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Changeset 5:aac02a3a395c (2025-08-04)

Previous changeset 4:998724a43694 (2025-05-13)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 31e7eb490fbaa2b1f34f0e0f154a6f82ad2f2f82

modified:
macros.xml
virAnnot_rps2tsv.xml

removed:
test-data/blast2tsv_output_with_rn.tab
test-data/blast2tsv_reads_with_rn.txt
test-data/rps_test.tab

diff -r 998724a43694 -r aac02a3a395c macros.xml
--- a/macros.xml Tue May 13 11:52:07 2025 +0000
+++ b/macros.xml Mon Aug 04 19:14:00 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>

diff -r 998724a43694 -r aac02a3a395c test-data/blast2tsv_output_with_rn.tab
--- a/test-data/blast2tsv_output_with_rn.tab Tue May 13 11:52:07 2025 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,13 +0,0 @@\n-#algo\tquery_id\tnb_reads\tquery_length\taccession\tdescription\torganism\tpercentIdentity\tnb_hsps\tqueryOverlap\thitOverlap\tevalue\tscore\ttax_id\ttaxonomy\tsequence\n-TBLASTX\tNODE_13_length_295_cov_0.945833\t264\t295\t316155\tpfam13603, 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.\tTursiops truncatus papillomavirus 2\t41.5\t1\t100\t67.0\t2.277e-05\t38.6378\t316155\tViruses;Monodnaviria;Shotokuvirae;Cossaviricota;Papovaviricetes;Zurhausenvirales;Papillomaviridae;Firstpapillomavirinae;Upsilonpapillomavirus;Upsilonpapillomavirus 2;Tursiops truncatus papillomavirus 2\tTGTGTTGGGTGTGTTTGGTTTCCGGTTACCATAATCGCTATTCTTTCAAACAGAAAGCGCATGCTAAGTATTCTCACCCAGAGGAATATGCTGACAAGCCCTCCTCAAAAGGCTATTTTTACAATGCCACCTATGAGAATGCACGAACTCTTATTCACTTCATTAAGCAATATGGATTGCCCTTCAATCCTGTTATTGCACCAGAAGATGCTGAACTAACTGATGAACAGATTCAATCTTACATCAACACAGCAAACTCCTTCTTTAATGATTATCCGACGTTACTGTTCACCCG\n-TBLASTX\tNODE_16_length_278_cov_0.901345\t377\t278\t306845\tpfam00421, PSII, Photosystem II protein. \t\t65.8\t1\t100\t47.0\t7.65615e-39\t132.634\t\t\tGTCTAACCTGTGTTGGGTGTGTTTGGGCTGTAATCGAGGTATAGTGTCGAACAAGTCGGTGTCACTGTTGAATTCTATGGCGGCGAACTCAATGGAGTCAGTTATAGTGATCCTGCTACTGTGAAAAAATATGCTAGACGTGCTCAATTGGGTGAAATTTTTGAATTAGATCGTGCTACTTTAAAATCGGATGGTGTTTTTCGTAGCAGTCCAAGGGGTTGGTTTACTTTTGGACATGCGTCGTTTGCTCTGCTCTTCTTCCAAACACACCCAACACA\n-TBLASTX\tNODE_19_length_271_cov_0.879630\t67\t271\t306845\tpfam00421, PSII, Photosystem II protein. \t\t32.9\t1\t100\t42.0\t1.69015e-11\t56.3644\t\t\tGTCTAACCTGTGTTGGGTGTGTTTGGTATGGAGGGAGGTGTATATGATACCTGGGCACCCGGAGGGGGAGATGTAAGAAAAATTACCAACTTGACCCTTAACCCAAGCGTGATATTTGGTTATTTACTAAAATCTCCTTTTGGGGGAGAAGGATGGATTGTTAGTGTGGACGATTTAGAAGATATAATTGGAGGACATGTCTGGTTAGGCTCCATTTGTATACTTGGTGGAATTTGGCATATCTTAACCAAACACACCCAACACAGGTTAG\n-TBLASTX\tNODE_20_length_267_cov_1.429245\t2\t267\t287774\tpfam10839, DUF2647, Protein of unknown function (DUF2647). This eukaryotic family of proteins are annotated as ycf68 but have no known function.\tDesulfovibrio sp. G100IX\t91.3\t1\t100\t99.0\t7.70073e-10\t48.4966\t287774\tcellular organisms;Bacteria;Pseudomonadati;Thermodesulfobacteriota;Desulfovibrionia;Desulfovibrionales;Desulfovibrionaceae;Desulfovibrio;unclassified Desulfovibrio;Desulfovibrio sp. G100IX\tCTGTGTTGGGTGTGTTTGGACTTGGTATGTGAAGATACGTTGTTAGGTGCTCCGTTTTATTTTCCCATTGAGGCCGAACCTAAACCTGTGCTCGAGAGATAGCTGTCCATATACTGATAAGGGATGTATGGATTCTCGAGAAGAGAGGAGCCATGGTGGTCCCTCCCGGACCGCCCGGATCCCACGAGTGAATAGAAAGTTGGATCTACATTGGATCTCACCTGAATCGCCCCATAAACAACCAAACACACCCAACACAGGTTAGAC\n-TBLASTX\tNODE_22_length_262_cov_1.053140\t262\t262\t306604\tpfam00124, Photo_RC, Photosynthetic reaction centre protein. \tHeterotermes sp. TMJ-2004j\t40.9\t1\t100\t77.0\t4.94039e-28\t99.6256\t306604\tcellular 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\tGTCTAACCTGTGTTGGGTGTGTTTGGCTAGTCAGTAGCTTGTTATATGGGTCGTGAGTGGGAAGTTAGCTTCCGTCTGGGTATGCGCCCGTGGATTGCTGTTGCATATTCAGCTCCTGTTGCAGCTGCTACTGCTGTTTTCTTGATTTACCCAATTGGTCAAGGAAGTTTTTCTGATGGTATGCCTCTAGGAATCTCTGGTACTTTCAACTTCATGATTGTATTCCAGGAGAGCACCCAAACACACCCAACACAGGTTAGAC\n-TBLASTX\tNODE_24_length_258_cov_0.935961\t101\t258\t307679\tpfam01660, 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, '..b'GAAAACTGCAAGCATAGATCTTTCGGCCCTTTCGAAGCTACCGCTTCCGAGAGCCTGGCTAAACTCTGCCCAGATTATCCGATCTGCTTGCCTGTACCTTACGACGTGATCAATAAAGTGTATAGGTATCTCAGAACGCTTAAGAAGCCTGATGTGCAGTCGCCCCACTACCAAACACACCCAACACAGGTTAGAC\n-TBLASTX\tNODE_29_length_250_cov_0.851282\t428\t250\t278700\tpfam00283, Cytochrom_B559, Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits. \tuncultured archaeon CRE-PA11a\t58.6\t1\t100\t100\t7.31211e-08\t42.0012\t278700\tcellular organisms;Archaea;environmental samples;uncultured archaeon CRE-PA11a\tGTCTAACCTGTGTTGGGTGTGTTTGGGTTTCTTTGGAGCAACTCGATGAATTTAGTAAATCCTTTTAGGAGGTTCCCAATGACCATAGATCGAACCTATCCAATTTTTACAGTGCGATGGTTGGCTGTTCACGGACTGGCTGTACCTACTGTTTCTTTTTTAGGGTCAATATCAGCAATGCAGTTCATCCAACGATAAACCTAATTCAAATTATAGAGCTAGCACACCAAACACACCCAACACAGGTTAG\n-TBLASTX\tNODE_34_length_245_cov_1.000000\t183\t245\t250270\tpfam00978, 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.\tNocardia sp. 431D04\t37.5\t1\t100\t38.0\t6.42106e-08\t45.7137\t250270\tcellular organisms;Bacteria;Bacillati;Actinomycetota;Actinomycetes;Mycobacteriales;Nocardiaceae;Nocardia;unclassified Nocardia;Nocardia sp. 431D04\tGTCTAACCTGTGTTGGGTGTGTTTGGATGGTGATCGGCAATTTAAAGGAATGTGTGCGATATTTTCACCAATATTCAAGGAGCTTAAAAATCGACTAAAAAGCGTGTTAGATATTAAATACATGTATGCAGACGGATTGAGACCTGATCAGTTGTCGGAGCGCATGTCACAGATAGGTGCAGGTAAATATTTTATAGAGAATGATATGGAACAGCATCTCGCCAAACACACCCAACACAGGTTAG\n-TBLASTX\tNODE_46_length_229_cov_1.091954\t471\t229\t306604\tpfam00124, Photo_RC, Photosynthetic reaction centre protein. \tHeterotermes sp. TMJ-2004j\t43.9\t1\t100\t66.0\t4.26406e-23\t86.1436\t306604\tcellular 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\tTGTGTTGGGTGTGTTTGGTTGGATGCCTGGAATACAATCATGAAATTGAAAGTACCAGATATTCCTAAAGGCATGCCATCTGAAAAACTTCCTTGACCAATAGGGTAGATCAAGAAAACAGCTGTAGCAGCCGCGACAGGAGCTGAATATGCAACAGCAATCCAAGGACGCATACCCAGACGGAAACTAAGCTCCCTCTCGCTCCAAACACACCCAACACAGGTTAGAC\n-TBLASTX\tNODE_47_length_229_cov_0.816092\t470\t229\t306687\tpfam00223, PsaA_PsaB, Photosystem I psaA/psaB protein. \t\t66.7\t1\t100\t14.0\t1.79906e-13\t61.3066\t\t\tTTGGTAAATTGGCGGAAAGAGGAGGACTCAATGATTATTCGTTCGCCGGAACCAGAAGTAAAAATTTTGGTAGATAGGGATCACATAAAAACTTCTTTCGAGGAATGGGCCAGGCCGGGTCATTTCTCAAGAACACTAGCTAAAGGCCCTGACACTACCACTTGGATCTGGAACCTACATGCTGATGCTCACGATCTTAATAGCCAAACACACCCAACACAGGTTAGAC\n-TBLASTX\tNODE_50_length_226_cov_2.269006\t315\t226\t306845\tpfam00421, PSII, Photosystem II protein. \t\t60.3\t1\t100\t41.0\t2.77182e-23\t89.1064\t\t\tGTCAACGGTGTGTTGGGTGTGTTTGGGAAAGGTCCTGGAATATGGGTGTCCGATCCTTATGGACTAACCGGAACAGTGCAACCTGTAAATCCGGCGTGGGGCGTGGAAGGTTTTGATCCTTTTGTCCCGGGAGGAATAGCTTCTCATCATATTGCAGCAGGTACATTGGGCATATTAGCGGGCCTATTCCATCTTAGCGTACGGTCACCCCAGCCAAACACACCCA\n-TBLASTX\tNODE_56_length_216_cov_1.180124\t166\t216\t306795\tpfam00361, 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.\t\t26.7\t1\t100\t62.0\t5.23486e-07\t42.6815\t\t\tGTGTTGGGTGTGTTTGGGGTCTATGTGGTTTATTTGGTTCTACTGAACCAACATTAAATTTTGAAATATTAACTAATCAGTCCTATCCTGTGGCCTTGGAAATAATATTTTATATTGGATTTTTTCTTGCTTTTGCTGTAAAATTACCAATCATACCCCTACATACATGGTTACCAGATACCCACGAGAGCCAAACACACCCAACACAGGTTAGAC\n'

diff -r 998724a43694 -r aac02a3a395c test-data/blast2tsv_reads_with_rn.txt
--- a/test-data/blast2tsv_reads_with_rn.txt Tue May 13 11:52:07 2025 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r 998724a43694 -r aac02a3a395c test-data/rps_test.tab
--- a/test-data/rps_test.tab Tue May 13 11:52:07 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

diff -r 998724a43694 -r aac02a3a395c virAnnot_rps2tsv.xml
--- a/virAnnot_rps2tsv.xml Tue May 13 11:52:07 2025 +0000
+++ b/virAnnot_rps2tsv.xml Mon Aug 04 19:14:00 2025 +0000

@@ -1,4 +1,4 @@
-<tool id="virAnnot_rps2tsv" name="virAnnot Rps2tsv" version="@TOOL_VERSION@+galaxy0" profile="21.05">
+<tool id="virAnnot_rps2tsv" name="virAnnot Rps2tsv" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
     <description>Convert xml rpstblast results to tab file with taxonomic informations</description>
     <macros>
         <import>macros.xml</import>
@@ -28,7 +28,7 @@
         <test>
             <param name="rps_xml" value="rps_test.xml"/>
             <param name="max_evalue" value="0.0001"/>
-            <output name="output" file="rps_test.tab">
+            <output name="output">
                 <assert_contents>
                     <has_n_columns n="11" />
                     <has_n_lines n="5" />