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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 48a3a1fa033745898a131f9dca7132947683c02f |
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modified:
macros.xml test-data/rps_test.tab virAnnot_blast2tsv.xml |
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| diff -r e889010415a1 -r 88ebde55bef8 macros.xml --- a/macros.xml Mon Mar 04 19:55:52 2024 +0000 +++ b/macros.xml Sat May 18 18:14:54 2024 +0000 |
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| @@ -1,4 +1,9 @@ <macros> + <xml name="xrefs"> + <xrefs> + <xref type="bio.tools">virannot</xref> + </xrefs> + </xml> <xml name="requirements"> <requirements> <requirement type="package" version="1.83">biopython</requirement> |
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| diff -r e889010415a1 -r 88ebde55bef8 test-data/rps_test.tab --- a/test-data/rps_test.tab Mon Mar 04 19:55:52 2024 +0000 +++ b/test-data/rps_test.tab Sat May 18 18:14:54 2024 +0000 |
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| b'@@ -1,6 +1,6 @@\n #query_id\tquery_length\tcdd_id\thit_id\tevalue\tstartQ\tendQ\tframe\tdescription\tsuperkingdom\n ds2020-267_120\t339\tpfam01333\tgnl|CDD|366578\t0.000848733\t197\t325\t-3\tpfam01333, Apocytochr_F_C, Apocytochrome F, C-terminal. This is a sub-family of cytochrome C. See pfam00034.\tEukaryota(19);Bacteria(1)\n-ds2020-267_374\t242\tpfam00124\tgnl|CDD|365890\t5.09126e-07\t21\t125\t3\tpfam00124, Photo_RC, Photosynthetic reaction centre protein. \tBacteria(9);Eukaryota(6);Viruses(4);unclassified sequences(1)\n+ds2020-267_374\t242\tpfam00124\tgnl|CDD|365890\t5.09126e-07\t21\t125\t3\tpfam00124, Photo_RC, Photosynthetic reaction centre protein. \tBacteria(10);Eukaryota(5);Viruses(4);unclassified sequences(1)\n ds2020-267_471\t230\tpfam00201\tgnl|CDD|278624\t3.12575e-07\t46\t210\t1\tpfam00201, UDPGT, UDP-glucoronosyl and UDP-glucosyl transferase. \tEukaryota(20)\n ds2020-267_710\t213\tpfam01127\tgnl|CDD|366480\t0.000723904\t46\t210\t1\tpfam01127, Sdh_cyt, Succinate dehydrogenase/Fumarate reductase transmembrane subunit. This family includes a transmembrane protein from both the Succinate dehydrogenase and Fumarate reductase complexes.\tBacteria(20)\n ds2020-267_692\t214\tpfam00680\tgnl|CDD|366242\t4.79875e-05\t70\t180\t1\tpfam00680, RdRP_1, RNA dependent RNA polymerase. \tViruses(20)\n@@ -11,7 +11,7 @@\n ds2020-267_773\t210\tpfam01641\tgnl|CDD|376583\t5.23903e-34\t16\t174\t1\tpfam01641, SelR, SelR domain. Methionine sulfoxide reduction is an important process, by which cells regulate biological processes and cope with oxidative stress. MsrA, a protein involved in the reduction of methionine sulfoxides in proteins, has been known for four decades and has been extensively characterized with respect to structure and function. However, recent studies revealed that MsrA is only specific for methionine-S-sulfoxides. Because oxidized methionines occur in a mixture of R and S isomers in vivo, it was unclear how stereo-specific MsrA could be responsible for the reduction of all protein methionine sulfoxides. It appears that a second methionine sulfoxide reductase, SelR, evolved that is specific for methionine-R-sulfoxides, the activity that is different but complementary to that of MsrA. Thus, these proteins, working together, could reduce both stereoisomers of methionine sulfoxide. This domain is found both in SelR proteins and fused with the peptide methionine sulfoxide reductase enzymatic domain pfam01625. The domain has two conserved cysteine and histidines. The domain binds both selenium and zinc. The final cysteine is found to be replaced by the rare amino acid selenocysteine in some members of the family. This family has methionine-R-sulfoxide reductase activity.\tBacteria(18);Archaea(1);unclassified sequences(1)\n ds2020-267_287\t256\tpfam00115\tgnl|CDD|376293\t2.8946e-26\t13\t237\t1\tpfam00115, COX1, Cytochrome C and Quinol oxidase polypeptide I. \tEukaryota(18);Bacteria(2)\n ds2020-267_139\t320\tpfam05860\tgnl|CDD|368641\t1.34887e-13\t167\t298\t2\tpfam05860, Haemagg_act, haemagglutination activity domain. This domain is suggested to be a carbohydrate- dependent haemagglutination activity site. It is found in a range of haemagglutinins and haemolysins.\tBacteria(20)\n-ds2020-267_763\t211\tpfam00557\tgnl|CDD|376349\t0.000231782\t167\t298\t2\tpfam00557, Peptidase_M24, Metallopeptidase family M24. This family contains metallopeptidases. It also contains non-peptidase homologs such as the N terminal domain of Spt16 which is a histone H3-H4 binding module.\tBacteria(18);Archaea(2)\n+ds2020-267_763\t211\tpfam00557\tgnl|CDD|376349\t0.000231782\t167\t298\t2\tpfam00557, Peptidase_M24, Metallopeptidase family M24. This family contains metallopeptidases. It also contains non-peptidase homologs such as the N terminal domain of Spt16 which is a histone H3-H4 binding module.\tBacteria(17);Archaea(2);unclassified sequences(1)\n ds2020-267_571\t221\tpfam00501\tgnl|CDD|366135\t2.61467e-07\t34\t201\t1\tpfam00501, AMP-binding, AMP-binding enzyme. \tBacteria(17);Eukaryota(2);unclassified sequences(1)\n ds2020-267_565\t222\tpfam03950\tgnl|CDD|377172\t9.52435e'..b" involved in Golgi to endosome trafficking. EAP30 is a subunit of the ELL complex. The ELL is an 80-kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity.\tEukaryota(17);Archaea(3)\n ds2020-267_6\t1860\tpfam02123\tgnl|CDD|280316\t1.35634e-17\t1147\t1764\t-1\tpfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.\tViruses(19);unclassified sequences(1)\n-ds2020-267_555\t222\tpfam00124\tgnl|CDD|365890\t7.71427e-08\t48\t203\t3\tpfam00124, Photo_RC, Photosynthetic reaction centre protein. \tBacteria(9);Eukaryota(6);Viruses(4);unclassified sequences(1)\n+ds2020-267_555\t222\tpfam00124\tgnl|CDD|365890\t7.71427e-08\t48\t203\t3\tpfam00124, Photo_RC, Photosynthetic reaction centre protein. \tBacteria(10);Eukaryota(5);Viruses(4);unclassified sequences(1)\n ds2020-267_550\t223\tpfam05694\tgnl|CDD|377548\t0.00097637\t48\t203\t3\tpfam05694, SBP56, 56kDa selenium binding protein (SBP56). This family consists of several eukaryotic selenium binding proteins as well as three sequences from archaea. The exact function of this protein is unknown although it is thought that SBP56 participates in late stages of intra-Golgi protein transport. The Lotus japonicus homolog of SBP56, LjSBP is thought to have more than one physiological role and can be implicated in controlling the oxidation/reduction status of target proteins, in vesicular Golgi transport.\tBacteria(12);Eukaryota(8)\n ds2020-267_65\t462\tpfam13406\tgnl|CDD|372592\t4.82338e-27\t145\t360\t-1\tpfam13406, SLT_2, Transglycosylase SLT domain. This family is related to the SLT domain pfam01464.\tBacteria(19);unclassified sequences(1)\n ds2020-267_729\t212\tpfam01405\tgnl|CDD|279713\t5.43744e-05\t19\t99\t-3\tpfam01405, PsbT, Photosystem II reaction centre T protein. The exact function of this protein is unknown. It probably consists of a single transmembrane spanning helix. The Chlamydomonas reinhardtii psbT protein appears to be (i) a novel photosystem II subunit and (ii) required for maintaining optimal photosystem II activity under adverse growth conditions.\tEukaryota(17);Bacteria(3)\n@@ -102,4 +102,4 @@\n ds2020-267_274\t258\tpfam03713\tgnl|CDD|367619\t9.45376e-09\t24\t173\t-2\tpfam03713, DUF305, Domain of unknown function (DUF305). Domain found in small family of bacterial secreted proteins with no known function. Also found in Paramecium bursaria chlorella virus 1. This domain is short and found in one or two copies. The domain has a conserved HH motif that may be functionally important. This domain belongs to the ferritin superfamily. It contains two sequence similar repeats each of which is composed of two alpha helices.\tBacteria(18);unclassified sequences(2)\n ds2020-267_42\t575\tpfam00283\tgnl|CDD|365999\t2.95472e-07\t325\t411\t1\tpfam00283, Cytochrom_B559, Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits. \tEukaryota(18);Bacteria(2)\n ds2020-267_283\t257\tpfam13041\tgnl|CDD|372443\t3.148e-06\t13\t114\t1\tpfam13041, PPR_2, PPR repeat family. This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR.\tEukaryota(20)\n-ds2020-267_685\t214\tpfam09334\tgnl|CDD|370442\t1.80219e-14\t16\t117\t-2\tpfam09334, tRNA-synt_1g, tRNA synthetases class I (M). This family includes methionyl tRNA synthetases.\tBacteria(17);Archaea(2);unclassified sequences(1)\n+ds2020-267_685\t214\tpfam09334\tgnl|CDD|370442\t1.80219e-14\t16\t117\t-2\tpfam09334, tRNA-synt_1g, tRNA synthetases class I (M). This family includes methionyl tRNA synthetases.\tBacteria(16);Archaea(3);unclassified sequences(1)\n" |
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| diff -r e889010415a1 -r 88ebde55bef8 virAnnot_blast2tsv.xml --- a/virAnnot_blast2tsv.xml Mon Mar 04 19:55:52 2024 +0000 +++ b/virAnnot_blast2tsv.xml Sat May 18 18:14:54 2024 +0000 |
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| @@ -3,6 +3,7 @@ <macros> <import>macros.xml</import> </macros> + <expand macro="xrefs"/> <expand macro="requirements" /> <required_files> <include path="blast2tsv.py" /> |