# HG changeset patch
# User iuc
# Date 1770738823 0
# Node ID 9fdd3e97db8df42e6cd17ee9834abafd1b6588b5
# Parent  3d4ae4eb3e981600cb206eeefda5efdd1129b65f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder commit 13f722da1a2d95586490e8534b9884abe61ba7cd

diff -r 3d4ae4eb3e98 -r 9fdd3e97db8d integron_finder.xml
--- a/integron_finder.xml	Fri Feb 17 18:35:52 2023 +0000
+++ b/integron_finder.xml	Tue Feb 10 15:53:43 2026 +0000
@@ -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>
@@ -38,43 +38,43 @@
         <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"/>
     </inputs>
     <outputs>
-        <collection type="list" label="Genbank files from [$tool.name] on $[on_string]" name="genbank_out">
-            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.gbk" format="gbk" visible="false" directory="Results_Integron_Finder/" />
+        <collection type="list" label="${tool.name} on ${on_string}: Genbank " name="genbank_out">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.gbk" format="genbank" visible="false" directory="Results_Integron_Finder/" />
             <filter>gbk</filter>
         </collection>
-	      <data format="txt" name="integron_log" from_work_dir="Results_Integron_Finder/integron_finder.out" label="Log from [$tool.name] on $[on_string]">
+	    <data format="txt" name="integron_log" from_work_dir="Results_Integron_Finder/integron_finder.out" label="${tool.name} on ${on_string}: Log">
             <filter> no_logfile == False</filter>
         </data>
-        <data format="tsv" name="integrons_table" from_work_dir="Results_Integron_Finder/*.integrons" label="Integrons annotations from [$tool.name] on $[on_string]"/>
-        <data format="tsv" name="summary" from_work_dir="Results_Integron_Finder/*.summary" label="Summary from [$tool.name] on $[on_string]"/>
-        <collection type="list" label="Graphic from [$tool.name] on $[on_string]" name="pdf_out">
+        <data format="tsv" name="integrons_table" from_work_dir="Results_Integron_Finder/*.integrons" label="${tool.name} on ${on_string}: Integron annotations"/>
+        <data format="tsv" name="summary" from_work_dir="Results_Integron_Finder/*.summary" label="${tool.name} on ${on_string}: Summary"/>
+        <collection name="pdf_out" type="list" label="${tool.name} on ${on_string}: Graphic">
             <discover_datasets pattern="(?P&lt;designation&gt;.+)\.pdf" format="pdf" visible="false" directory="Results_Integron_Finder/" />
             <filter>pdf</filter>
         </collection>
@@ -146,7 +146,7 @@
                     <param name="calin_threshold" value="3"/>
                     <param name="max_attc_size" value="188"/>
                     <param name="min_attc_size" value="30"/>
-                    <param name="keep_palindromes" value=""/>
+                    <param name="keep_palindromes" value="false"/>
                 </section>
             </section>
             <output name="integrons_table" value="test7_integrons_table.tsv" lines_diff="3" />
diff -r 3d4ae4eb3e98 -r 9fdd3e97db8d macro.xml
--- a/macro.xml	Fri Feb 17 18:35:52 2023 +0000
+++ b/macro.xml	Tue Feb 10 15:53:43 2026 +0000
@@ -1,13 +1,10 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.0.2</token>
+    <token name="@TOOL_VERSION@">2.0.5</token>
     <token name="@VERSION_SUFFIX@">1</token>
-    <token name="@PROFILE@">21.05</token>
+    <token name="@PROFILE@">24.2</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>
diff -r 3d4ae4eb3e98 -r 9fdd3e97db8d test-data/integron_log
--- a/test-data/integron_log	Fri Feb 17 18:35:52 2023 +0000
+++ b/test-data/integron_log	Tue Feb 10 15:53:43 2026 +0000
@@ -9,13 +9,13 @@
 
 **************************************************************************
 
-integron_finder version 2.0.2
+integron_finder version 2.0.5 
 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 3.12.3 | packaged by conda-forge | (main, Apr 15 2024, 18:38:13) [GCC 12.3.0]
+ - numpy 1.26.4
+ - pandas 2.2.2
+ - matplolib 3.8.4
+ - biopython 1.83
 
  - Prodigal V2.6.3: February, 2016
  - INFERNAL 1.1.4 (Dec 2020)
@@ -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/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/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
 
                      =======================
 
diff -r 3d4ae4eb3e98 -r 9fdd3e97db8d test-data/summary.tsv
--- a/test-data/summary.tsv	Fri Feb 17 18:35:52 2023 +0000
+++ b/test-data/summary.tsv	Tue Feb 10 15:53:43 2026 +0000
@@ -1,3 +1,4 @@
-# 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
+# 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
diff -r 3d4ae4eb3e98 -r 9fdd3e97db8d test-data/test10_integrons_table.tsv
--- a/test-data/test10_integrons_table.tsv	Fri Feb 17 18:35:52 2023 +0000
+++ b/test-data/test10_integrons_table.tsv	Tue Feb 10 15:53:43 2026 +0000
@@ -1,9 +1,10 @@
-# 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
+# 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	1.9000000000000001e-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
diff -r 3d4ae4eb3e98 -r 9fdd3e97db8d test-data/test1_integrons_table.tsv
--- a/test-data/test1_integrons_table.tsv	Fri Feb 17 18:35:52 2023 +0000
+++ b/test-data/test1_integrons_table.tsv	Tue Feb 10 15:53:43 2026 +0000
@@ -1,6 +1,7 @@
-# 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
+# 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	1.9000000000000001e-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
diff -r 3d4ae4eb3e98 -r 9fdd3e97db8d test-data/test2_integrons_table.tsv
--- a/test-data/test2_integrons_table.tsv	Fri Feb 17 18:35:52 2023 +0000
+++ b/test-data/test2_integrons_table.tsv	Tue Feb 10 15:53:43 2026 +0000
@@ -1,6 +1,7 @@
-# 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
+# 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	1.9000000000000001e-25	protein	intI	intersection_tyr_intI	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	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
diff -r 3d4ae4eb3e98 -r 9fdd3e97db8d test-data/test3_integrons_table.tsv
--- a/test-data/test3_integrons_table.tsv	Fri Feb 17 18:35:52 2023 +0000
+++ b/test-data/test3_integrons_table.tsv	Tue Feb 10 15:53:43 2026 +0000
@@ -1,6 +1,7 @@
-# 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
+# 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	1.9000000000000001e-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
diff -r 3d4ae4eb3e98 -r 9fdd3e97db8d test-data/test4_integrons_table.tsv
--- a/test-data/test4_integrons_table.tsv	Fri Feb 17 18:35:52 2023 +0000
+++ b/test-data/test4_integrons_table.tsv	Tue Feb 10 15:53:43 2026 +0000
@@ -1,6 +1,7 @@
-# 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
+# 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	1.9000000000000001e-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
diff -r 3d4ae4eb3e98 -r 9fdd3e97db8d test-data/test5_integrons_table.tsv
--- a/test-data/test5_integrons_table.tsv	Fri Feb 17 18:35:52 2023 +0000
+++ b/test-data/test5_integrons_table.tsv	Tue Feb 10 15:53:43 2026 +0000
@@ -1,7 +1,8 @@
-# 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
+# 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	1.9000000000000001e-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
diff -r 3d4ae4eb3e98 -r 9fdd3e97db8d test-data/test6_integrons_table.tsv
--- a/test-data/test6_integrons_table.tsv	Fri Feb 17 18:35:52 2023 +0000
+++ b/test-data/test6_integrons_table.tsv	Tue Feb 10 15:53:43 2026 +0000
@@ -1,6 +1,7 @@
-# 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
+# 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	1.9000000000000001e-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
diff -r 3d4ae4eb3e98 -r 9fdd3e97db8d test-data/test7_integrons_table.tsv
--- a/test-data/test7_integrons_table.tsv	Fri Feb 17 18:35:52 2023 +0000
+++ b/test-data/test7_integrons_table.tsv	Tue Feb 10 15:53:43 2026 +0000
@@ -1,6 +1,7 @@
-# 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
+# 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	1.9000000000000001e-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
diff -r 3d4ae4eb3e98 -r 9fdd3e97db8d test-data/test8_integrons_table.tsv
--- a/test-data/test8_integrons_table.tsv	Fri Feb 17 18:35:52 2023 +0000
+++ b/test-data/test8_integrons_table.tsv	Tue Feb 10 15:53:43 2026 +0000
@@ -1,10 +1,11 @@
-# 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
+# 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	1.9000000000000001e-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_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_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_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_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_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
diff -r 3d4ae4eb3e98 -r 9fdd3e97db8d test-data/test9_integrons_table.tsv
--- a/test-data/test9_integrons_table.tsv	Fri Feb 17 18:35:52 2023 +0000
+++ b/test-data/test9_integrons_table.tsv	Tue Feb 10 15:53:43 2026 +0000
@@ -1,4 +1,5 @@
-# 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
+# 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
diff -r 3d4ae4eb3e98 -r 9fdd3e97db8d test-data/test9_summary.tsv
--- a/test-data/test9_summary.tsv	Fri Feb 17 18:35:52 2023 +0000
+++ b/test-data/test9_summary.tsv	Tue Feb 10 15:53:43 2026 +0000
@@ -1,3 +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
+# 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