0.002229085)0.952:0.101287628)1.000:0.225059008,(((((gnl_Orysa6.0_PACid_16843526:0.000000007,gnl_Orysa6.0_PACid_16843528:0.000000007)0.960:0.104692276,(gnl_Bradi1.2_Bradi3g60090.1:0.251215525,gnl_Sorbi1.4_PACid_1968370:0.202676729)0.470:0.035571250)0.964:0.220529391,(gnl_Orysa6.0_PACid_16864430:0.468545028,gnl_Sorbi1.4_PACid_1982925:0.504608123)0.995:0.341396682)0.999:0.333764302,((gnl_Musac1.0_GSMUA_Achr6T31040_001:0.257705603,gnl_Musac1.0_GSMUA_Achr9T18140_001:0.233035596)0.837:0.090223569,(gnl_Musac1.0_GSMUA_Achr8T23700_001:0.288734161,gnl_Musac1.0_GSMUA_AchrUn_randomT02210_001:0.550828541)0.916:0.084755065)0.866:0.093086055)0.999:0.343576670,(((gnl_Mimgu1.0_PACid_17694730:0.627920829,((gnl_Soltu3.4_PGSC0003DMP400016106:0.060397140,(gnl_Soltu3.4_PGSC0003DMP400016105:0.000000007,gnl_Solly2.3_Solyc03g123560.2.1:0.117851013)0.917:0.075604816)0.676:0.104109587,(gnl_Selmo1.0_PACid_15401289:0.393757146,gnl_Nelnu1.0_NNU_000115-RA:1.006137326)0.989:1.057259060)0.804:0.231585972)0.632:0.070827174,(gnl_Nelnu1.0_NNU_010544-RA:0.445330506,(gnl_Ambtr1.0.27_AmTr_v1.0_scaffold00007.329:0.481404311,gnl_Aquco1.0_PACid_18141277:0.569001355)0.869:0.111238919)0.913:0.101469446)0.876:0.061617758,(gnl_Frave2.0_gene05408:0.298252983,gnl_Vitvi12X_PACid_17827068:0.183978617)0.975:0.124539672)0.258:0.016419054)0.666:0.050639012,(((contig_7:0.847311108,gnl_Theca1.0_Tc06_g010450:0.107098111)0.806:0.076702503,((gnl_Arath10_AT3G14200.1:0.118641618,gnl_Thepa2.0_Tp3g12470:0.089890295)1.000:0.506633729,gnl_Carpa1.181_PACid_16420351:0.140839270)0.773:0.074226625)0.858:0.037834597,(gnl_Poptr2.2_PACid_18217800:0.237912037,(gnl_Poptr2.2_PACid_18234651:0.048333265,(gnl_Poptr2.2_PACid_18234649:0.000000007,gnl_Poptr2.2_PACid_18234650:0.000000007)0.962:0.063277271)0.890:0.133521212)0.996:0.168273995)0.846:0.051958868); diff -r 34ca28db0a5d -r a7867769a706 test-data/tool-data/plant_tribes/scaffolds/README.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tool-data/plant_tribes/scaffolds/README.txt Mon Oct 30 09:53:46 2017 -0400 @@ -0,0 +1,3 @@ +For functional tests to work, this directory must contain symlinks to the scaffolds data +installed into the Galaxy instance to which planemo points via the --galaxy_root parameter. +This would typically be something like ~/galaxy/tool-data/plant_tribes/scaffolds/22Gv1.1. diff -r 34ca28db0a5d -r a7867769a706 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Mon Oct 30 09:53:46 2017 -0400 @@ -0,0 +1,6 @@ + + + value, name, path, description + +

+ diff -r 34ca28db0a5d -r a7867769a706 utils.py --- a/utils.py Wed Aug 30 13:11:48 2017 -0400 +++ b/utils.py Mon Oct 30 09:53:46 2017 -0400 @@ -27,7 +27,7 @@ return fstderr, fherr, fstdout, fhout -def move_directory_files(source_dir, destination_dir, copy=False): +def move_directory_files(source_dir, destination_dir, copy=False, remove_source_dir=False): source_directory = os.path.abspath(source_dir) destination_directory = os.path.abspath(destination_dir) if not os.path.isdir(destination_directory): @@ -38,6 +38,8 @@ shutil.copy(source_entry, destination_directory) else: shutil.move(source_entry, destination_directory) + if remove_source_dir: + os.rmdir(source_directory) def run_command(cmd): @@ -52,29 +54,3 @@ def stop_err(msg): sys.exit(msg) - - -def write_html_output(output, title, dir): - with open(output, 'w') as fh: - dir_items = sorted(os.listdir(dir)) - # Directories can only contain either files or directories, - # but not both. - if len(dir_items) > 0: - item_path = os.path.join(dir, dir_items[0]) - if os.path.isdir(item_path): - header = 'Directories' - else: - header = 'Datasets' - else: - header = '' - fh.write('

%s: %d items

\n' % (title, len(dir_items))) - fh.write('

\n') - fh.write('%s\n' % header) - for index, fname in enumerate(dir_items): - if index % 2 == 0: - bgcolor = '#D8D8D8' - else: - bgcolor = '#FFFFFF' - link = '%s\n' % (fname, fname) - fh.write('\n' % (bgcolor, link)) - fh.write('
%s
\n')