| Previous changeset 2:48228f4ad1d5 (2016-04-21) Next changeset 4:a0d092f27fdf (2018-01-23) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 0ddf7187a84073a5e01170106e6c1cbab18d23e5 |
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modified:
bp_genbank2gff3.xml macros.xml test-data/seq.gb.0.gff test-data/seq.gb.1.gff |
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| diff -r 48228f4ad1d5 -r 19c318403f13 bp_genbank2gff3.xml --- a/bp_genbank2gff3.xml Thu Apr 21 14:04:02 2016 -0400 +++ b/bp_genbank2gff3.xml Sat Aug 19 08:44:34 2017 -0400 |
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| @@ -24,7 +24,7 @@ $genbank > $gff3]]></command> <inputs> - <param label="Genbank file" name="genbank" type="data" format="gb"/> + <param label="Genbank file" name="genbank" type="data" format="genbank"/> <param name="noinfer" truevalue="" falsevalue="--noinfer" checked="true" type="boolean" label="Infer exon/mRNA subfeatures"/> <conditional name="sofile" label="Sequence Ontology"> <param name="sofile" label="Sequence Ontology File" type="select"> |
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| diff -r 48228f4ad1d5 -r 19c318403f13 macros.xml --- a/macros.xml Thu Apr 21 14:04:02 2016 -0400 +++ b/macros.xml Sat Aug 19 08:44:34 2017 -0400 |
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| @@ -2,6 +2,8 @@ <xml name="requirements"> <requirements> <requirement type="package" version="1.6.922">bioperl</requirement> + <!-- conda bioperl dependency --> + <requirement type="package" version="1.6.924">perl-bioperl</requirement> <yield/> </requirements> </xml> |
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| diff -r 48228f4ad1d5 -r 19c318403f13 test-data/seq.gb.0.gff --- a/test-data/seq.gb.0.gff Thu Apr 21 14:04:02 2016 -0400 +++ b/test-data/seq.gb.0.gff Sat Aug 19 08:44:34 2017 -0400 |
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| @@ -1,10 +1,12 @@ +# Input: /tmp/tmp1YCbBQ/files/000/dataset_1.dat ##gff-version 3 ##sequence-region NC_014662 1 165540 # conversion-by bp_genbank2gff3.pl # organism Enterobacteria phage CC31 # Note Enterobacteria phage CC31, complete genome. # date 12-NOV-2010 -NC_014662 GenBank region 1 165540 . + 1 ID=NC_014662;Dbxref=BioProject:PRJNA60119,taxon:709484;Name=NC_014662;Note=Enterobacteria phage CC31%2C complete genome.,PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI review. The reference sequence is identical to GU323318. COMPLETENESS: full length. ;comment1=PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI review. The reference sequence is identical to GU323318. COMPLETENESS: full length. ;date=12-NOV-2010;host=Escherichia coli;mol_type=genomic DNA;organism=Enterobacteria phage CC31 +# working on contig:NC_014662, Enterobacteria phage CC31, Enterobacteria phage CC31, complete genome., 12-NOV-2010 +NC_014662 GenBank contig 1 165540 . + 1 ID=NC_014662;Dbxref=BioProject:PRJNA60119,taxon:709484;Name=NC_014662;Note=Enterobacteria phage CC31%2C complete genome.,PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI review. The reference sequence is identical to GU323318. COMPLETENESS: full length. ;comment1=PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI review. The reference sequence is identical to GU323318. COMPLETENESS: full length. ;date=12-NOV-2010;host=Escherichia coli;mol_type=genomic DNA;organism=Enterobacteria phage CC31 NC_014662 GenBank gene 1 2214 . - 1 ID=CC31p001;Dbxref=GeneID:9926434;Name=rIIA;locus_tag=CC31p001 NC_014662 GenBank mRNA 1 2214 . - 1 ID=CC31p001.t01;Parent=CC31p001 NC_014662 GenBank CDS 1 2214 . - 1 ID=CC31p001.p01;Parent=CC31p001.t01;Dbxref=GI:311992993,GeneID:9926434;Name=rIIA;codon_start=1;locus_tag=CC31p001;product=membrane-associated affects host membrane ATPase;protein_id=YP_004009859.1;transl_table=11;translation=length.737 @@ -1145,6 +1147,7 @@ NC_014662 GenBank mRNA 164610 165521 . - 1 ID=CC31p279.t01;Parent=CC31p279 NC_014662 GenBank CDS 164610 165521 . - 1 ID=CC31p279.p01;Parent=CC31p279.t01;Dbxref=GI:311993271,GeneID:9926433;Name=rIIB;codon_start=1;locus_tag=CC31p279;product=protector from prophage-induced early lysis;protein_id=YP_004010137.1;transl_table=11;translation=length.303 NC_014662 GenBank exon 164610 165521 . - 1 Parent=CC31p279.t01 +# GFF3 saved to stdout2829 ##FASTA >NC_014662 TTACTCATCTTCATCTTTACCTTTTAAGGAAGGAGCGCTTTCCAGCGCTCTCATAATACG |
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| diff -r 48228f4ad1d5 -r 19c318403f13 test-data/seq.gb.1.gff --- a/test-data/seq.gb.1.gff Thu Apr 21 14:04:02 2016 -0400 +++ b/test-data/seq.gb.1.gff Sat Aug 19 08:44:34 2017 -0400 |
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| b'@@ -1,4 +1,4 @@\n-# Input: test-data/seq.gb\n+# Input: /tmp/tmp1YCbBQ/files/000/dataset_3.dat\n ##gff-version 3\n ##sequence-region NC_014662 1 165540\n # conversion-by bp_genbank2gff3.pl\n@@ -7,581 +7,1147 @@\n # date 12-NOV-2010\n # working on contig:NC_014662, Enterobacteria phage CC31, Enterobacteria phage CC31, complete genome., 12-NOV-2010\n NC_014662\tGenBank\tcontig\t1\t165540\t.\t+\t1\tID=NC_014662;Dbxref=BioProject:PRJNA60119,taxon:709484;Name=NC_014662;Note=Enterobacteria phage CC31%2C complete genome.,PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI review. The reference sequence is identical to GU323318. COMPLETENESS: full length. ;comment1=PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI review. The reference sequence is identical to GU323318. COMPLETENESS: full length. ;date=12-NOV-2010;host=Escherichia coli;mol_type=genomic DNA;organism=Enterobacteria phage CC31\n-NC_014662\tGenBank\tCDS\t1\t2214\t.\t-\t1\tID=CC31p001;Dbxref=GI:311992993,GeneID:9926434;Name=rIIA;codon_start=1;locus_tag=CC31p001;product=membrane-associated affects host membrane ATPase;protein_id=YP_004009859.1;transl_table=11;translation=length.737\n-NC_014662\tGenBank\tgene\t1\t2214\t.\t-\t1\tID=CC31p001.gene;Alias=CC31p001;Dbxref=GeneID:9926434;Name=rIIA;locus_tag=CC31p001\n-NC_014662\tGenBank\tCDS\t2220\t2426\t.\t-\t1\tID=CC31p002;Dbxref=GI:311992994,GeneID:9926148;Name=rIIA.1;codon_start=1;locus_tag=CC31p002;product=hypothetical protein;protein_id=YP_004009860.1;transl_table=11;translation=length.68\n-NC_014662\tGenBank\tgene\t2220\t2426\t.\t-\t1\tID=CC31p002.gene;Alias=CC31p002;Dbxref=GeneID:9926148;Name=rIIA.1;locus_tag=CC31p002\n-NC_014662\tGenBank\tCDS\t2420\t2704\t.\t-\t1\tID=CC31p003;Dbxref=GI:311992995,GeneID:9926149;Name=CC31p003;Note=predicted by GenMarkS;codon_start=1;product=hypothetical protein;protein_id=YP_004009861.1;transl_table=11;translation=length.94\n-NC_014662\tGenBank\tgene\t2420\t2704\t.\t-\t1\tID=CC31p003.gene;Alias=CC31p003;Dbxref=GeneID:9926149;Name=CC31p003\n-NC_014662\tGenBank\tCDS\t2750\t2905\t.\t-\t1\tID=CC31p004;Dbxref=GI:311992996,GeneID:9926150;Name=CC31p004;Note=predicted by GenMarkS;codon_start=1;product=hypothetical protein;protein_id=YP_004009862.1;transl_table=11;translation=length.51\n-NC_014662\tGenBank\tgene\t2750\t2905\t.\t-\t1\tID=CC31p004.gene;Alias=CC31p004;Dbxref=GeneID:9926150;Name=CC31p004\n-NC_014662\tGenBank\tCDS\t2945\t4789\t.\t-\t1\tID=CC31p005;Dbxref=GI:311992997,GeneID:9926151;Name=60plus39;codon_start=1;locus_tag=CC31p005;product=DNA topoisomerase subunit;protein_id=YP_004009863.1;transl_table=11;translation=length.614\n-NC_014662\tGenBank\tgene\t2945\t4789\t.\t-\t1\tID=CC31p005.gene;Alias=CC31p005;Dbxref=GeneID:9926151;Name=60plus39;locus_tag=CC31p005\n-NC_014662\tGenBank\tCDS\t4835\t5302\t.\t-\t1\tID=CC31p006;Dbxref=GI:311992998,GeneID:9926152;Name=CC31p006;Note=predicted by GenMarkS;codon_start=1;product=hypothetical protein;protein_id=YP_004009864.1;transl_table=11;translation=length.155\n-NC_014662\tGenBank\tgene\t4835\t5302\t.\t-\t1\tID=CC31p006.gene;Alias=CC31p006;Dbxref=GeneID:9926152;Name=CC31p006\n-NC_014662\tGenBank\tCDS\t5302\t6837\t.\t-\t1\tID=CC31p007;Dbxref=GI:311992999,GeneID:9926153;Name=CC31p007;Note=N-terminal part is similar to Hoc protein and C-terminal part is similar to lipolytic enzyme%2C G-D-S-L;codon_start=1;product=hypothetical protein;protein_id=YP_004009865.1;transl_table=11;translation=length.511\n-NC_014662\tGenBank\tgene\t5302\t6837\t.\t-\t1\tID=CC31p007.gene;Alias=CC31p007;Dbxref=GeneID:9926153;Name=CC31p007\n-NC_014662\tGenBank\tCDS\t6870\t7130\t.\t-\t1\tID=CC31p008;Dbxref=GI:311993000,GeneID:9926154;Name=39.1;codon_start=1;locus_tag=CC31p008;product=gp39.1 hypothetical protein;protein_id=YP_004009866.1;transl_table=11;translation=length.86\n-NC_014662\tGenBank\tgene\t6870\t7130\t.\t-\t1\tID=CC31p008.gene;Alias=CC31p008;Dbxref=GeneID:9926154;Name=39.1;locus_tag=CC31p008\n-NC_014662\tGenBank\tCDS\t7127\t7222\t.\t-\t1\tID=CC31p009;Dbxref=GI:311993001,GeneID:9926155;Name=CC31p009;Note=predicted by GenMarkS;codon_start=1;product=hypothetical protein;protein_id=YP_004009867.1;trans'..b'VLGKFLYDEAGRVYSPGNKPNNVDVGLGNVSNDAQVKINTTTLQTMAG\n PLAAPNLSSLNAASAPQHVPRFDQIVVRDSIQDFGTY\n->CC31p257\n+>CC31p257.p01\n MATIKQIQFKRSNVAGKRPLPADIAEGELAINIKDSTLFTKNADGQIIDLGFAKGGRIDG\n DVVQVGNYTQTGNYITSGDVSAKTILASAGVSSNGDIVAERGVIRTRAASSGNAHLWFEG\n EEITGENRNKERGVLYATQQTDTDGRVNLRVYNGKAHAANTNNALFVFNGAGDFAAPKDL\n@@ -4559,54 +5125,54 @@\n GAYHIAAMDVYAPSGNGYVRLVIRNGGAHIWNNSSYTSPVQINAPEFYLTSDISLKKDIR\n SIEDSRSNLHKVEIKRYAMKDGSNDNAIGVIAQEVQEVYPELVNENKDTGKLSVNYRGLS\n SVLWKIVQEQDKELEDVKSRLARIEELLSK\n->CC31p258\n+>CC31p258.p01\n MAIAGPNIGTSWFRETGQRPMSAARVAVRLPARPGGARQMVGLSKEVNYNIGANNSYNKD\n TLINYLRSQGSTPVVVTITGNLVSYSSGVACLEFPANLPNAYVHLIINGGVTLYGRGGNG\n GVKGNGAAGGHAINNQFGTRLRITNNGAIAGGGGGGGGNSANGGMGGGGRPFGYADKTHP\n PAAATSRAATDGTLTSPGIGAEYKIGTAVQYTCGSGGNVGANGGASTGRLGTNYGGGSAG\n RAVIGNAPTWNKVGTIYGSRV\n->CC31p259\n+>CC31p259.p01\n MTQRTPLPGISDILFGVLDRLFKDNATGRVLASRIVALIVVFILSLTWYRLDAIMQVWKE\n SRYETYTKVLQQDKEAKFEASALEQLQIAHVSSNADFSAIYSFRPRNLNYFVDLIAYEGR\n LPSTVNEKNLGGFPVDKTSNEYSAHLRGAYFSSEDEFVFLPTKKKDGELKYMYSCPYFNL\n DNVYAGTVSMYWYSKPLLNENRLAAICSQAARTLGRAK\n->CC31p260\n+>CC31p260.p01\n MSKLEIVREIVTVASVLIKFGSEHILEKREHFIAFLNEIGIKNDLGRPLNQSNFRKMIEE\n MTAEEKQQLVEEFNEGFESVYRYMMMYSKP\n->CC31p261\n+>CC31p261.p01\n MNQTVEIQRYLEGMMNKLALGDMVDYSYQEAMEICHWMKRRVRVVGAEWYISAELIDGRY\n AIRYDSGDEYVTLPGHVLQRWEVVN\n->CC31p262\n+>CC31p262.p01\n MNKISHIEAERKAWDEHTSVVDAITPVYHLVVWFSLSQEEQDCSWKYFEDTTFQKFVNAI\n NHPESLLTHCEIKASEETFCYFTVSSKRSVSDVMQGYQFLKGVADEFELKINYEKI\n->CC31p263\n+>CC31p263.p01\n MSTSEIKMVPYVTYTSERLREFQDQFNGTGIFYDTLSEIENDVKSDINDNDFIIRMFLNG\n TFEIVAISDKRIEDAIAHIDNIIDEMTEGYYE\n->CC31p264\n+>CC31p264.p01\n MNNPVAKHDFNKGGAHKDMKRQEKESRRKQKHKGKGYEHI\n->CC31p265\n+>CC31p265.p01\n MSDLSCLRHNIILIKTQIASLQRANEMMDENWGTYANDPGFRMAEHPFMKKLLGKDYICP\n FETPYNGGVKPFLLDIYKAMNNEMIKELERRLEQLNENNTQKE\n->CC31p266\n+>CC31p266.p01\n MNGDLIETQNIGERIPEICFIKADWWDGRLLQRVIVCAANRFKLKDGGELVIPGTRHYSK\n DMALVLDQMRDKVVSEQVYGDDQGFLDQWGNYLTRKEALIIATHAGQINTRRQKGGPADT\n LFSEDLY\n->CC31p267\n+>CC31p267.p01\n MNMKNLNAQIDRVKKSMNRPAILNELQRCAERVTDEHYLPTEAWEVWFRGTHLGSIERKY\n KGCYAVHSSLGRHCGDCATYMQALARFIDSCSVVIAKKELEEVEEWINEVVKEPELRVWG\n IREPKTLWQKIKGFFK\n->CC31p268\n+>CC31p268.p01\n MSKVIYIVKASENSISENAANVLIVVAKKDFITSSEVRDVLADKLSAASVNSNIGVLIKK\n GLIEKSGDGLIVSAEGQEIINQAAVIYAEENAPELLEKRNTRKARPITDQMEADKNLMME\n ILATKDNLFTIKKLDVYRSNFIAVLEKRTFGIRSFEVSNKGNFRISGYKMTEEQVKHFED\n LGMVAKHSKNGNVYLDIPRTQENIENIIHAVDTL\n->CC31p269\n+>CC31p269.p01\n MKTLINNLNALLANSGVDLDDTMHAARLHSSNTDSNSYLTIWYNTESENYVLVWVYVNNY\n DMVAVLDAEVEDVAETLNEAKKLFADFFRG\n->CC31p270\n+>CC31p270.p01\n MISIIVAALKNGGVITETSDFAYVKFNRMSIDKDTQARYWVMVYDHNESQYILTEVLVDL\n ETMEADFVGCPELEGTFEEVLEAYVAK\n->CC31p271\n+>CC31p271.p01\n MTTIFDMMAKQVDDSIGQLNLRDLQSIIDNEAKEFAIYTVENRAIPNLIDGFKPVQRFVI\n ARALDLSRGNKEKFHKLASVAGGVADLGYHHGEGSAQDAGALMANTWNNNYPLLDGQGNF\n GSRLVQKAAASRYIFCRISDNFRKVYKDTEIAPEHKDKEHVPPAFYLPIIPTVLLNGVQG\n@@ -4615,28 +5181,28 @@\n DEKYRHEKIMRDFKLVEKMSQFIVVIDENGKLNDKFQSSSELIKHFVEVRKTYIVKRIEH\n KIKECDEAFKLALAKAMFIKEVIEGSIVIQGKTRKQLTSELESRPTYAPFADKLVSMNIY\n HITSDEAKKLAQQAKDLKAELKYWQETTPETEYMKDLEAL\n->CC31p272\n+>CC31p272.p01\n MKLTVSIILALIIASAGFVGVCYVIYEIMLFLACVMMDLGNLIW\n->CC31p273\n+>CC31p273.p01\n MSPFKQIWALVFLLMAPLFIASGIFIWEGLTPPPRVIGSMCFGVAALAVERLFYYTGLTK\n \n->CC31p274\n+>CC31p274.p01\n MRDYMTRGDILAAGGTHVVSVKNGETVGYVDPSVLAEPGFYFMVKGASAWRAVAARFYVG\n RQRSKSGFMNVLSQIRQGRSQLGRTMRSNNVIYDVYFIPADKMKPLTTGFGKGQLALAFT\n RKHNDSYQNLEEMNRMLNDNFKFILQAY\n->CC31p275\n+>CC31p275.p01\n MGRKVYSSSMNKMQKIFWIFFSIIAIMVFVGIGFSIWATVEIVNVIQTEGLKGAVEVLMN\n GAQQSSGL\n->CC31p276\n+>CC31p276.p01\n MNIIKKILKAIWTLTLLMVLFGAFAFALAHDVVMAWINF\n->CC31p277\n+>CC31p277.p01\n MKALKTFTRAFSDLTPEDRVKIKSTAAYSLRQDPDQDKTEVINRCAIAQLAEKAVADWMD\n GYVAGGQENHDDPYTYAWDVLAHPRFCGLRVEVKTHQSDSKWISVTTGYSGDYPGGSGIN\n LGPFLTHRIADCIIILDVVESGPSVYQFTLKFAGDHEDLKSVVRKSNYQGWYLNL\n->CC31p278\n+>CC31p278.p01\n MINPFNVSDSAVVNLRGDHYAKSVYCRKLVKHPGDVHYAWLHCDEVVNEIPPADAEYLEE\n DDRIYFGELHIRGIYGKDESRPVEIESPEDFYPGVQ\n->CC31p279\n+>CC31p279.p01\n MFNDVEKVAIHDEFMQGYTQTELAEIYSCSVDTIRRVVNEIKSRKAEVEPEVKVTSPVKV\n FNPEDVVWAGSSKFLSITVGRDTYAADKDHPNFKEALQFCVDGDFESAINLINIEKAITS\n YVDGNIRIENGQLFYQDIEIKSGLVDRIINDMQNGEDFEFYLPFLENLLENPSKTAVTRL\n' |