# HG changeset patch # User genouest # Date 1695646032 0 # Node ID 7bc75dd0f78284a030fce4be6c9e00365807b4bd # Parent 1b08e39cc52d696cb08db25276a445737723db4c planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/helixer commit e516933a2c3aa6bcd336a0b5c072893fe9019dd9 diff -r 1b08e39cc52d -r 7bc75dd0f782 helixer.xml --- a/helixer.xml Wed Jun 28 08:39:38 2023 +0000 +++ b/helixer.xml Mon Sep 25 12:47:12 2023 +0000 @@ -6,16 +6,12 @@ - + [0-9a-zA-Z_]+ - +
@@ -82,26 +78,45 @@ - - - - - - - - - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - 0.3.1 + 0.3.2 @@ -9,9 +9,9 @@ - gglyptodon/helixer-docker:helixer_v@TOOL_VERSION@_cuda_11.2.0-cudnn8 + gglyptodon/helixer-docker:helixer_v@TOOL_VERSION@_cuda_11.8.0-cudnn8 - + @@ -26,6 +26,5 @@ - diff -r 1b08e39cc52d -r 7bc75dd0f782 test-data/fungi.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fungi.gff3 Mon Sep 25 12:47:12 2023 +0000 @@ -0,0 +1,4 @@ +##gff-version 3.2.1 +##species +# c62d9615e722c2f927a0de3f4fcf5b70 /shared/ifbstor1/galaxy/jobs/003/517/3517616/home/.local/share/Helixer/models/fungi/fungi_v0.3_a_0100.h5 +##sequence-region NC_034365.1:c72045-70009 1 2037 diff -r 1b08e39cc52d -r 7bc75dd0f782 test-data/invertebrate.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/invertebrate.gff3 Mon Sep 25 12:47:12 2023 +0000 @@ -0,0 +1,13 @@ +##gff-version 3.2.1 +##species +# fdd5a925728cf56e2470d96beeeb797b /shared/ifbstor1/galaxy/jobs/003/517/3517615/home/.local/share/Helixer/models/invertebrate/invertebrate_v0.3_m_0100.h5 +##sequence-region NC_034365.1:c72045-70009 1 2037 +NC_034365.1:c72045-70009 Helixer gene 1029 2037 . + . ID=_NC_034365.1:c72045-70009_000001 +NC_034365.1:c72045-70009 Helixer mRNA 1029 2037 . + . ID=_NC_034365.1:c72045-70009_000001.1;Parent=_NC_034365.1:c72045-70009_000001 +NC_034365.1:c72045-70009 Helixer exon 1029 1228 . + . ID=_NC_034365.1:c72045-70009_000001.1.exon.1;Parent=_NC_034365.1:c72045-70009_000001.1 +NC_034365.1:c72045-70009 Helixer five_prime_UTR 1029 1035 . + . ID=_NC_034365.1:c72045-70009_000001.1.five_prime_UTR.1;Parent=_NC_034365.1:c72045-70009_000001.1 +NC_034365.1:c72045-70009 Helixer CDS 1036 1228 . + 0 ID=_NC_034365.1:c72045-70009_000001.1.CDS.1;Parent=_NC_034365.1:c72045-70009_000001.1 +NC_034365.1:c72045-70009 Helixer exon 1595 1598 . + . ID=_NC_034365.1:c72045-70009_000001.1.exon.2;Parent=_NC_034365.1:c72045-70009_000001.1 +NC_034365.1:c72045-70009 Helixer CDS 1595 1598 . + 2 ID=_NC_034365.1:c72045-70009_000001.1.CDS.2;Parent=_NC_034365.1:c72045-70009_000001.1 +NC_034365.1:c72045-70009 Helixer exon 1812 2037 . + . ID=_NC_034365.1:c72045-70009_000001.1.exon.3;Parent=_NC_034365.1:c72045-70009_000001.1 +NC_034365.1:c72045-70009 Helixer CDS 1812 2037 . + 1 ID=_NC_034365.1:c72045-70009_000001.1.CDS.3;Parent=_NC_034365.1:c72045-70009_000001.1 diff -r 1b08e39cc52d -r 7bc75dd0f782 test-data/land_plant.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/land_plant.gff3 Mon Sep 25 12:47:12 2023 +0000 @@ -0,0 +1,17 @@ +##gff-version 3.2.1 +##species +# f0e00efcbea83c66b69258d11119a691 /shared/ifbstor1/galaxy/jobs/003/517/3517613/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5 +##sequence-region NC_034365.1:c72045-70009 1 2037 +NC_034365.1:c72045-70009 Helixer gene 1035 1269 . + . ID=_NC_034365.1:c72045-70009_000001 +NC_034365.1:c72045-70009 Helixer mRNA 1035 1269 . + . ID=_NC_034365.1:c72045-70009_000001.1;Parent=_NC_034365.1:c72045-70009_000001 +NC_034365.1:c72045-70009 Helixer exon 1035 1269 . + . ID=_NC_034365.1:c72045-70009_000001.1.exon.1;Parent=_NC_034365.1:c72045-70009_000001.1 +NC_034365.1:c72045-70009 Helixer five_prime_UTR 1035 1035 . + . ID=_NC_034365.1:c72045-70009_000001.1.five_prime_UTR.1;Parent=_NC_034365.1:c72045-70009_000001.1 +NC_034365.1:c72045-70009 Helixer CDS 1036 1260 . + 0 ID=_NC_034365.1:c72045-70009_000001.1.CDS.1;Parent=_NC_034365.1:c72045-70009_000001.1 +NC_034365.1:c72045-70009 Helixer three_prime_UTR 1261 1269 . + . ID=_NC_034365.1:c72045-70009_000001.1.three_prime_UTR.1;Parent=_NC_034365.1:c72045-70009_000001.1 +NC_034365.1:c72045-70009 Helixer gene 1603 2037 . + . ID=_NC_034365.1:c72045-70009_000002 +NC_034365.1:c72045-70009 Helixer mRNA 1603 2037 . + . ID=_NC_034365.1:c72045-70009_000002.1;Parent=_NC_034365.1:c72045-70009_000002 +NC_034365.1:c72045-70009 Helixer exon 1603 1725 . + . ID=_NC_034365.1:c72045-70009_000002.1.exon.1;Parent=_NC_034365.1:c72045-70009_000002.1 +NC_034365.1:c72045-70009 Helixer five_prime_UTR 1603 1606 . + . ID=_NC_034365.1:c72045-70009_000002.1.five_prime_UTR.1;Parent=_NC_034365.1:c72045-70009_000002.1 +NC_034365.1:c72045-70009 Helixer CDS 1607 1725 . + 0 ID=_NC_034365.1:c72045-70009_000002.1.CDS.1;Parent=_NC_034365.1:c72045-70009_000002.1 +NC_034365.1:c72045-70009 Helixer exon 1812 2037 . + . ID=_NC_034365.1:c72045-70009_000002.1.exon.2;Parent=_NC_034365.1:c72045-70009_000002.1 +NC_034365.1:c72045-70009 Helixer CDS 1812 2037 . + 1 ID=_NC_034365.1:c72045-70009_000002.1.CDS.2;Parent=_NC_034365.1:c72045-70009_000002.1 diff -r 1b08e39cc52d -r 7bc75dd0f782 test-data/ouput_species.gff3 --- a/test-data/ouput_species.gff3 Wed Jun 28 08:39:38 2023 +0000 +++ b/test-data/ouput_species.gff3 Mon Sep 25 12:47:12 2023 +0000 @@ -14,4 +14,4 @@ NC_034365.1:c72045-70009 Helixer five_prime_UTR 1603 1606 . + . ID=Arabidopsis_NC_034365.1:c72045-70009_000002.1.five_prime_UTR.1;Parent=Arabidopsis_NC_034365.1:c72045-70009_000002.1 NC_034365.1:c72045-70009 Helixer CDS 1607 1725 . + 0 ID=Arabidopsis_NC_034365.1:c72045-70009_000002.1.CDS.1;Parent=Arabidopsis_NC_034365.1:c72045-70009_000002.1 NC_034365.1:c72045-70009 Helixer exon 1812 2037 . + . ID=Arabidopsis_NC_034365.1:c72045-70009_000002.1.exon.2;Parent=Arabidopsis_NC_034365.1:c72045-70009_000002.1 -NC_034365.1:c72045-70009 Helixer CDS 1812 2037 . + 1 ID=Arabidopsis_NC_034365.1:c72045-70009_000002.1.CDS.2;Parent=Arabidopsis_NC_034365.1:c72045-70009_000002.1 +NC_034365.1:c72045-70009 Helixer CDS 1812 2037 . + 1 ID=Arabidopsis_NC_034365.1:c72045-70009_000002.1.CDS.2;Parent=Arabidopsis_NC_034365.1:c72045-70009_000002.1 \ No newline at end of file diff -r 1b08e39cc52d -r 7bc75dd0f782 test-data/output.gff3 --- a/test-data/output.gff3 Wed Jun 28 08:39:38 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,17 +0,0 @@ -##gff-version 3.2.1 -##species -# f0e00efcbea83c66b69258d11119a691 /tmp/tmpyabgcmro/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5 -##sequence-region NC_034365.1:c72045-70009 1 2037 -NC_034365.1:c72045-70009 Helixer gene 1035 1269 . + . ID=_NC_034365.1:c72045-70009_000001 -NC_034365.1:c72045-70009 Helixer mRNA 1035 1269 . + . ID=_NC_034365.1:c72045-70009_000001.1;Parent=_NC_034365.1:c72045-70009_000001 -NC_034365.1:c72045-70009 Helixer exon 1035 1269 . + . ID=_NC_034365.1:c72045-70009_000001.1.exon.1;Parent=_NC_034365.1:c72045-70009_000001.1 -NC_034365.1:c72045-70009 Helixer five_prime_UTR 1035 1035 . + . ID=_NC_034365.1:c72045-70009_000001.1.five_prime_UTR.1;Parent=_NC_034365.1:c72045-70009_000001.1 -NC_034365.1:c72045-70009 Helixer CDS 1036 1260 . + 0 ID=_NC_034365.1:c72045-70009_000001.1.CDS.1;Parent=_NC_034365.1:c72045-70009_000001.1 -NC_034365.1:c72045-70009 Helixer three_prime_UTR 1261 1269 . + . ID=_NC_034365.1:c72045-70009_000001.1.three_prime_UTR.1;Parent=_NC_034365.1:c72045-70009_000001.1 -NC_034365.1:c72045-70009 Helixer gene 1603 2037 . + . ID=_NC_034365.1:c72045-70009_000002 -NC_034365.1:c72045-70009 Helixer mRNA 1603 2037 . + . ID=_NC_034365.1:c72045-70009_000002.1;Parent=_NC_034365.1:c72045-70009_000002 -NC_034365.1:c72045-70009 Helixer exon 1603 1725 . + . ID=_NC_034365.1:c72045-70009_000002.1.exon.1;Parent=_NC_034365.1:c72045-70009_000002.1 -NC_034365.1:c72045-70009 Helixer five_prime_UTR 1603 1606 . + . ID=_NC_034365.1:c72045-70009_000002.1.five_prime_UTR.1;Parent=_NC_034365.1:c72045-70009_000002.1 -NC_034365.1:c72045-70009 Helixer CDS 1607 1725 . + 0 ID=_NC_034365.1:c72045-70009_000002.1.CDS.1;Parent=_NC_034365.1:c72045-70009_000002.1 -NC_034365.1:c72045-70009 Helixer exon 1812 2037 . + . ID=_NC_034365.1:c72045-70009_000002.1.exon.2;Parent=_NC_034365.1:c72045-70009_000002.1 -NC_034365.1:c72045-70009 Helixer CDS 1812 2037 . + 1 ID=_NC_034365.1:c72045-70009_000002.1.CDS.2;Parent=_NC_034365.1:c72045-70009_000002.1 diff -r 1b08e39cc52d -r 7bc75dd0f782 test-data/vertebrate.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vertebrate.gff3 Mon Sep 25 12:47:12 2023 +0000 @@ -0,0 +1,4 @@ +##gff-version 3.2.1 +##species +# acedf94d7c4f811e877da07844bc58f4 /shared/ifbstor1/galaxy/jobs/003/517/3517614/home/.local/share/Helixer/models/vertebrate/vertebrate_v0.3_m_0080.h5 +##sequence-region NC_034365.1:c72045-70009 1 2037