Mercurial > repos > iuc > integron_finder
changeset 3:bfd290fe1588 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder commit cbb56e087d23446b8159622e2e4b7a709c8529ad
| author | iuc |
|---|---|
| date | Fri, 14 Jun 2024 21:19:29 +0000 |
| parents | 392f100eebcd |
| children | |
| files | macro.xml test-data/integron_log test-data/summary.tsv test-data/test10_integrons_table.tsv test-data/test1_integrons_table.tsv test-data/test2_integrons_table.tsv test-data/test3_integrons_table.tsv test-data/test4_integrons_table.tsv test-data/test5_integrons_table.tsv test-data/test6_integrons_table.tsv test-data/test7_integrons_table.tsv test-data/test8_integrons_table.tsv test-data/test9_integrons_table.tsv test-data/test9_summary.tsv |
| diffstat | 14 files changed, 42 insertions(+), 23 deletions(-) [+] |
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--- a/macro.xml Sun Feb 25 16:08:08 2024 +0000 +++ b/macro.xml Fri Jun 14 21:19:29 2024 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">2.0.3</token> + <token name="@TOOL_VERSION@">2.0.5</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">22.05</token> <token name="@THREADS@">\${GALAXY_SLOTS:-2}</token>
--- a/test-data/integron_log Sun Feb 25 16:08:08 2024 +0000 +++ b/test-data/integron_log Fri Jun 14 21:19:29 2024 +0000 @@ -9,12 +9,12 @@ ************************************************************************** -integron_finder version 2.0.3 +integron_finder version 2.0.5 Using: - - Python 3.12.1 | packaged by conda-forge | (main, Dec 23 2023, 08:03:24) [GCC 12.3.0] + - Python 3.12.3 | packaged by conda-forge | (main, Apr 15 2024, 18:38:13) [GCC 12.3.0] - numpy 1.26.4 - - pandas 2.2.0 - - matplolib 3.8.2 + - pandas 2.2.2 + - matplolib 3.8.4 - biopython 1.83 - Prodigal V2.6.3: February, 2016 @@ -34,7 +34,7 @@ Haft, DH et al., Nucleic Acids Res. 2018 Jan 4;46(D1):D851-D860 PMID: 29112715 - + ======================= @@ -54,7 +54,7 @@ ======================= -command used: integron_finder /tmp/tmpx8hgxvv4/files/4/8/1/dataset_481be4e5-1005-4f8f-8196-c85c63664801.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 +command used: integron_finder /tmp/tmphy8ici_1/files/3/c/0/dataset_3c0e648b-467e-4d54-a0da-908f237d87ff.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 =======================
--- a/test-data/summary.tsv Sun Feb 25 16:08:08 2024 +0000 +++ b/test-data/summary.tsv Fri Jun 14 21:19:29 2024 +0000 @@ -1,3 +1,4 @@ -# cmd: integron_finder /tmp/tmpx8hgxvv4/files/b/e/e/dataset_bee350c4-08fc-401b-b91f-5769817c474a.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 --union-integrases --func-annot +# integron_finder 2.0.5 +# cmd: integron_finder /tmp/tmphy8ici_1/files/2/e/b/dataset_2ebb353a-12c6-4a70-b30a-5bd0ab3efdce.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 --union-integrases --func-annot ID_replicon CALIN complete In0 topology size ACBA.007.P01_13 0 1 0 circ 20301
--- a/test-data/test10_integrons_table.tsv Sun Feb 25 16:08:08 2024 +0000 +++ b/test-data/test10_integrons_table.tsv Fri Jun 14 21:19:29 2024 +0000 @@ -1,4 +1,5 @@ -# cmd: integron_finder /tmp/tmpx8hgxvv4/files/b/e/e/dataset_bee350c4-08fc-401b-b91f-5769817c474a.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 --union-integrases --func-annot +# integron_finder 2.0.5 +# cmd: integron_finder /tmp/tmphy8ici_1/files/2/e/b/dataset_2ebb353a-12c6-4a70-b30a-5bd0ab3efdce.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 --union-integrases --func-annot ID_integron ID_replicon element pos_beg pos_end strand evalue type_elt annotation model type default distance_2attC considered_topology integron_01 ACBA.007.P01_13 ACBA.007.P01_13_1 55 1014 1 1.9e-25 protein intI intersection_tyr_intI complete Yes NA circ integron_01 ACBA.007.P01_13 ACBA.007.P01_13_20 17375 17722 -1 9.800000000000001e-65 protein SMR_qac_E-NCBIFAM NF000276.2 complete Yes NA circ
--- a/test-data/test1_integrons_table.tsv Sun Feb 25 16:08:08 2024 +0000 +++ b/test-data/test1_integrons_table.tsv Fri Jun 14 21:19:29 2024 +0000 @@ -1,4 +1,5 @@ -# cmd: integron_finder /tmp/tmpx8hgxvv4/files/4/8/1/dataset_481be4e5-1005-4f8f-8196-c85c63664801.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 +# integron_finder 2.0.5 +# cmd: integron_finder /tmp/tmphy8ici_1/files/3/c/0/dataset_3c0e648b-467e-4d54-a0da-908f237d87ff.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 ID_integron ID_replicon element pos_beg pos_end strand evalue type_elt annotation model type default distance_2attC considered_topology integron_01 ACBA.007.P01_13 ACBA.007.P01_13_1 55 1014 1 1.9e-25 protein intI intersection_tyr_intI complete Yes NA circ integron_01 ACBA.007.P01_13 ACBA.007.P01_13_20 17375 17722 -1 NA protein protein NA complete Yes NA circ
--- a/test-data/test2_integrons_table.tsv Sun Feb 25 16:08:08 2024 +0000 +++ b/test-data/test2_integrons_table.tsv Fri Jun 14 21:19:29 2024 +0000 @@ -1,6 +1,14 @@ -# cmd: integron_finder /tmp/tmpx8hgxvv4/files/9/c/7/dataset_9c7b9167-33f0-4cb0-8bad-0edb132a2f75.dat --cpu 1 --keep-tmp --local-max --linear -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 +# integron_finder 2.0.5 +# cmd: integron_finder /tmp/tmphy8ici_1/files/8/1/3/dataset_8137b4e1-31db-4985-96ff-fe68cc586a9d.dat --cpu 1 --keep-tmp --local-max --linear -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 ID_integron ID_replicon element pos_beg pos_end strand evalue type_elt annotation model type default distance_2attC considered_topology -integron_01 ACBA.007.P01_13 ACBA.007.P01_13_1 55 1014 1 1.9e-25 protein intI intersection_tyr_intI In0 No NA lin +integron_01 ACBA.007.P01_13 ACBA.007.P01_13_1 55 1014 1 1.9e-25 protein intI intersection_tyr_intI complete No NA lin +integron_01 ACBA.007.P01_13 ACBA.007.P01_13_2 905 1609 -1 NA protein protein NA complete No NA lin +integron_01 ACBA.007.P01_13 attc_001 1453 1504 1 0.31 attC attC attc_4 complete No NA lin +integron_01 ACBA.007.P01_13 ACBA.007.P01_13_3 1722 2537 -1 NA protein protein NA complete No NA lin +integron_01 ACBA.007.P01_13 ACBA.007.P01_13_4 2667 2900 1 NA protein protein NA complete No NA lin +integron_01 ACBA.007.P01_13 ACBA.007.P01_13_5 2791 3495 -1 NA protein protein NA complete No NA lin +integron_01 ACBA.007.P01_13 attc_002 3339 3390 1 0.31 attC attC attc_4 complete No 1835.0 lin +integron_01 ACBA.007.P01_13 ACBA.007.P01_13_6 3546 4313 1 NA protein protein NA complete No NA lin integron_02 ACBA.007.P01_13 ACBA.007.P01_13_20 17375 17722 -1 NA protein protein NA CALIN No NA lin integron_02 ACBA.007.P01_13 attc_001 17825 17884 -1 5.1e-10 attC attC attc_4 CALIN No NA lin integron_02 ACBA.007.P01_13 ACBA.007.P01_13_21 17886 18665 -1 NA protein protein NA CALIN No NA lin
--- a/test-data/test3_integrons_table.tsv Sun Feb 25 16:08:08 2024 +0000 +++ b/test-data/test3_integrons_table.tsv Fri Jun 14 21:19:29 2024 +0000 @@ -1,4 +1,5 @@ -# cmd: integron_finder /tmp/tmpx8hgxvv4/files/8/7/c/dataset_87c30394-7ae6-4ec3-af50-dbfc9664d83d.dat --cpu 1 --keep-tmp --circ -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 +# integron_finder 2.0.5 +# cmd: integron_finder /tmp/tmphy8ici_1/files/0/1/8/dataset_0187fbc1-f208-45ff-ac2b-92c4e97c18eb.dat --cpu 1 --keep-tmp --circ -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 ID_integron ID_replicon element pos_beg pos_end strand evalue type_elt annotation model type default distance_2attC considered_topology integron_01 ACBA.007.P01_13 ACBA.007.P01_13_1 55 1014 1 1.9e-25 protein intI intersection_tyr_intI complete Yes NA circ integron_01 ACBA.007.P01_13 ACBA.007.P01_13_20 17375 17722 -1 NA protein protein NA complete Yes NA circ
--- a/test-data/test4_integrons_table.tsv Sun Feb 25 16:08:08 2024 +0000 +++ b/test-data/test4_integrons_table.tsv Fri Jun 14 21:19:29 2024 +0000 @@ -1,4 +1,5 @@ -# cmd: integron_finder /tmp/tmpx8hgxvv4/files/0/6/1/dataset_061a0fee-1c9e-49b2-949c-3c47f53e6db1.dat --cpu 1 --keep-tmp --topology-file /tmp/tmpx8hgxvv4/files/4/e/0/dataset_4e02f977-0c6a-4062-89ef-148bf2871520.dat -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 +# integron_finder 2.0.5 +# cmd: integron_finder /tmp/tmphy8ici_1/files/e/0/d/dataset_e0daeffa-7968-4ff7-babf-1f3f24a5c8f3.dat --cpu 1 --keep-tmp --topology-file /tmp/tmphy8ici_1/files/0/b/f/dataset_0bfb6d07-f1e7-4e45-ac12-719cf99e8532.dat -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 ID_integron ID_replicon element pos_beg pos_end strand evalue type_elt annotation model type default distance_2attC considered_topology integron_01 ACBA.007.P01_13 ACBA.007.P01_13_1 55 1014 1 1.9e-25 protein intI intersection_tyr_intI In0 Yes NA lin integron_02 ACBA.007.P01_13 ACBA.007.P01_13_20 17375 17722 -1 NA protein protein NA CALIN Yes NA lin
--- a/test-data/test5_integrons_table.tsv Sun Feb 25 16:08:08 2024 +0000 +++ b/test-data/test5_integrons_table.tsv Fri Jun 14 21:19:29 2024 +0000 @@ -1,4 +1,5 @@ -# cmd: integron_finder /tmp/tmpx8hgxvv4/files/f/5/6/dataset_f56693b9-7a23-459d-b14d-f33b5dbcd9cc.dat --cpu 1 --keep-tmp --promoter-attI -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 +# integron_finder 2.0.5 +# cmd: integron_finder /tmp/tmphy8ici_1/files/4/5/6/dataset_456847c3-0e81-4c5c-b3f2-6b14a0da2b45.dat --cpu 1 --keep-tmp --promoter-attI -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 ID_integron ID_replicon element pos_beg pos_end strand evalue type_elt annotation model type default distance_2attC considered_topology integron_01 ACBA.007.P01_13 Pc_int1 25 51 -1 NA Promoter Pc_1 NA complete Yes NA circ integron_01 ACBA.007.P01_13 ACBA.007.P01_13_1 55 1014 1 1.9e-25 protein intI intersection_tyr_intI complete Yes NA circ
--- a/test-data/test6_integrons_table.tsv Sun Feb 25 16:08:08 2024 +0000 +++ b/test-data/test6_integrons_table.tsv Fri Jun 14 21:19:29 2024 +0000 @@ -1,4 +1,5 @@ -# cmd: integron_finder /tmp/tmpx8hgxvv4/files/a/c/d/dataset_acd74005-21a2-4e86-bd45-517444a3e845.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 --gbk --pdf +# integron_finder 2.0.5 +# cmd: integron_finder /tmp/tmphy8ici_1/files/5/b/f/dataset_5bf66ab8-ec42-4ea2-8498-e5cf2432cddc.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 --gbk --pdf ID_integron ID_replicon element pos_beg pos_end strand evalue type_elt annotation model type default distance_2attC considered_topology integron_01 ACBA.007.P01_13 ACBA.007.P01_13_1 55 1014 1 1.9e-25 protein intI intersection_tyr_intI complete Yes NA circ integron_01 ACBA.007.P01_13 ACBA.007.P01_13_20 17375 17722 -1 NA protein protein NA complete Yes NA circ
--- a/test-data/test7_integrons_table.tsv Sun Feb 25 16:08:08 2024 +0000 +++ b/test-data/test7_integrons_table.tsv Fri Jun 14 21:19:29 2024 +0000 @@ -1,4 +1,5 @@ -# cmd: integron_finder /tmp/tmpx8hgxvv4/files/c/7/6/dataset_c7633788-caf8-4572-a154-afd0b927a73e.dat --cpu 1 --keep-tmp -dt 2000 --calin-threshold 3 --max-attc-size 188 --min-attc-size 30 +# integron_finder 2.0.5 +# cmd: integron_finder /tmp/tmphy8ici_1/files/4/1/e/dataset_41ebaaee-9c5d-4eb1-bf50-d61a66c4f74a.dat --cpu 1 --keep-tmp -dt 2000 --calin-threshold 3 --max-attc-size 188 --min-attc-size 30 ID_integron ID_replicon element pos_beg pos_end strand evalue type_elt annotation model type default distance_2attC considered_topology integron_01 ACBA.007.P01_13 ACBA.007.P01_13_1 55 1014 1 1.9e-25 protein intI intersection_tyr_intI complete Yes NA circ integron_01 ACBA.007.P01_13 ACBA.007.P01_13_20 17375 17722 -1 NA protein protein NA complete Yes NA circ
--- a/test-data/test8_integrons_table.tsv Sun Feb 25 16:08:08 2024 +0000 +++ b/test-data/test8_integrons_table.tsv Fri Jun 14 21:19:29 2024 +0000 @@ -1,10 +1,11 @@ -# cmd: integron_finder /tmp/tmpx8hgxvv4/files/5/9/0/dataset_590dbd5b-cca8-402e-84b0-5e38a7557de0.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 --attc-model /tmp/tmpx8hgxvv4/files/c/0/1/dataset_c0189f7e-8116-49cb-a925-803cedaa57d7.dat +# integron_finder 2.0.5 +# cmd: integron_finder /tmp/tmphy8ici_1/files/e/5/2/dataset_e52d2948-5751-485a-b1ed-0842a2a60fed.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 --attc-model /tmp/tmphy8ici_1/files/d/0/b/dataset_d0b5f9f9-1d2b-4bd8-934f-2ddb10bd9e6b.dat ID_integron ID_replicon element pos_beg pos_end strand evalue type_elt annotation model type default distance_2attC considered_topology integron_01 ACBA.007.P01_13 ACBA.007.P01_13_1 55 1014 1 1.9e-25 protein intI intersection_tyr_intI complete Yes NA circ integron_01 ACBA.007.P01_13 ACBA.007.P01_13_20 17375 17722 -1 NA protein protein NA complete Yes NA circ -integron_01 ACBA.007.P01_13 attc_001 17825 17884 -1 1e-09 attC attC dataset_c0189f7e-8116-49cb-a925-803cedaa57d7 complete Yes NA circ +integron_01 ACBA.007.P01_13 attc_001 17825 17884 -1 1e-09 attC attC dataset_d0b5f9f9-1d2b-4bd8-934f-2ddb10bd9e6b complete Yes NA circ integron_01 ACBA.007.P01_13 ACBA.007.P01_13_21 17886 18665 -1 NA protein protein NA complete Yes NA circ -integron_01 ACBA.007.P01_13 attc_002 19080 19149 -1 0.0001 attC attC dataset_c0189f7e-8116-49cb-a925-803cedaa57d7 complete Yes 1196.0 circ +integron_01 ACBA.007.P01_13 attc_002 19080 19149 -1 0.0001 attC attC dataset_d0b5f9f9-1d2b-4bd8-934f-2ddb10bd9e6b complete Yes 1196.0 circ integron_01 ACBA.007.P01_13 ACBA.007.P01_13_22 19090 19749 -1 NA protein protein NA complete Yes NA circ -integron_01 ACBA.007.P01_13 attc_003 19618 19726 -1 1.1e-07 attC attC dataset_c0189f7e-8116-49cb-a925-803cedaa57d7 complete Yes 469.0 circ +integron_01 ACBA.007.P01_13 attc_003 19618 19726 -1 1.1e-07 attC attC dataset_d0b5f9f9-1d2b-4bd8-934f-2ddb10bd9e6b complete Yes 469.0 circ integron_01 ACBA.007.P01_13 ACBA.007.P01_13_23 19721 20254 -1 NA protein protein NA complete Yes NA circ
--- a/test-data/test9_integrons_table.tsv Sun Feb 25 16:08:08 2024 +0000 +++ b/test-data/test9_integrons_table.tsv Fri Jun 14 21:19:29 2024 +0000 @@ -1,4 +1,5 @@ -# cmd: integron_finder /tmp/tmpx8hgxvv4/files/3/c/d/dataset_3cd5ad7d-e5e7-4256-b7e8-3a043e5973b4.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 --no-proteins +# integron_finder 2.0.5 +# cmd: integron_finder /tmp/tmphy8ici_1/files/5/e/e/dataset_5eeb02f0-3703-48bc-a3a4-d7b4b476cf46.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 --no-proteins ID_integron ID_replicon element pos_beg pos_end strand evalue type_elt annotation model type default distance_2attC considered_topology integron_01 ACBA.007.P01_13 attc_001 17825 17884 -1 1e-09 attC attC attc_4 CALIN Yes NA circ integron_01 ACBA.007.P01_13 attc_002 19080 19149 -1 0.0001 attC attC attc_4 CALIN Yes 1196.0 circ
--- a/test-data/test9_summary.tsv Sun Feb 25 16:08:08 2024 +0000 +++ b/test-data/test9_summary.tsv Fri Jun 14 21:19:29 2024 +0000 @@ -1,3 +1,4 @@ -# cmd: integron_finder /tmp/tmpx8hgxvv4/files/3/c/d/dataset_3cd5ad7d-e5e7-4256-b7e8-3a043e5973b4.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 --no-proteins +# integron_finder 2.0.5 +# cmd: integron_finder /tmp/tmphy8ici_1/files/5/e/e/dataset_5eeb02f0-3703-48bc-a3a4-d7b4b476cf46.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 --no-proteins ID_replicon CALIN complete In0 topology size ACBA.007.P01_13 1 0 0 circ 20301