| Previous changeset 1:4768f7f8e93f (2023-02-17) Next changeset 3:bfd290fe1588 (2024-06-14) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder commit bf94533e76d4253a734333e33c2f14f6634f0e79 |
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modified:
integron_finder.xml 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 |
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| diff -r 4768f7f8e93f -r 392f100eebcd integron_finder.xml --- a/integron_finder.xml Fri Feb 17 18:36:09 2023 +0000 +++ b/integron_finder.xml Sun Feb 25 16:08:08 2024 +0000 |
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| @@ -1,5 +1,5 @@ <tool id="integron_finder" name="Integron Finder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> - <description> is a program that detects integrons in DNA sequences</description> + <description>is a program that detects integrons in DNA sequences</description> <macros> <import>macro.xml</import> </macros> @@ -38,28 +38,28 @@ <param type="data" name="sequence" format="fasta" label="Replicon file" help="Replicon can be entire chromosome, contif, PCR fragments..."> <validator type="expression" message="Integron Finder has problems with large multi FASTA files. Please assembly your sequences or split them up into files smaller 10.000 sequences."><![CDATA[value is not None and value.metadata.sequences <= 10000]]></validator> </param> - <param name="local_max" argument="--local-max" type="boolean" checked="false" truevalue="--local-max" falsevalue="" label="Thorough local detection" help="This option allows a more sensitive search. I will be slower (dependant on the number of hits) if integrons are found, but will be as fast if nothing is detected and will not increase the false positive rate." /> + <param argument="--local-max" type="boolean" checked="false" truevalue="--local-max" falsevalue="" label="Thorough local detection" help="This option allows a more sensitive search. I will be slower (dependant on the number of hits) if integrons are found, but will be as fast if nothing is detected and will not increase the false positive rate." /> <param name="type_replicon" type="select" optional="true" label="Default replicons topology" help="Set the default topology for replicons, linear, circular (deault: no topology)"> <option value="--linear">linear (--linear)</option> <option value="--circ">circular (--circ)</option> </param> - <param name="topology_file" argument="--topology-file" type="data" format="txt" optional="true" label="Select a topology file from your history"/> - <param name="promoter_attI" argument="--promoter-attI" type="boolean" checked="false" truevalue="--promoter-attI" falsevalue="" label="Search also for promoter and attI sites?" /> + <param argument="--topology-file" type="data" format="txt" optional="true" label="Select a topology file from your history"/> + <param argument="--promoter-attI" type="boolean" checked="false" truevalue="--promoter-attI" falsevalue="" label="Search also for promoter and attI sites?" /> <param argument="--gbk" type="boolean" checked="false" truevalue="--gbk" falsevalue="" label="Genbank output?" help="Generate a GenBank file with the sequence annotated with the same annotations than .integrons file."/> - <param argument="--pdf" type="boolean" checked="false" truevalue="--pdf" falsevalue="" label="pdf output?" help="For each complete integron, a simple graphic of the region is depicted (in pdf format)"/> + <param argument="--pdf" type="boolean" checked="false" truevalue="--pdf" falsevalue="" label="PDF output?" help="For each complete integron, a simple graphic of the region is depicted (in pdf format)"/> <section name="settings" title="Advanced Parameters" expanded="False"> <section name="attc_settings" title="Attc options" expanded="False"> <param name="dist_thresh" argument="--distance-thresh" type="integer" value="4000" label="Threshold for clustering (in base)" min="0" help="By default, to cluster an array of attC sites and an integron integrase, they must be less than 4 kb apart. You can here change this value." /> <param name="calin_threshold" type="integer" value="2" label="Threshold to filter CALIN" min="0" help="Keep 'CALIN' only if attC sites number >= calin-threshold" /> <param name="max_attc_size" type="integer" value="200" label="Maximum value for attC size" min="0"/> <param name="min_attc_size" type="integer" value="40" label="Minimum value for attC size" min="0" /> - <param name="keep_palindromes" argument="--keep-palindromes" type="boolean" checked="false" truevalue="--keep-palindromes" falsevalue="" label="Keep palindromes with the highest evalue" help="For a given hit, if the palindromic version is found, don't remove the one with highest evalue"/> + <param argument="--keep-palindromes" type="boolean" checked="false" truevalue="--keep-palindromes" falsevalue="" label="Keep palindromes with the highest evalue" help="For a given hit, if the palindromic version is found, don't remove the one with highest evalue"/> <param name="covar_matrix" argument="--attc-model" type="data" optional="true" format="txt" label="Covariance Matrix" /> </section> <section name="protein_settings" title="Protein options" expanded="False"> - <param name="no_proteins" argument="--no-proteins" type="boolean" checked="false" truevalue="--no-proteins" falsevalue="" label="Just look for attC sites" help="When enabled, it does not annotate CDS and does not find integrase."/> - <param name="union_integrases" argument="--union-integrases" type="boolean" checked="false" truevalue="--union-integrases" falsevalue="" label="Use the union of the hits" help="Instead of taking intersection of hits from Phage_int profile (Tyr recombinases) and integron_integrase profile, use the union of the hits" /> - <param name="func_annot" argument="--func-annot" type="boolean" checked="false" truevalue="--func-annot" falsevalue="" label="Annotate cassettes given HMM profiles" /> + <param argument="--no-proteins" type="boolean" checked="false" truevalue="--no-proteins" falsevalue="" label="Just look for attC sites" help="When enabled, it does not annotate CDS and does not find integrase."/> + <param argument="--union-integrases" type="boolean" checked="false" truevalue="--union-integrases" falsevalue="" label="Use the union of the hits" help="Instead of taking intersection of hits from Phage_int profile (Tyr recombinases) and integron_integrase profile, use the union of the hits" /> + <param argument="--func-annot" type="boolean" checked="false" truevalue="--func-annot" falsevalue="" label="Annotate cassettes given HMM profiles" /> </section> </section> <param name="no_logfile" type="boolean" truevalue="true" falsevalue="false" label="Remove log file"/> |
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| diff -r 4768f7f8e93f -r 392f100eebcd macro.xml --- a/macro.xml Fri Feb 17 18:36:09 2023 +0000 +++ b/macro.xml Sun Feb 25 16:08:08 2024 +0000 |
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| @@ -1,13 +1,10 @@ <macros> - <token name="@TOOL_VERSION@">2.0.2</token> - <token name="@VERSION_SUFFIX@">1</token> - <token name="@PROFILE@">21.05</token> + <token name="@TOOL_VERSION@">2.0.3</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">22.05</token> <token name="@THREADS@">\${GALAXY_SLOTS:-2}</token> <xml name="requirements"> <requirements> - <requirement type="package" version="3.3.2">hmmer</requirement> - <requirement type="package" version="1.1.4">infernal</requirement> - <requirement type="package" version="2.6.3">prodigal</requirement> <requirement type="package" version="@TOOL_VERSION@">integron_finder</requirement> </requirements> </xml> |
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| diff -r 4768f7f8e93f -r 392f100eebcd test-data/integron_log --- a/test-data/integron_log Fri Feb 17 18:36:09 2023 +0000 +++ b/test-data/integron_log Sun Feb 25 16:08:08 2024 +0000 |
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| @@ -9,13 +9,13 @@ ************************************************************************** -integron_finder version 2.0.2 +integron_finder version 2.0.3 Using: - - Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:58:50) [GCC 10.3.0] - - numpy 1.19.4 - - pandas 1.1.5 - - matplolib 3.3.3 - - biopython 1.78 + - Python 3.12.1 | packaged by conda-forge | (main, Dec 23 2023, 08:03:24) [GCC 12.3.0] + - numpy 1.26.4 + - pandas 2.2.0 + - matplolib 3.8.2 + - biopython 1.83 - Prodigal V2.6.3: February, 2016 - INFERNAL 1.1.4 (Dec 2020) @@ -54,7 +54,7 @@ ======================= -command used: integron_finder /tmp/tmp3_ir6t5a/files/7/8/a/dataset_78ad162b-8ddf-4d54-a7e8-be6ee3804d0a.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 +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 ======================= |
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| diff -r 4768f7f8e93f -r 392f100eebcd test-data/summary.tsv --- a/test-data/summary.tsv Fri Feb 17 18:36:09 2023 +0000 +++ b/test-data/summary.tsv Sun Feb 25 16:08:08 2024 +0000 |
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| @@ -1,3 +1,3 @@ -# cmd: integron_finder /tmp/tmp3_ir6t5a/files/c/d/d/dataset_cdd097ee-d7c0-4424-9c3c-3ddd5d20887a.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 --union-integrases --func-annot +# 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 ID_replicon CALIN complete In0 topology size ACBA.007.P01_13 0 1 0 circ 20301 |
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| diff -r 4768f7f8e93f -r 392f100eebcd test-data/test10_integrons_table.tsv --- a/test-data/test10_integrons_table.tsv Fri Feb 17 18:36:09 2023 +0000 +++ b/test-data/test10_integrons_table.tsv Sun Feb 25 16:08:08 2024 +0000 |
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| @@ -1,9 +1,9 @@ -# cmd: integron_finder /tmp/tmp3_ir6t5a/files/c/d/d/dataset_cdd097ee-d7c0-4424-9c3c-3ddd5d20887a.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 --union-integrases --func-annot +# 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 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 1.9000000000000001e-25 protein intI intersection_tyr_intI complete Yes NA circ -integron_01 ACBA.007.P01_13 ACBA.007.P01_13_20 17375 17722 -1 9.799999999999998e-65 protein SMR_qac_E-NCBIFAM NF000276.2 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 +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 integron_01 ACBA.007.P01_13 attc_001 17825 17884 -1 1e-09 attC attC attc_4 complete Yes NA circ -integron_01 ACBA.007.P01_13 ACBA.007.P01_13_21 17886 18665 -1 2.7999999999999994e-183 protein ANT_3pp_AadA1-NCBIFAM NF033126.1 complete Yes NA circ +integron_01 ACBA.007.P01_13 ACBA.007.P01_13_21 17886 18665 -1 2.8e-183 protein ANT_3pp_AadA1-NCBIFAM NF033126.1 complete Yes NA circ integron_01 ACBA.007.P01_13 attc_002 19080 19149 -1 0.0001 attC attC attc_4 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 attc_4 complete Yes 469.0 circ |
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| diff -r 4768f7f8e93f -r 392f100eebcd test-data/test1_integrons_table.tsv --- a/test-data/test1_integrons_table.tsv Fri Feb 17 18:36:09 2023 +0000 +++ b/test-data/test1_integrons_table.tsv Sun Feb 25 16:08:08 2024 +0000 |
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| @@ -1,6 +1,6 @@ -# cmd: integron_finder /tmp/tmp3_ir6t5a/files/7/8/a/dataset_78ad162b-8ddf-4d54-a7e8-be6ee3804d0a.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 +# 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 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 1.9000000000000001e-25 protein intI intersection_tyr_intI 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 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 attc_4 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 |
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| diff -r 4768f7f8e93f -r 392f100eebcd test-data/test2_integrons_table.tsv --- a/test-data/test2_integrons_table.tsv Fri Feb 17 18:36:09 2023 +0000 +++ b/test-data/test2_integrons_table.tsv Sun Feb 25 16:08:08 2024 +0000 |
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| @@ -1,13 +1,6 @@ -# cmd: integron_finder /tmp/tmp3_ir6t5a/files/d/8/b/dataset_d8bd8cc0-78f5-4a59-b73a-d6819c72d20b.dat --cpu 1 --keep-tmp --local-max --linear -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 +# 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 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 1.9000000000000001e-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_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_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 |
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| diff -r 4768f7f8e93f -r 392f100eebcd test-data/test3_integrons_table.tsv --- a/test-data/test3_integrons_table.tsv Fri Feb 17 18:36:09 2023 +0000 +++ b/test-data/test3_integrons_table.tsv Sun Feb 25 16:08:08 2024 +0000 |
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| @@ -1,6 +1,6 @@ -# cmd: integron_finder /tmp/tmp3_ir6t5a/files/2/9/7/dataset_2978faa9-7392-48d8-9759-c12e419d7fe1.dat --cpu 1 --keep-tmp --circ -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 +# 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 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 1.9000000000000001e-25 protein intI intersection_tyr_intI 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 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 attc_4 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 |
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| diff -r 4768f7f8e93f -r 392f100eebcd test-data/test4_integrons_table.tsv --- a/test-data/test4_integrons_table.tsv Fri Feb 17 18:36:09 2023 +0000 +++ b/test-data/test4_integrons_table.tsv Sun Feb 25 16:08:08 2024 +0000 |
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| @@ -1,6 +1,6 @@ -# cmd: integron_finder /tmp/tmp3_ir6t5a/files/8/8/3/dataset_883ade04-f62d-4f17-85e7-122e7b43d339.dat --cpu 1 --keep-tmp --topology-file /tmp/tmp3_ir6t5a/files/d/7/c/dataset_d7c8e07c-4b44-480f-9059-a9bff8bf5be6.dat -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 +# 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 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 1.9000000000000001e-25 protein intI intersection_tyr_intI In0 Yes NA lin +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 integron_02 ACBA.007.P01_13 attc_001 17825 17884 -1 1e-09 attC attC attc_4 CALIN Yes NA lin integron_02 ACBA.007.P01_13 ACBA.007.P01_13_21 17886 18665 -1 NA protein protein NA CALIN Yes NA lin |
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| diff -r 4768f7f8e93f -r 392f100eebcd test-data/test5_integrons_table.tsv --- a/test-data/test5_integrons_table.tsv Fri Feb 17 18:36:09 2023 +0000 +++ b/test-data/test5_integrons_table.tsv Sun Feb 25 16:08:08 2024 +0000 |
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| @@ -1,7 +1,7 @@ -# cmd: integron_finder /tmp/tmp3_ir6t5a/files/a/8/c/dataset_a8c83ef3-ab8b-416f-adb8-54a6ba99e378.dat --cpu 1 --keep-tmp --promoter-attI -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 +# 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 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 1.9000000000000001e-25 protein intI intersection_tyr_intI 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 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 attc_4 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 |
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| diff -r 4768f7f8e93f -r 392f100eebcd test-data/test6_integrons_table.tsv --- a/test-data/test6_integrons_table.tsv Fri Feb 17 18:36:09 2023 +0000 +++ b/test-data/test6_integrons_table.tsv Sun Feb 25 16:08:08 2024 +0000 |
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| @@ -1,6 +1,6 @@ -# cmd: integron_finder /tmp/tmp3_ir6t5a/files/4/3/2/dataset_432b6fe2-79b8-45f0-a295-e5ab18425476.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 --gbk --pdf +# 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 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 1.9000000000000001e-25 protein intI intersection_tyr_intI 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 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 attc_4 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 |
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| diff -r 4768f7f8e93f -r 392f100eebcd test-data/test7_integrons_table.tsv --- a/test-data/test7_integrons_table.tsv Fri Feb 17 18:36:09 2023 +0000 +++ b/test-data/test7_integrons_table.tsv Sun Feb 25 16:08:08 2024 +0000 |
| b |
| @@ -1,6 +1,6 @@ -# cmd: integron_finder /tmp/tmp3_ir6t5a/files/7/e/3/dataset_7e32f99d-dba8-4527-9e8f-4ac9ca88d7db.dat --cpu 1 --keep-tmp -dt 2000 --calin-threshold 3 --max-attc-size 188 --min-attc-size 30 +# 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 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 1.9000000000000001e-25 protein intI intersection_tyr_intI 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 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 attc_4 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 |
| b |
| diff -r 4768f7f8e93f -r 392f100eebcd test-data/test8_integrons_table.tsv --- a/test-data/test8_integrons_table.tsv Fri Feb 17 18:36:09 2023 +0000 +++ b/test-data/test8_integrons_table.tsv Sun Feb 25 16:08:08 2024 +0000 |
| b |
| @@ -1,10 +1,10 @@ -# cmd: integron_finder /tmp/tmp3_ir6t5a/files/e/4/5/dataset_e459a473-6554-4525-9ec1-505e63711366.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 --attc-model /tmp/tmp3_ir6t5a/files/3/0/3/dataset_303db187-2a98-45e2-8c99-3d5694175a98.dat +# 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 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 1.9000000000000001e-25 protein intI intersection_tyr_intI 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 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_303db187-2a98-45e2-8c99-3d5694175a98 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 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_303db187-2a98-45e2-8c99-3d5694175a98 complete Yes 1196.0 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 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_303db187-2a98-45e2-8c99-3d5694175a98 complete Yes 469.0 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 ACBA.007.P01_13_23 19721 20254 -1 NA protein protein NA complete Yes NA circ |
| b |
| diff -r 4768f7f8e93f -r 392f100eebcd test-data/test9_integrons_table.tsv --- a/test-data/test9_integrons_table.tsv Fri Feb 17 18:36:09 2023 +0000 +++ b/test-data/test9_integrons_table.tsv Sun Feb 25 16:08:08 2024 +0000 |
| b |
| @@ -1,4 +1,4 @@ -# cmd: integron_finder /tmp/tmp3_ir6t5a/files/5/5/a/dataset_55aed596-7c76-44f2-817c-e12d708ca8b9.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 --no-proteins +# 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 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 |
| b |
| diff -r 4768f7f8e93f -r 392f100eebcd test-data/test9_summary.tsv --- a/test-data/test9_summary.tsv Fri Feb 17 18:36:09 2023 +0000 +++ b/test-data/test9_summary.tsv Sun Feb 25 16:08:08 2024 +0000 |
| b |
| @@ -1,3 +1,3 @@ -# cmd: integron_finder /tmp/tmp3_ir6t5a/files/5/5/a/dataset_55aed596-7c76-44f2-817c-e12d708ca8b9.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 --no-proteins +# 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 ID_replicon CALIN complete In0 topology size ACBA.007.P01_13 1 0 0 circ 20301 |