| Previous changeset 1:9e61bc67866f (2018-03-16) Next changeset 3:4383070d29ed (2020-08-14) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit 4aa8226ad3031636041eaa6f29a7fb4721dcdc43 |
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modified:
test-data/trinotate_annotation_report.xls test-data/trinotate_annotation_report_minus_tmhmm_signalp.xls trinotate.xml |
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| diff -r 9e61bc67866f -r 6fd16fad465d test-data/trinotate_annotation_report.xls --- a/test-data/trinotate_annotation_report.xls Fri Mar 16 21:52:26 2018 -0400 +++ b/test-data/trinotate_annotation_report.xls Mon Aug 06 06:52:04 2018 -0400 |
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| b'@@ -1,168 +1,168 @@\n #gene_id\ttranscript_id\tsprot_Top_BLASTX_hit\tRNAMMER\tprot_id\tprot_coords\tsprot_Top_BLASTP_hit\tPfam\tSignalP\tTmHMM\teggnog\tKegg\tgene_ontology_blast\tgene_ontology_pfam\ttranscript\tpeptide\n-TRINITY_DN596_c0_g1\tTRINITY_DN596_c0_g1_i1\tYB92_SCHPO^YB92_SCHPO^Q:102-1910,H:1-603^100%ID^E:0^RecName: Full=Uncharacterized ubiquitin-like protein C1E8.02;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\t.\tTRINITY_DN596_c0_g1_i1|m.607\t102-1913[+]\tYB92_SCHPO^YB92_SCHPO^Q:1-603,H:1-603^100%ID^E:0^RecName: Full=Uncharacterized ubiquitin-like protein C1E8.02;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\tPF13881.3^Rad60-SLD_2^Ubiquitin-2 like Rad60 SUMO-like^5-77^E:0.0063`PF00240.20^ubiquitin^Ubiquitin family^6-77^E:1.7e-13\t.\t.\t.\tKEGG:spo:SPBC1E8.02\tGO:0005783^cellular_component^endoplasmic reticulum`GO:0005789^cellular_component^endoplasmic reticulum membrane`GO:0016021^cellular_component^integral component of membrane`GO:0032446^biological_process^protein modification by small protein conjugation\tGO:0005515^molecular_function^protein binding\t.\t.\n-TRINITY_DN549_c0_g1\tTRINITY_DN549_c0_g1_i1\tGAA1_SCHPO^GAA1_SCHPO^Q:2-1363,H:121-574^100%ID^E:0^RecName: Full=GPI transamidase component gaa1;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\t.\tTRINITY_DN549_c0_g1_i1|m.608\t2-1387[+]\tGAA1_SCHPO^GAA1_SCHPO^Q:1-461,H:121-581^100%ID^E:0^RecName: Full=GPI transamidase component gaa1;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\tPF04114.11^Gaa1^Gaa1-like, GPI transamidase component^2-434^E:1.5e-135\t.\tExpAA=140.37^PredHel=6^Topology=i247-269o284-302i309-331o346-368i381-403o428-450i\t.\tKEGG:spo:SPAC1002.11`KO:K05289\tGO:0005783^cellular_component^endoplasmic reticulum`GO:0042765^cellular_component^GPI-anchor transamidase complex`GO:0016255^biological_process^attachment of GPI anchor to protein\tGO:0016021^cellular_component^integral component of membrane`GO:0042765^cellular_component^GPI-anchor transamidase complex\t.\t.\n-TRINITY_DN594_c0_g1\tTRINITY_DN594_c0_g1_i1\tERG27_SCHPO^ERG27_SCHPO^Q:1275-349,H:46-338^94.82%ID^E:0^RecName: Full=3-keto-steroid reductase;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\t.\tTRINITY_DN594_c0_g1_i1|m.612\t346-1275[-]\tERG27_SCHPO^ERG27_SCHPO^Q:1-309,H:46-338^94.82%ID^E:0^RecName: Full=3-keto-steroid reductase;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\t.\t.\t.\t.\tKEGG:spo:SPBC1709.07`KO:K09827\tGO:0005789^cellular_component^endoplasmic reticulum membrane`GO:0000253^molecular_function^3-keto sterol reductase activity`GO:0006696^biological_process^ergosterol biosynthetic process\t.\t.\t.\n-TRINITY_DN594_c0_g2\tTRINITY_DN594_c0_g2_i1\tERG27_SCHPO^ERG27_SCHPO^Q:1207-680,H:46-205^90.91%ID^E:2e-141^RecName: Full=3-keto-steroid reductase;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces`ERG27_SCHPO^ERG27_SCHPO^Q:681-349,H:228-338^100%ID^E:2e-141^RecName: Full=3-keto-steroid reductase;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\t.\tTRINITY_DN594_c0_g2_i1|m.614\t346-651[-]\tERG27_SCHPO^ERG27_SCHPO^Q:1-101,H:238-338^100%ID^E:7e-68^RecName: Full=3-keto-steroid reductase;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\t.\t'..b'llular_component^cytoplasm`GO:0005635^cellular_component^nuclear envelope`GO:0005643^cellular_component^nuclear pore`GO:0044611^cellular_component^nuclear pore inner ring`GO:0017056^molecular_function^structural constituent of nuclear pore`GO:0006606^biological_process^protein import into nucleus`GO:0036228^biological_process^protein localization to nuclear inner membrane`GO:0006405^biological_process^RNA export from nucleus`GO:0006407^biological_process^rRNA export from nucleus`GO:0000972^biological_process^transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery\t.\t.\t.\n+TRINITY_DN54_c0_g2\tTRINITY_DN54_c0_g2_i1\tNG06_SCHPO^NG06_SCHPO^Q:49-3783,H:1-1245^100%ID^E:0^RecName: Full=Probable nucleoporin C890.06;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces`NG06_SCHPO^NG06_SCHPO^Q:3758-3994,H:1239-1315^93.67%ID^E:2e-35^RecName: Full=Probable nucleoporin C890.06;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\t.\tTRINITY_DN54_c0_g2_i1|m.8842\t1-3825[+]\tNG06_SCHPO^NG06_SCHPO^Q:17-1261,H:1-1245^100%ID^E:0^RecName: Full=Probable nucleoporin C890.06;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\t.\t.\t.\t.\tKEGG:spo:SPAC890.06`KO:K14312\tGO:0005737^cellular_component^cytoplasm`GO:0005635^cellular_component^nuclear envelope`GO:0005643^cellular_component^nuclear pore`GO:0044611^cellular_component^nuclear pore inner ring`GO:0017056^molecular_function^structural constituent of nuclear pore`GO:0006606^biological_process^protein import into nucleus`GO:0036228^biological_process^protein localization to nuclear inner membrane`GO:0006405^biological_process^RNA export from nucleus`GO:0006407^biological_process^rRNA export from nucleus`GO:0000972^biological_process^transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery\t.\t.\t.\n+TRINITY_DN59_c0_g1\tTRINITY_DN59_c0_g1_i1\tRNG3_SCHPO^RNG3_SCHPO^Q:1950-1060,H:450-746^100%ID^E:0^RecName: Full=Ring assembly protein 3;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\t.\tTRINITY_DN59_c0_g1_i1|m.8862\t1057-1950[-]\tRNG3_SCHPO^RNG3_SCHPO^Q:1-297,H:450-746^100%ID^E:0^RecName: Full=Ring assembly protein 3;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\t.\t.\t.\t.\tKEGG:spo:SPCC613.04c`KO:K21991\tGO:0005826^cellular_component^actomyosin contractile ring`GO:0005829^cellular_component^cytosol`GO:0005634^cellular_component^nucleus`GO:0005844^cellular_component^polysome`GO:0017022^molecular_function^myosin binding`GO:0034613^biological_process^cellular protein localization`GO:0000917^biological_process^division septum assembly`GO:1903475^biological_process^mitotic actomyosin contractile ring assembly\t.\t.\t.\n+TRINITY_DN59_c0_g1\tTRINITY_DN59_c0_g1_i1\tRNG3_SCHPO^RNG3_SCHPO^Q:1950-1060,H:450-746^100%ID^E:0^RecName: Full=Ring assembly protein 3;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\t.\tTRINITY_DN59_c0_g1_i1|m.8863\t2-619[+]\tYCS3_SCHPO^YCS3_SCHPO^Q:17-205,H:1-189^100%ID^E:3e-137^RecName: Full=Uncharacterized calcium-binding protein C613.03;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\t.\t.\t.\t.\tKEGG:spo:SPCC613.03\tGO:0005783^cellular_component^endoplasmic reticulum`GO:0005788^cellular_component^endoplasmic reticulum lumen`GO:0005794^cellular_component^Golgi apparatus`GO:0005796^cellular_component^Golgi lumen`GO:0005509^molecular_function^calcium ion binding\t.\t.\t.\n' |
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| diff -r 9e61bc67866f -r 6fd16fad465d test-data/trinotate_annotation_report_minus_tmhmm_signalp.xls --- a/test-data/trinotate_annotation_report_minus_tmhmm_signalp.xls Fri Mar 16 21:52:26 2018 -0400 +++ b/test-data/trinotate_annotation_report_minus_tmhmm_signalp.xls Mon Aug 06 06:52:04 2018 -0400 |
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| b'@@ -1,168 +1,168 @@\n #gene_id\ttranscript_id\tsprot_Top_BLASTX_hit\tRNAMMER\tprot_id\tprot_coords\tsprot_Top_BLASTP_hit\tPfam\tSignalP\tTmHMM\teggnog\tKegg\tgene_ontology_blast\tgene_ontology_pfam\ttranscript\tpeptide\n-TRINITY_DN596_c0_g1\tTRINITY_DN596_c0_g1_i1\tYB92_SCHPO^YB92_SCHPO^Q:102-1910,H:1-603^100%ID^E:0^RecName: Full=Uncharacterized ubiquitin-like protein C1E8.02;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\t.\tTRINITY_DN596_c0_g1_i1|m.607\t102-1913[+]\tYB92_SCHPO^YB92_SCHPO^Q:1-603,H:1-603^100%ID^E:0^RecName: Full=Uncharacterized ubiquitin-like protein C1E8.02;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\tPF13881.3^Rad60-SLD_2^Ubiquitin-2 like Rad60 SUMO-like^5-77^E:0.0063`PF00240.20^ubiquitin^Ubiquitin family^6-77^E:1.7e-13\t.\t.\t.\tKEGG:spo:SPBC1E8.02\tGO:0005783^cellular_component^endoplasmic reticulum`GO:0005789^cellular_component^endoplasmic reticulum membrane`GO:0016021^cellular_component^integral component of membrane`GO:0032446^biological_process^protein modification by small protein conjugation\tGO:0005515^molecular_function^protein binding\tTGTGATTCGTGCCGCTCAACATTTCTTCAAGTGATTCCTAACATTGCTGTACATTCTCTTGAAAAGCGTTTTAACCTTTTCAATTCTGAAACTTGTAAAGAATGTCAGAGTATCGTATTCGAGTGACAACTGTGGACCAGAAGGTTGGTATTTTTCAAGTTCCTAGGACAAAAACGGTTTTAGAATTAAAGGAACTGATTGCTGTAACATTTGAAGCTCCTGCAGATCGATTAAAGTTGATTCACGCTGGTCGTGTATTGAGGAATGAAACTCCCCTCGAGGAAATTTTGCATGACGCTACTGATCTGGTCACTTTTCATCTTGTAATTGCGGTTTTTAATTCTACAAGCACAACCTTGCCATCAGCGACATCATCTTCTGTTCCTCAAAGTAGGACCAGCGAATTATCATCGACTAATTCAATTCCAACTCCTCGAATCACCAGTTTGAACCCGGAAGAATTGTCAAGACGTGAACGTGCCCAACGTTTATTACAGACATACAACAGTTTCCATGGATCTGGCTTAGGAGGACTTTTTCCAAACATACACCGGGAACTAGAAAGTCACGGATTTTCATTGCCAACCCATGAGCAATCATCACCCGTTGCTGAATCTCTGGATAATTCGGTATCGTCTGCTTTATCTCCACATTTGGAAACGCTGCGTCGCCGCAATCTCAGTATTCATCATCAACATATACAAGCTCACGAAATGGCACAAGAGTCCTTGGAGACCAGAAATCCAGGAAACATTTCTTCCTCGAGTGCTCCTTTAGCTAGTGATCAATCCCCGACTGTATCATCTAACCATATCCATGCATCCGGTAATTTGGCTTTAGGATCAAATTCGGGGTTAAATCCACGAAGCCCTAATTCTTTTTCTTCCCCATTGGACAATCCTGCACTTCATACTGTTGACTCAACCAACGTCAATGGTTCGCTTTCACCTCTATCAAATTCTTCATCTATCAATCAAGTTCACCAAAATGAAACTCATGGTTCTACCATCTCAGTACCTAACCCGAACTTAAGTCAAATGGGCCCTTCACACTCTTCTTCTGTGCCCTCAAATCTGTCACCAAATCCTGCCCAAAATGAAAATCCTAGTACAACCTCTATTCCATCAATAAATAATCAACCATTCCCGTCTGGTCTTTCTGCTTCTAACTCTAATTTTGCCTCTTCCTCGTTTATCCCTCAGAGCGTTCCGCAACTATTGCCTATATATTATCAAACTATCTTTTACAACGGTAACTATTATTTACAGCAGCTCCCATCTGCATCGCCTCCCACTATGTTTCGAGATCACTCATTTGCTCCTTTAGTTTCCCCTTCTATTGTTTCTCCGTATGGTGTTTTAGAAAATGAAGAAACTGGCGAATGTGCCTTTTTGTTTTCACCAAATGCCTCCCAACCCCATTTTCAGCCGAGAGCCCCCACGTTTGGCATTCCACGAAATGTGAGATCCCTCTTCACCTTACCGTTCTTCCATACTATCCGTAATATTGAGAGACATTTCCGATTATTTATTCGTTTAGCCCTGTTTTGTGTATTAACGACTTATAATGTTTCTCTCTCACAAACAATTTTGCTAACATCTATAATGTCTGTTGTGTTTTTGTTACAGACCGGTGCTCTAGCTCCATTCATCAATGACAATCCACTCATCCAGTCTGGTATGCGTCATATTCGTAATCTTCAAGATGAATACCGGCGGCGTCGAAACCGAACGGCTCAAAGAGTAGTTGAAATTCCTAATGAGACACAGACTGAAGATGAACAAGATGGTACAAATACGCCGGATAATAGGGCTGACGCTGAAGAACGCGAACTAACTCGAAGTCAAAGAATATACCGGACGGTAGTAAGAACCATAGTTGCCTTCGCATTAAGCTTTGTACCTCGAGCGTAACATTTTTTTCTTAAAAACAAAAGTGATAATATAGCTGTAAAGTCATTTTTCATTACTAATTAGAAATATTGTCTAAGCTTGCTATTAATAAAAGAGTTCTAGCTAGACTAAATTTTGACAGTGTCGAAATATCATTCCAAGGTACCCCATCAGATTAACAAATTTATAA\tMSEYRIRVTTVDQKVGIFQVPRTKTVLELKELIAVTFEAPADRLKLIHAGRVLRNETPLEEILHDATDLVTFHLVIAVFNSTSTTLPSATSSSVPQSRTSELSSTNSIPTPRITSLNPEELSRRERAQRLLQTYNSFHGSGLGGLFPNIHRELESHGFSLPTHEQSSPVAESLDNSVSSALSPHLETLRRRNLSIHHQHIQAHEMAQESLETRNPGNISSSSAPLASDQSPTVSSNHIHASGNLALGSNSGLNPRSPNSFSSPLDNPALHTVDSTNVNGSLSPLSNSSSINQVHQNETHGSTISVPNPNLSQMGPSHSSSVPSNLSPNPAQNENPSTTSIPSINNQPFPSGLSASNSNFASSSFIPQSVPQLLPIYYQTIFYNGNYYLQQLPSASPPTMFRDHSFAPLVSPSIVSPYGVLENEETGECAFLFSPNASQPHFQPRAPTFGIPRNVRSLFTLPFFHTIRNIERHFRLFIRLALFCVLTTYNVSLSQTILLTSIMSVVFLLQTGALAPFINDNPLIQSGMRHIRNLQDEYRRRRNRTAQRVVEIPNETQTEDEQDGTNTPDNRADAEERELTRSQRIYRTVVRTIVAFALSFVPRA*\n-TRINITY_DN549_c0_g1\tTRINITY_DN549_c0_g1_i1\tGA'..b'TTAAAATCGTTCTGGAGACTTAAAATTTTCTTGCACCCTTCATCAACACTAGTAATTTGAACAAGAATTCCGCATGCTGCTAATCTCGTGGGAGTGTCTTCGGTATCTGAGAGTGCTAGTACAATGTGTAAACGAGTATTTTCAAAATCCGAGTCCTTGTCTCCTATAAACTTAATTAAGCAATAAGGTGATAAAGAAAGGTTGTTAATAAGTTCCGTGGTTGCCCTCTGAATTAAAGGATTTGTTTCTATAATTAGTTCATCCAATTCTCTCCAACATTCTTGAACTATGGCTTGCCGACTTTCTTCATCATGTGAAGCAAGATTTGTTAGCGCAAGTAACACTTCAAATTTCCCCAAGAGAATTGGATACTCAGTATCAGCAGAATTAGTACTTAGTAACTTTGACATAGGATGAATTGCTCGGTTCGATGGAAACGCCTTAGTAAATATACTATGAGGAGCCACACTGATAAGAATTTTCGCTAATGCAAAAGCCGCATTCGAATCCTGGGTTTGGATAAAACATTGTCTAGTAAGGAATTTCAATGCACCTATTTGTACTAGCTTGCGACGTGCCAGCTTGTAATTAGCCATGTGTACAAGTATCATTGCTAATAACCCGTTTAGGCTATTATAGTGCTTGGCCGCTGAAAAGAGTTTTGAC\tSKLFSAAKHYNSLNGLLAMILVHMANYKLARRKLVQIGALKFLTRQCFIQTQDSNAAFALAKILISVAPHSIFTKAFPSNRAIHPMSKLLSTNSADTEYPILLGKFEVLLALTNLASHDEESRQAIVQECWRELDELIIETNPLIQRATTELINNLSLSPYCLIKFIGDKDSDFENTRLHIVLALSDTEDTPTRLAACGILVQITSVDEGCKKILSLQNDFNYIVRMLTDQDEGIQHRGLVCICNIVYSKDQEIFNKFIKTPKAVETLRTYITKQAALKELQHEALVMIDSRLQGSK*\n+TRINITY_DN59_c0_g1\tTRINITY_DN59_c0_g1_i1\tRNG3_SCHPO^RNG3_SCHPO^Q:1950-1060,H:450-746^100%ID^E:0^RecName: Full=Ring assembly protein 3;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\t.\tTRINITY_DN59_c0_g1_i1|m.8863\t2-619[+]\tYCS3_SCHPO^YCS3_SCHPO^Q:17-205,H:1-189^100%ID^E:3e-137^RecName: Full=Uncharacterized calcium-binding protein C613.03;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\t.\t.\t.\t.\tKEGG:spo:SPCC613.03\tGO:0005783^cellular_component^endoplasmic reticulum`GO:0005788^cellular_component^endoplasmic reticulum lumen`GO:0005794^cellular_component^Golgi apparatus`GO:0005796^cellular_component^Golgi lumen`GO:0005509^molecular_function^calcium ion binding\t.\tAGAACTTGACCGCAGCGCACATCAACTACACCTTGAGGCAATTCAAAATATGAAGTTTTCTACCGTAGGGTTTTTGTTTTCAACAATTTTATTCAAAAGTGCGTTTGCAGGATGGATGGATACACACATGAAAGATGAACATCACATTGATAAGTACACAGATGAATCTTTTTTTCGTCTTCACGATTTAGGAAAAAAGGGATACTGGTCAGATCAAGATATACTTAGTTTATATGGATTATTTGAAAATGATGAGGTCCCATTCGTCAAAAAGAATGAGGTTTTGGTTGATGTTCTAAAAAAATGCGATCCATCGGGCAATCGCCGGATAACACTTGATGAATTTCTTGCATTTCGTAAAAATGGAGGAGAGTTAACGGATTTTGGATTTCCAGGGCACCATGGTGATGAGGAAGAGGAATTTGAAATGCATCATGTGGAAAAATATCACCCAGCTGGCCTCGATGAACCAGATGAAAACTGGAATCATCCTGAAGATATCGAACATTTTCAAAAACACGATGAGATATTTCATGGTGATAAGAAACCTGAGGAACGACGCAAACATTTTGTAAAATACAATAATATCCCTGACAAGTATCGTCGTGTGAGCATTTAAATTTTCCCATTGATAGATTTACTTGCTTCTCCTTGGGACGTTTTATTTTTATTTTTATTTTTCCGTTTATTTTTGGATTGTCGTGTTCCGATATATATCCGTGTTTACAAACAATAGCTTCAACATTTTTGAACGGGTCCTTCCAATACTAATGCCATATCTTATTTCTTTGTCAATACAAAATCACTTTTGTTCGTTAAACTCATTTTGGTTTGCAGATATTATCATATTCTTACCAATTATACATACACTCACAATTTGTTTTACATTTCCGCTCCCTTCTTCAATAAGCTGATTGCTTATAAAAAATCAAACATTCATATGATTCAAGTTCAAATATTATCATCTGAAAACTGACAAGTTCCATTCATTACTATATTAATATCATTTATTCGTTAAACCGATATCATTAAAAATGGAAAATTAAAGAAATCAATTCATTTGCTTCCTTGAAGTCTAGAGTCGATCATAACGAGAGCTTCATGTTGAAGCTCTTTAAGTGCAGCTTGCTTAGTAATATAAGTGCGTAATGTTTCAACAGCCTTTGGTGTTTTTATGAACTTGTTAAATATTTCTTGATCTTTGGAATATACGATATTGCATATGCAAACTAATCCACGATGTTGAATTCCTTCATCTTGGTCGGTTAACATTCTGACTATGTAGTTAAAATCGTTCTGGAGACTTAAAATTTTCTTGCACCCTTCATCAACACTAGTAATTTGAACAAGAATTCCGCATGCTGCTAATCTCGTGGGAGTGTCTTCGGTATCTGAGAGTGCTAGTACAATGTGTAAACGAGTATTTTCAAAATCCGAGTCCTTGTCTCCTATAAACTTAATTAAGCAATAAGGTGATAAAGAAAGGTTGTTAATAAGTTCCGTGGTTGCCCTCTGAATTAAAGGATTTGTTTCTATAATTAGTTCATCCAATTCTCTCCAACATTCTTGAACTATGGCTTGCCGACTTTCTTCATCATGTGAAGCAAGATTTGTTAGCGCAAGTAACACTTCAAATTTCCCCAAGAGAATTGGATACTCAGTATCAGCAGAATTAGTACTTAGTAACTTTGACATAGGATGAATTGCTCGGTTCGATGGAAACGCCTTAGTAAATATACTATGAGGAGCCACACTGATAAGAATTTTCGCTAATGCAAAAGCCGCATTCGAATCCTGGGTTTGGATAAAACATTGTCTAGTAAGGAATTTCAATGCACCTATTTGTACTAGCTTGCGACGTGCCAGCTTGTAATTAGCCATGTGTACAAGTATCATTGCTAATAACCCGTTTAGGCTATTATAGTGCTTGGCCGCTGAAAAGAGTTTTGAC\tELDRSAHQLHLEAIQNMKFSTVGFLFSTILFKSAFAGWMDTHMKDEHHIDKYTDESFFRLHDLGKKGYWSDQDILSLYGLFENDEVPFVKKNEVLVDVLKKCDPSGNRRITLDEFLAFRKNGGELTDFGFPGHHGDEEEEFEMHHVEKYHPAGLDEPDENWNHPEDIEHFQKHDEIFHGDKKPEERRKHFVKYNNIPDKYRRVSI*\n' 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| diff -r 9e61bc67866f -r 6fd16fad465d trinotate.xml --- a/trinotate.xml Fri Mar 16 21:52:26 2018 -0400 +++ b/trinotate.xml Mon Aug 06 06:52:04 2018 -0400 |
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| @@ -1,6 +1,6 @@ -<tool id="trinotate" name="Trinotate" version="3.0.1.0"> +<tool id="trinotate" name="Trinotate" version="3.1.1"> <requirements> - <requirement type="package" version="3.0.1">trinotate</requirement> + <requirement type="package" version="3.1.1">trinotate</requirement> <requirement type="package" version="1.18">gnu-wget</requirement> </requirements> <stdio> @@ -8,16 +8,15 @@ </stdio> <version_command> <![CDATA[ - Trinotate version 3.0.1 + Trinotate version 3.1.1 ]]> </version_command> <command><![CDATA[ #if str($cond_download.select_download) == "yes": - wget --no-verbose 'https://data.broadinstitute.org/Trinity/__deprecated_trinotate_resources/Trinotate_v3_RESOURCES/Trinotate_v3.sqlite.gz' -O Trinotate.sqlite.gz && - gunzip Trinotate.sqlite.gz && + Build_Trinotate_Boilerplate_SQLite_db.pl Trinotate && #else: - ln -s '$cond_download.trinotate_sqlite_in' Trinotate.sqlite + ln -s '$cond_download.trinotate_sqlite_in' Trinotate.sqlite && #end if Trinotate Trinotate.sqlite init --gene_trans_map '$gene_trans_map' --transcript_fasta $trinity --transdecoder_pep '$transdecoder' && @@ -37,7 +36,7 @@ Trinotate Trinotate.sqlite LOAD_signalp '$signalp' && #end if -Trinotate Trinotate.sqlite report -E $report_option.E --pfam_cutoff $report_option.pfam_cutoff $report_option.incl_pep $report_option.incl_trans > '$trinotate_out'; +Trinotate Trinotate.sqlite report -E $report_option.E --pfam_cutoff $report_option.pfam_cutoff $report_option.incl_pep $report_option.incl_trans > '$trinotate_out' ]]></command> <inputs> @@ -48,7 +47,7 @@ <param name="blastx" type="data" format="tabular" optional="true" label="BLASTX: Transcripts vs Uniprot.SwissProt" help="[optional] NCBI BLAST+ blastx output. Output format: Tabular (standard 12 columns)" /> <param name="hmmscan" type="data" format="txt" optional="true" label="HMMER hmmscan: Peptides vs PFAM" help="[optional] HMMER hmmscan output: Table of per-domain hits. Output format: Table of per-domain hits (--domtblout)" /> <param name="tmhmm" type="data" format="tabular" optional="true" label="TMHMM on Peptides" help="[optional]"/> - <param name="signalp" type="data" format="tabular" optional="true" label="SignalP on Peptides" help="[optional]" /> + <param name="signalp" type="data" format="tabular" optional="true" label="SignalP on Peptides" help="[optional]" /> <conditional name="cond_download"> <param name="select_download" type="select" label="Let Galaxy downloading the Trinotate Pre-generated Resource SQLite database"> @@ -60,7 +59,7 @@ </when> <when value="yes" /> </conditional> - + <section name="report_option" title="Report options" expanded="False"> <param argument="-E" type="float" value="1e-5" label="Maximum E-value for reporting best blast hit and associated annotations." /> <param argument="--pfam_cutoff" type="select" label="PFAM cutoff"> @@ -97,6 +96,7 @@ <param name="tmhmm" ftype="tabular" value="tmhmm.out" /> <param name="signalp" ftype="tabular" value="signalp.out" /> <output name="trinotate_out" file="trinotate_annotation_report.xls" /> + <output name="trinotate_out" file="trinotate_annotation_report.xls" /> </test> <test> <param name="trinity" ftype="fasta" value="Trinity.fasta" /> @@ -174,11 +174,6 @@ .. _tmhmm_and_signalp: https://toolshed.g2.bx.psu.edu/repository?repository_id=292389a45f1a238a - -Trinotate Pre-generated Resource SQLite database - -- You can provide the SQLite database yourself, if Galaxy have trouble to download it : https://data.broadinstitute.org/Trinity/__deprecated_trinotate_resources/Trinotate_v3_RESOURCES/Trinotate_v3.sqlite.gz - -------- **Output** |