Mercurial > repos > iuc > virannot_blast2tsv
changeset 5:5c53a5baaf72 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 31e7eb490fbaa2b1f34f0e0f154a6f82ad2f2f82
| author | iuc |
|---|---|
| date | Mon, 04 Aug 2025 19:14:12 +0000 |
| parents | bb29ae8708b5 |
| children | |
| files | macros.xml test-data/blast2tsv_output_with_rn.tab test-data/blast2tsv_reads_with_rn.txt test-data/rps_test.tab virAnnot_blast2tsv.xml |
| diffstat | 5 files changed, 7 insertions(+), 35 deletions(-) [+] |
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--- a/macros.xml Tue May 13 11:52:17 2025 +0000 +++ b/macros.xml Mon Aug 04 19:14:12 2025 +0000 @@ -21,6 +21,7 @@ </requirements> </xml> <token name="@TOOL_VERSION@">1.2.0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@HEADLESS@"><![CDATA[export QT_QPA_PLATFORM='offscreen' &&]]></token> <xml name="citations"> <citations>
--- a/test-data/blast2tsv_output_with_rn.tab Tue May 13 11:52:17 2025 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -#algo query_id nb_reads query_length accession description organism percentIdentity nb_hsps queryOverlap hitOverlap evalue score tax_id taxonomy sequence -TBLASTX NODE_13_length_295_cov_0.945833 264 295 316155 pfam13603, tRNA-synt_1_2, Leucyl-tRNA synthetase, Domain 2. This is a family of the conserved region of Leucine-tRNA ligase or Leucyl-tRNA synthetase, EC:6.1.1.4. Tursiops truncatus papillomavirus 2 41.5 1 100 67.0 2.277e-05 38.6378 316155 Viruses;Monodnaviria;Shotokuvirae;Cossaviricota;Papovaviricetes;Zurhausenvirales;Papillomaviridae;Firstpapillomavirinae;Upsilonpapillomavirus;Upsilonpapillomavirus 2;Tursiops truncatus papillomavirus 2 TGTGTTGGGTGTGTTTGGTTTCCGGTTACCATAATCGCTATTCTTTCAAACAGAAAGCGCATGCTAAGTATTCTCACCCAGAGGAATATGCTGACAAGCCCTCCTCAAAAGGCTATTTTTACAATGCCACCTATGAGAATGCACGAACTCTTATTCACTTCATTAAGCAATATGGATTGCCCTTCAATCCTGTTATTGCACCAGAAGATGCTGAACTAACTGATGAACAGATTCAATCTTACATCAACACAGCAAACTCCTTCTTTAATGATTATCCGACGTTACTGTTCACCCG -TBLASTX NODE_16_length_278_cov_0.901345 377 278 306845 pfam00421, PSII, Photosystem II protein. 65.8 1 100 47.0 7.65615e-39 132.634 GTCTAACCTGTGTTGGGTGTGTTTGGGCTGTAATCGAGGTATAGTGTCGAACAAGTCGGTGTCACTGTTGAATTCTATGGCGGCGAACTCAATGGAGTCAGTTATAGTGATCCTGCTACTGTGAAAAAATATGCTAGACGTGCTCAATTGGGTGAAATTTTTGAATTAGATCGTGCTACTTTAAAATCGGATGGTGTTTTTCGTAGCAGTCCAAGGGGTTGGTTTACTTTTGGACATGCGTCGTTTGCTCTGCTCTTCTTCCAAACACACCCAACACA -TBLASTX NODE_19_length_271_cov_0.879630 67 271 306845 pfam00421, PSII, Photosystem II protein. 32.9 1 100 42.0 1.69015e-11 56.3644 GTCTAACCTGTGTTGGGTGTGTTTGGTATGGAGGGAGGTGTATATGATACCTGGGCACCCGGAGGGGGAGATGTAAGAAAAATTACCAACTTGACCCTTAACCCAAGCGTGATATTTGGTTATTTACTAAAATCTCCTTTTGGGGGAGAAGGATGGATTGTTAGTGTGGACGATTTAGAAGATATAATTGGAGGACATGTCTGGTTAGGCTCCATTTGTATACTTGGTGGAATTTGGCATATCTTAACCAAACACACCCAACACAGGTTAG -TBLASTX NODE_20_length_267_cov_1.429245 2 267 287774 pfam10839, DUF2647, Protein of unknown function (DUF2647). This eukaryotic family of proteins are annotated as ycf68 but have no known function. Desulfovibrio sp. G100IX 91.3 1 100 99.0 7.70073e-10 48.4966 287774 cellular organisms;Bacteria;Pseudomonadati;Thermodesulfobacteriota;Desulfovibrionia;Desulfovibrionales;Desulfovibrionaceae;Desulfovibrio;unclassified Desulfovibrio;Desulfovibrio sp. G100IX CTGTGTTGGGTGTGTTTGGACTTGGTATGTGAAGATACGTTGTTAGGTGCTCCGTTTTATTTTCCCATTGAGGCCGAACCTAAACCTGTGCTCGAGAGATAGCTGTCCATATACTGATAAGGGATGTATGGATTCTCGAGAAGAGAGGAGCCATGGTGGTCCCTCCCGGACCGCCCGGATCCCACGAGTGAATAGAAAGTTGGATCTACATTGGATCTCACCTGAATCGCCCCATAAACAACCAAACACACCCAACACAGGTTAGAC -TBLASTX NODE_22_length_262_cov_1.053140 262 262 306604 pfam00124, Photo_RC, Photosynthetic reaction centre protein. Heterotermes sp. TMJ-2004j 40.9 1 100 77.0 4.94039e-28 99.6256 306604 cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Protostomia;Ecdysozoa;Panarthropoda;Arthropoda;Mandibulata;Pancrustacea;Hexapoda;Insecta;Dicondylia;Pterygota;Neoptera;Polyneoptera;Dictyoptera;Blattodea;Blattoidea;Termitoidae;Rhinotermitidae;Heterotermitinae;Heterotermes;unclassified Heterotermes;Heterotermes sp. TMJ-2004j GTCTAACCTGTGTTGGGTGTGTTTGGCTAGTCAGTAGCTTGTTATATGGGTCGTGAGTGGGAAGTTAGCTTCCGTCTGGGTATGCGCCCGTGGATTGCTGTTGCATATTCAGCTCCTGTTGCAGCTGCTACTGCTGTTTTCTTGATTTACCCAATTGGTCAAGGAAGTTTTTCTGATGGTATGCCTCTAGGAATCTCTGGTACTTTCAACTTCATGATTGTATTCCAGGAGAGCACCCAAACACACCCAACACAGGTTAGAC -TBLASTX NODE_24_length_258_cov_0.935961 101 258 307679 pfam01660, Vmethyltransf, Viral methyltransferase. This RNA methyltransferase domain is found in a wide range of ssRNA viruses, including Hordei-, Tobra-, Tobamo-, Bromo-, Clostero- and Caliciviruses. This methyltransferase is involved in mRNA capping. Capping of mRNA enhances its stability. This usually occurs in the nucleus. Therefore, many viruses that replicate in the cytoplasm encode their own. This is a specific guanine-7-methyltransferase domain involved in viral mRNA cap0 synthesis. Specificity for guanine 7 position is shown by NMR in and in vivo role in cap synthesis. Based on secondary structure prediction, the basic fold is believed to be similar to the common AdoMet-dependent methyltransferase fold. A curious feature of this methyltransferase domain is that it together with flanking sequences seems to have guanylyltransferase activity coupled to the methyltransferase activity. The domain is found throughout the so-called Alphavirus superfamily, (including alphaviruses and several other groups). It forms the defining, unique feature of this superfamily. Tetrastemma peltatum 39.4 1 100 70.0 8.38713e-15 65.0021 307679 cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Protostomia;Spiralia;Lophotrochozoa;Nemertea;Enopla;Hoplonemertea;Monostilifera;Eumonostilifera;Tetrastemmatidae;Tetrastemma;Tetrastemma peltatum GTGTTGGGTGTGTTTGGTTGGTGAACGCGCACCATTTAGTGGCAATCACGCGCGGGGAGGCTGAAAACTGCAAGCATAGATCTTTCGGCCCTTTCGAAGCTACCGCTTCCGAGAGCCTGGCTAAACTCTGCCCAGATTATCCGATCTGCTTGCCTGTACCTTACGACGTGATCAATAAAGTGTATAGGTATCTCAGAACGCTTAAGAAGCCTGATGTGCAGTCGCCCCACTACCAAACACACCCAACACAGGTTAGAC -TBLASTX NODE_29_length_250_cov_0.851282 428 250 278700 pfam00283, Cytochrom_B559, Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits. uncultured archaeon CRE-PA11a 58.6 1 100 100 7.31211e-08 42.0012 278700 cellular organisms;Archaea;environmental samples;uncultured archaeon CRE-PA11a GTCTAACCTGTGTTGGGTGTGTTTGGGTTTCTTTGGAGCAACTCGATGAATTTAGTAAATCCTTTTAGGAGGTTCCCAATGACCATAGATCGAACCTATCCAATTTTTACAGTGCGATGGTTGGCTGTTCACGGACTGGCTGTACCTACTGTTTCTTTTTTAGGGTCAATATCAGCAATGCAGTTCATCCAACGATAAACCTAATTCAAATTATAGAGCTAGCACACCAAACACACCCAACACAGGTTAG -TBLASTX NODE_34_length_245_cov_1.000000 183 245 250270 pfam00978, RdRP_2, RNA dependent RNA polymerase. This family may represent an RNA dependent RNA polymerase. The family also contains the following proteins: 2A protein from bromoviruses putative RNA dependent RNA polymerase from tobamoviruses Non structural polyprotein from togaviruses. Nocardia sp. 431D04 37.5 1 100 38.0 6.42106e-08 45.7137 250270 cellular organisms;Bacteria;Bacillati;Actinomycetota;Actinomycetes;Mycobacteriales;Nocardiaceae;Nocardia;unclassified Nocardia;Nocardia sp. 431D04 GTCTAACCTGTGTTGGGTGTGTTTGGATGGTGATCGGCAATTTAAAGGAATGTGTGCGATATTTTCACCAATATTCAAGGAGCTTAAAAATCGACTAAAAAGCGTGTTAGATATTAAATACATGTATGCAGACGGATTGAGACCTGATCAGTTGTCGGAGCGCATGTCACAGATAGGTGCAGGTAAATATTTTATAGAGAATGATATGGAACAGCATCTCGCCAAACACACCCAACACAGGTTAG -TBLASTX NODE_46_length_229_cov_1.091954 471 229 306604 pfam00124, Photo_RC, Photosynthetic reaction centre protein. Heterotermes sp. TMJ-2004j 43.9 1 100 66.0 4.26406e-23 86.1436 306604 cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Protostomia;Ecdysozoa;Panarthropoda;Arthropoda;Mandibulata;Pancrustacea;Hexapoda;Insecta;Dicondylia;Pterygota;Neoptera;Polyneoptera;Dictyoptera;Blattodea;Blattoidea;Termitoidae;Rhinotermitidae;Heterotermitinae;Heterotermes;unclassified Heterotermes;Heterotermes sp. TMJ-2004j TGTGTTGGGTGTGTTTGGTTGGATGCCTGGAATACAATCATGAAATTGAAAGTACCAGATATTCCTAAAGGCATGCCATCTGAAAAACTTCCTTGACCAATAGGGTAGATCAAGAAAACAGCTGTAGCAGCCGCGACAGGAGCTGAATATGCAACAGCAATCCAAGGACGCATACCCAGACGGAAACTAAGCTCCCTCTCGCTCCAAACACACCCAACACAGGTTAGAC -TBLASTX NODE_47_length_229_cov_0.816092 470 229 306687 pfam00223, PsaA_PsaB, Photosystem I psaA/psaB protein. 66.7 1 100 14.0 1.79906e-13 61.3066 TTGGTAAATTGGCGGAAAGAGGAGGACTCAATGATTATTCGTTCGCCGGAACCAGAAGTAAAAATTTTGGTAGATAGGGATCACATAAAAACTTCTTTCGAGGAATGGGCCAGGCCGGGTCATTTCTCAAGAACACTAGCTAAAGGCCCTGACACTACCACTTGGATCTGGAACCTACATGCTGATGCTCACGATCTTAATAGCCAAACACACCCAACACAGGTTAGAC -TBLASTX NODE_50_length_226_cov_2.269006 315 226 306845 pfam00421, PSII, Photosystem II protein. 60.3 1 100 41.0 2.77182e-23 89.1064 GTCAACGGTGTGTTGGGTGTGTTTGGGAAAGGTCCTGGAATATGGGTGTCCGATCCTTATGGACTAACCGGAACAGTGCAACCTGTAAATCCGGCGTGGGGCGTGGAAGGTTTTGATCCTTTTGTCCCGGGAGGAATAGCTTCTCATCATATTGCAGCAGGTACATTGGGCATATTAGCGGGCCTATTCCATCTTAGCGTACGGTCACCCCAGCCAAACACACCCA -TBLASTX NODE_56_length_216_cov_1.180124 166 216 306795 pfam00361, Proton_antipo_M, Proton-conducting membrane transporter. This is a family of membrane transporters that inlcudes some 7 of potentially 14-16 TM regions. In many instances the family forms part of complex I that catalyzes the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane, and in this context is a combination predominantly of subunits 2, 4, 5, 14, L, M and N. In many bacterial species these proteins are probable stand-alone transporters not coupled with oxidoreduction. The family in total represents homologs across the phyla. 26.7 1 100 62.0 5.23486e-07 42.6815 GTGTTGGGTGTGTTTGGGGTCTATGTGGTTTATTTGGTTCTACTGAACCAACATTAAATTTTGAAATATTAACTAATCAGTCCTATCCTGTGGCCTTGGAAATAATATTTTATATTGGATTTTTTCTTGCTTTTGCTGTAAAATTACCAATCATACCCCTACATACATGGTTACCAGATACCCACGAGAGCCAAACACACCCAACACAGGTTAGAC
--- a/test-data/blast2tsv_reads_with_rn.txt Tue May 13 11:52:17 2025 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -#algo query_id nb_reads query_length accession description organism percentIdentity nb_hsps queryOverlap hitOverlap evalue score tax_id taxonomy sequence -TBLASTX NODE_13_length_295_cov_0.945833 264 295 316155 pfam13603, tRNA-synt_1_2, Leucyl-tRNA synthetase, Domain 2. This is a family of the conserved region of Leucine-tRNA ligase or Leucyl-tRNA synthetase, EC:6.1.1.4. Tursiops truncatus papillomavirus 2 41.5 1 100 67.0 2.277e-05 38.6378 316155 Viruses;Monodnaviria;Shotokuvirae;Cossaviricota;Papovaviricetes;Zurhausenvirales;Papillomaviridae;Firstpapillomavirinae;Upsilonpapillomavirus;Upsilonpapillomavirus 2;Tursiops truncatus papillomavirus 2 TGTGTTGGGTGTGTTTGGTTTCCGGTTACCATAATCGCTATTCTTTCAAACAGAAAGCGCATGCTAAGTATTCTCACCCAGAGGAATATGCTGACAAGCCCTCCTCAAAAGGCTATTTTTACAATGCCACCTATGAGAATGCACGAACTCTTATTCACTTCATTAAGCAATATGGATTGCCCTTCAATCCTGTTATTGCACCAGAAGATGCTGAACTAACTGATGAACAGATTCAATCTTACATCAACACAGCAAACTCCTTCTTTAATGATTATCCGACGTTACTGTTCACCCG -TBLASTX NODE_16_length_278_cov_0.901345 377 278 306845 pfam00421, PSII, Photosystem II protein. 65.8 1 100 47.0 7.65615e-39 132.634 GTCTAACCTGTGTTGGGTGTGTTTGGGCTGTAATCGAGGTATAGTGTCGAACAAGTCGGTGTCACTGTTGAATTCTATGGCGGCGAACTCAATGGAGTCAGTTATAGTGATCCTGCTACTGTGAAAAAATATGCTAGACGTGCTCAATTGGGTGAAATTTTTGAATTAGATCGTGCTACTTTAAAATCGGATGGTGTTTTTCGTAGCAGTCCAAGGGGTTGGTTTACTTTTGGACATGCGTCGTTTGCTCTGCTCTTCTTCCAAACACACCCAACACA -TBLASTX NODE_19_length_271_cov_0.879630 67 271 306845 pfam00421, PSII, Photosystem II protein. 32.9 1 100 42.0 1.69015e-11 56.3644 GTCTAACCTGTGTTGGGTGTGTTTGGTATGGAGGGAGGTGTATATGATACCTGGGCACCCGGAGGGGGAGATGTAAGAAAAATTACCAACTTGACCCTTAACCCAAGCGTGATATTTGGTTATTTACTAAAATCTCCTTTTGGGGGAGAAGGATGGATTGTTAGTGTGGACGATTTAGAAGATATAATTGGAGGACATGTCTGGTTAGGCTCCATTTGTATACTTGGTGGAATTTGGCATATCTTAACCAAACACACCCAACACAGGTTAG -TBLASTX NODE_20_length_267_cov_1.429245 2 267 287774 pfam10839, DUF2647, Protein of unknown function (DUF2647). This eukaryotic family of proteins are annotated as ycf68 but have no known function. Desulfovibrio sp. G100IX 91.3 1 100 99.0 7.70073e-10 48.4966 287774 cellular organisms;Bacteria;Pseudomonadati;Thermodesulfobacteriota;Desulfovibrionia;Desulfovibrionales;Desulfovibrionaceae;Desulfovibrio;unclassified Desulfovibrio;Desulfovibrio sp. G100IX CTGTGTTGGGTGTGTTTGGACTTGGTATGTGAAGATACGTTGTTAGGTGCTCCGTTTTATTTTCCCATTGAGGCCGAACCTAAACCTGTGCTCGAGAGATAGCTGTCCATATACTGATAAGGGATGTATGGATTCTCGAGAAGAGAGGAGCCATGGTGGTCCCTCCCGGACCGCCCGGATCCCACGAGTGAATAGAAAGTTGGATCTACATTGGATCTCACCTGAATCGCCCCATAAACAACCAAACACACCCAACACAGGTTAGAC -TBLASTX NODE_22_length_262_cov_1.053140 262 262 306604 pfam00124, Photo_RC, Photosynthetic reaction centre protein. Heterotermes sp. TMJ-2004j 40.9 1 100 77.0 4.94039e-28 99.6256 306604 cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Protostomia;Ecdysozoa;Panarthropoda;Arthropoda;Mandibulata;Pancrustacea;Hexapoda;Insecta;Dicondylia;Pterygota;Neoptera;Polyneoptera;Dictyoptera;Blattodea;Blattoidea;Termitoidae;Rhinotermitidae;Heterotermitinae;Heterotermes;unclassified Heterotermes;Heterotermes sp. TMJ-2004j GTCTAACCTGTGTTGGGTGTGTTTGGCTAGTCAGTAGCTTGTTATATGGGTCGTGAGTGGGAAGTTAGCTTCCGTCTGGGTATGCGCCCGTGGATTGCTGTTGCATATTCAGCTCCTGTTGCAGCTGCTACTGCTGTTTTCTTGATTTACCCAATTGGTCAAGGAAGTTTTTCTGATGGTATGCCTCTAGGAATCTCTGGTACTTTCAACTTCATGATTGTATTCCAGGAGAGCACCCAAACACACCCAACACAGGTTAGAC -TBLASTX NODE_24_length_258_cov_0.935961 101 258 307679 pfam01660, Vmethyltransf, Viral methyltransferase. This RNA methyltransferase domain is found in a wide range of ssRNA viruses, including Hordei-, Tobra-, Tobamo-, Bromo-, Clostero- and Caliciviruses. This methyltransferase is involved in mRNA capping. Capping of mRNA enhances its stability. This usually occurs in the nucleus. Therefore, many viruses that replicate in the cytoplasm encode their own. This is a specific guanine-7-methyltransferase domain involved in viral mRNA cap0 synthesis. Specificity for guanine 7 position is shown by NMR in and in vivo role in cap synthesis. Based on secondary structure prediction, the basic fold is believed to be similar to the common AdoMet-dependent methyltransferase fold. A curious feature of this methyltransferase domain is that it together with flanking sequences seems to have guanylyltransferase activity coupled to the methyltransferase activity. The domain is found throughout the so-called Alphavirus superfamily, (including alphaviruses and several other groups). It forms the defining, unique feature of this superfamily. Tetrastemma peltatum 39.4 1 100 70.0 8.38713e-15 65.0021 307679 cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Protostomia;Spiralia;Lophotrochozoa;Nemertea;Enopla;Hoplonemertea;Monostilifera;Eumonostilifera;Tetrastemmatidae;Tetrastemma;Tetrastemma peltatum GTGTTGGGTGTGTTTGGTTGGTGAACGCGCACCATTTAGTGGCAATCACGCGCGGGGAGGCTGAAAACTGCAAGCATAGATCTTTCGGCCCTTTCGAAGCTACCGCTTCCGAGAGCCTGGCTAAACTCTGCCCAGATTATCCGATCTGCTTGCCTGTACCTTACGACGTGATCAATAAAGTGTATAGGTATCTCAGAACGCTTAAGAAGCCTGATGTGCAGTCGCCCCACTACCAAACACACCCAACACAGGTTAGAC -TBLASTX NODE_29_length_250_cov_0.851282 428 250 278700 pfam00283, Cytochrom_B559, Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits. uncultured archaeon CRE-PA11a 58.6 1 100 100 7.31211e-08 42.0012 278700 cellular organisms;Archaea;environmental samples;uncultured archaeon CRE-PA11a GTCTAACCTGTGTTGGGTGTGTTTGGGTTTCTTTGGAGCAACTCGATGAATTTAGTAAATCCTTTTAGGAGGTTCCCAATGACCATAGATCGAACCTATCCAATTTTTACAGTGCGATGGTTGGCTGTTCACGGACTGGCTGTACCTACTGTTTCTTTTTTAGGGTCAATATCAGCAATGCAGTTCATCCAACGATAAACCTAATTCAAATTATAGAGCTAGCACACCAAACACACCCAACACAGGTTAG -TBLASTX NODE_34_length_245_cov_1.000000 183 245 250270 pfam00978, RdRP_2, RNA dependent RNA polymerase. This family may represent an RNA dependent RNA polymerase. The family also contains the following proteins: 2A protein from bromoviruses putative RNA dependent RNA polymerase from tobamoviruses Non structural polyprotein from togaviruses. Nocardia sp. 431D04 37.5 1 100 38.0 6.42106e-08 45.7137 250270 cellular organisms;Bacteria;Bacillati;Actinomycetota;Actinomycetes;Mycobacteriales;Nocardiaceae;Nocardia;unclassified Nocardia;Nocardia sp. 431D04 GTCTAACCTGTGTTGGGTGTGTTTGGATGGTGATCGGCAATTTAAAGGAATGTGTGCGATATTTTCACCAATATTCAAGGAGCTTAAAAATCGACTAAAAAGCGTGTTAGATATTAAATACATGTATGCAGACGGATTGAGACCTGATCAGTTGTCGGAGCGCATGTCACAGATAGGTGCAGGTAAATATTTTATAGAGAATGATATGGAACAGCATCTCGCCAAACACACCCAACACAGGTTAG -TBLASTX NODE_46_length_229_cov_1.091954 471 229 306604 pfam00124, Photo_RC, Photosynthetic reaction centre protein. Heterotermes sp. TMJ-2004j 43.9 1 100 66.0 4.26406e-23 86.1436 306604 cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Protostomia;Ecdysozoa;Panarthropoda;Arthropoda;Mandibulata;Pancrustacea;Hexapoda;Insecta;Dicondylia;Pterygota;Neoptera;Polyneoptera;Dictyoptera;Blattodea;Blattoidea;Termitoidae;Rhinotermitidae;Heterotermitinae;Heterotermes;unclassified Heterotermes;Heterotermes sp. TMJ-2004j TGTGTTGGGTGTGTTTGGTTGGATGCCTGGAATACAATCATGAAATTGAAAGTACCAGATATTCCTAAAGGCATGCCATCTGAAAAACTTCCTTGACCAATAGGGTAGATCAAGAAAACAGCTGTAGCAGCCGCGACAGGAGCTGAATATGCAACAGCAATCCAAGGACGCATACCCAGACGGAAACTAAGCTCCCTCTCGCTCCAAACACACCCAACACAGGTTAGAC -TBLASTX NODE_47_length_229_cov_0.816092 470 229 306687 pfam00223, PsaA_PsaB, Photosystem I psaA/psaB protein. 66.7 1 100 14.0 1.79906e-13 61.3066 TTGGTAAATTGGCGGAAAGAGGAGGACTCAATGATTATTCGTTCGCCGGAACCAGAAGTAAAAATTTTGGTAGATAGGGATCACATAAAAACTTCTTTCGAGGAATGGGCCAGGCCGGGTCATTTCTCAAGAACACTAGCTAAAGGCCCTGACACTACCACTTGGATCTGGAACCTACATGCTGATGCTCACGATCTTAATAGCCAAACACACCCAACACAGGTTAGAC -TBLASTX NODE_50_length_226_cov_2.269006 315 226 306845 pfam00421, PSII, Photosystem II protein. 60.3 1 100 41.0 2.77182e-23 89.1064 GTCAACGGTGTGTTGGGTGTGTTTGGGAAAGGTCCTGGAATATGGGTGTCCGATCCTTATGGACTAACCGGAACAGTGCAACCTGTAAATCCGGCGTGGGGCGTGGAAGGTTTTGATCCTTTTGTCCCGGGAGGAATAGCTTCTCATCATATTGCAGCAGGTACATTGGGCATATTAGCGGGCCTATTCCATCTTAGCGTACGGTCACCCCAGCCAAACACACCCA -TBLASTX NODE_56_length_216_cov_1.180124 166 216 306795 pfam00361, Proton_antipo_M, Proton-conducting membrane transporter. This is a family of membrane transporters that inlcudes some 7 of potentially 14-16 TM regions. In many instances the family forms part of complex I that catalyzes the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane, and in this context is a combination predominantly of subunits 2, 4, 5, 14, L, M and N. In many bacterial species these proteins are probable stand-alone transporters not coupled with oxidoreduction. The family in total represents homologs across the phyla. 26.7 1 100 62.0 5.23486e-07 42.6815 GTGTTGGGTGTGTTTGGGGTCTATGTGGTTTATTTGGTTCTACTGAACCAACATTAAATTTTGAAATATTAACTAATCAGTCCTATCCTGTGGCCTTGGAAATAATATTTTATATTGGATTTTTTCTTGCTTTTGCTGTAAAATTACCAATCATACCCCTACATACATGGTTACCAGATACCCACGAGAGCCAAACACACCCAACACAGGTTAGAC
--- a/test-data/rps_test.tab Tue May 13 11:52:17 2025 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -#query_id query_length cdd_id hit_id evalue startQ endQ frame description superkingdom pident -No definition line 211 pfam01490 gnl|CDD|279788 0.000177299 15 134 -2 pfam01490, Aa_trans, Transmembrane amino acid transporter protein. This transmembrane region is found in many amino acid transporters including UNC-47 and MTR. UNC-47 encodes a vesicular amino butyric acid (GABA) transporter, (VGAT). UNC-47 is predicted to have 10 transmembrane domains. MTR is a N system amino acid transporter system protein involved in methyltryptophan resistance. Other members of this family include proline transporters and amino acid permeases. cellular organisms(1);Eukaryota(1);Opisthokonta(1);Metazoa(1) 35.000 -ds2020-267_4 2297 pfam00680 gnl|CDD|279070 3.12197e-05 995 1873 -2 pfam00680, RdRP_1, RNA dependent RNA polymerase. Viruses(1);Riboviria(1);Orthornavirae(1);Pisuviricota(1) 16.986 -ds2020-267_5 2029 pfam00680 gnl|CDD|279070 8.86955e-06 840 1706 3 pfam00680, RdRP_1, RNA dependent RNA polymerase. Viruses(1);Riboviria(1);Orthornavirae(1);Pisuviricota(1) 17.974 -ds2020-267_6 1860 pfam02123 gnl|CDD|280316 1.27376e-17 1147 1764 -1 pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus. Viruses(1);Riboviria(1);Orthornavirae(1);Resentoviricetes(1) 23.671
--- a/virAnnot_blast2tsv.xml Tue May 13 11:52:17 2025 +0000 +++ b/virAnnot_blast2tsv.xml Mon Aug 04 19:14:12 2025 +0000 @@ -1,4 +1,4 @@ -<tool id="virannot_blast2tsv" name="virAnnot Blast2tsv" version="@TOOL_VERSION@+galaxy0" profile="21.05"> +<tool id="virannot_blast2tsv" name="virAnnot Blast2tsv" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>convert XML blast results to tabular file with taxonomic informations</description> <macros> <import>macros.xml</import> @@ -48,7 +48,7 @@ <param name="contigs" value="blast2tsv_contigs.fa"/> <param name="blast_type" value="TBLASTX"/> <param name="max_evalue" value="0.001"/> - <output name="out_annotation" file="blast2tsv_output.tab"> + <output name="out_annotation"> <assert_contents> <has_n_columns n="16" /> <has_n_lines n="13" /> @@ -62,16 +62,18 @@ <param name="blast_type" value="TBLASTX"/> <param name="max_evalue" value="0.001"/> <param name="read_nb" value="blast2tsv_read_nb.tab"/> - <output name="out_annotation" file="blast2tsv_output_with_rn.tab"> + <output name="out_annotation"> <assert_contents> <has_text text="pfam13603" /> <has_n_lines n="13" /> + <has_n_columns n="16"/> </assert_contents> </output> - <output name="out_annotation" file="blast2tsv_reads_with_rn.txt"> + <output name="out_annotation"> <assert_contents> <has_text text="Desulfovibrio" /> <has_n_lines n="13" /> + <has_n_columns n="16"/> </assert_contents> </output> </test>