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changeset 4:65b333eed5c2 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder commit 232de7b04558cf28e2caffb8a5e0520b7dd1b645
author iuc
date Tue, 10 Feb 2026 17:52:55 +0000
parents e9813d6ac5ab
children
files macro.xml plasmidfinder.xml test-data/test_1/data_test1.json test-data/test_1/logfile_test1.log test-data/test_2/data_test2.json test-data/test_2/logfile_test2.log test-data/test_2/results_tab_test2.tsv test-data/test_2/results_test2.txt
diffstat 8 files changed, 100 insertions(+), 29 deletions(-) [+]
line wrap: on
line diff
--- a/macro.xml	Thu Mar 02 14:57:54 2023 +0000
+++ b/macro.xml	Tue Feb 10 17:52:55 2026 +0000
@@ -1,8 +1,8 @@
 
 <macros>
   <token name="@TOOL_VERSION@">2.1.6</token>
-  <token name="@VERSION_SUFFIX@">1</token>
-  <token name="@PROFILE@">21.05</token>
+  <token name="@VERSION_SUFFIX@">2</token>
+  <token name="@PROFILE@">24.2</token>
   <token name="@THREADS@">\${GALAXY_SLOTS:-7}</token>
 
   <xml name="xrefs">
--- a/plasmidfinder.xml	Thu Mar 02 14:57:54 2023 +0000
+++ b/plasmidfinder.xml	Tue Feb 10 17:52:55 2026 +0000
@@ -78,7 +78,6 @@
         <test expect_num_outputs="6">
               <section name="input">
                   <param name="input_file" value="contigs.fasta"/>
-                  <param name="input_type" value="genome"/>
                   <param name="database_name" value="plasmidfinder_9002e7282dd0_2022-12-20"/>
               </section>
               <section name="output_files">
@@ -95,7 +94,6 @@
         <test expect_num_outputs="4">
               <section name="input">
                   <param name="input_file" value="data.fastq.gz"/>
-                  <param name="input_type" value="raw"/>
                   <param name="database_name" value="plasmidfinder_9002e7282dd0_2022-12-20"/>
               </section>
               <section name="output_files">
@@ -110,7 +108,6 @@
         <test expect_num_outputs="3">
               <section name="input">
                   <param name="input_file" value="contigs.fasta"/>
-                  <param name="input_type" value="genome"/>
                   <param name="database_name" value="plasmidfinder_9002e7282dd0_2022-12-20"/>
               </section>
               <section name="options">
--- a/test-data/test_1/data_test1.json	Thu Mar 02 14:57:54 2023 +0000
+++ b/test-data/test_1/data_test1.json	Tue Feb 10 17:52:55 2026 +0000
@@ -1,1 +1,1 @@
-{"plasmidfinder": {"user_input": {"filename(s)": ["/tmp/tmpj3aqa6lu/files/9/6/4/dataset_9649367d-27ab-42b3-8f51-56f81f942d9c.dat"], "method": "blast", "file_format": "fasta"}, "run_info": {"date": "09.09.2022", "time": "08:52:55"}, "results": {"Gram Positive": {"Inc18": "No hit found", "Rep3": {"contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302:308..1252:rep11a_1_repA(pB82)_AB178871:99.894180": {"plasmid": "rep11a", "identity": 99.89, "HSP_length": 945, "template_length": 945, "position_in_ref": "1..945", "contig_name": "contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302", "positions_in_contig": "308..1252", "note": "repA(pB82)", "accession": "AB178871", "coverage": 100.0, "hit_id": "contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302:308..1252:rep11a_1_repA(pB82)_AB178871:99.894180"}}, "Rep_trans": {"contig00008 len=2292 cov=2.6 corr=0 origname=NODE_11_length_2292_cov_2.631409_pilon sw=shovill-spades/1.1.0 date=20220302:1703..2104:rep14a_2_ORF1(pKQ10)_EFU01917:99.502488": {"plasmid": "rep14a", "identity": 99.5, "HSP_length": 402, "template_length": 402, "position_in_ref": "1..402", "contig_name": "contig00008 len=2292 cov=2.6 corr=0 origname=NODE_11_length_2292_cov_2.631409_pilon sw=shovill-spades/1.1.0 date=20220302", "positions_in_contig": "1703..2104", "note": "ORF1(pKQ10)", "accession": "EFU01917", "coverage": 100.0, "hit_id": "contig00008 len=2292 cov=2.6 corr=0 origname=NODE_11_length_2292_cov_2.631409_pilon sw=shovill-spades/1.1.0 date=20220302:1703..2104:rep14a_2_ORF1(pKQ10)_EFU01917:99.502488"}}}}}}
\ No newline at end of file
+{"plasmidfinder": {"user_input": {"filename(s)": ["/tmp/tmp1yi7ks0w/files/1/b/7/dataset_1b7d7582-03af-4303-8f60-ef2c3c433521.dat"], "method": "blast", "file_format": "fasta"}, "run_info": {"date": "10.02.2026", "time": "15:20:29"}, "results": {"Gram Positive": {"Inc18": "No hit found", "Rep3": {"contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302:308..1252:rep11a_1_repA(pB82)_AB178871:99.894180": {"plasmid": "rep11a", "identity": 99.89, "HSP_length": 945, "template_length": 945, "position_in_ref": "1..945", "contig_name": "contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302", "positions_in_contig": "308..1252", "note": "repA(pB82)", "accession": "AB178871", "coverage": 100.0, "hit_id": "contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302:308..1252:rep11a_1_repA(pB82)_AB178871:99.894180"}}, "Rep_trans": {"contig00008 len=2292 cov=2.6 corr=0 origname=NODE_11_length_2292_cov_2.631409_pilon sw=shovill-spades/1.1.0 date=20220302:1703..2104:rep14a_2_ORF1(pKQ10)_EFU01917:99.502488": {"plasmid": "rep14a", "identity": 99.5, "HSP_length": 402, "template_length": 402, "position_in_ref": "1..402", "contig_name": "contig00008 len=2292 cov=2.6 corr=0 origname=NODE_11_length_2292_cov_2.631409_pilon sw=shovill-spades/1.1.0 date=20220302", "positions_in_contig": "1703..2104", "note": "ORF1(pKQ10)", "accession": "EFU01917", "coverage": 100.0, "hit_id": "contig00008 len=2292 cov=2.6 corr=0 origname=NODE_11_length_2292_cov_2.631409_pilon sw=shovill-spades/1.1.0 date=20220302:1703..2104:rep14a_2_ORF1(pKQ10)_EFU01917:99.502488"}}}}}}
\ No newline at end of file
--- a/test-data/test_1/logfile_test1.log	Thu Mar 02 14:57:54 2023 +0000
+++ b/test-data/test_1/logfile_test1.log	Tue Feb 10 17:52:55 2026 +0000
@@ -1,9 +1,3 @@
-Found: rep2_2_repR(pEF1)_DQ198088
-Saving: contig00014 len=836 cov=2.5 corr=0 origname=NODE_172_length_836_cov_2.489422_pilon sw=shovill-spades/1.1.0 date=20220302:2..836:rep2_2_repR(pEF1)_DQ198088:55.890228
-Found: rep11a_1_repA(pB82)_AB178871
-Saving: contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302:308..1252:rep11a_1_repA(pB82)_AB178871:99.894180
-Found: rep14a_2_ORF1(pKQ10)_EFU01917
-Saving: contig00008 len=2292 cov=2.6 corr=0 origname=NODE_11_length_2292_cov_2.631409_pilon sw=shovill-spades/1.1.0 date=20220302:1703..2104:rep14a_2_ORF1(pKQ10)_EFU01917:99.502488
 {'plasmidfinder': {'results': {'Gram Positive': {'Inc18': 'No hit found',
                                                  'Rep3': {'contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302:308..1252:rep11a_1_repA(pB82)_AB178871:99.894180': {'HSP_length': 945,
                                                                                                                                                                                                                                         'accession': 'AB178871',
@@ -51,7 +45,7 @@
                                                                                                                                                                                                                                                 'position_in_ref': '1..402',
                                                                                                                                                                                                                                                 'positions_in_contig': '1703..2104',
                                                                                                                                                                                                                                                 'template_length': 402}}}},
-                   'run_info': {'date': '09.09.2022', 'time': '08:52:55'},
+                   'run_info': {'date': '10.02.2026', 'time': '15:20:29'},
                    'user_input': {'file_format': 'fasta',
-                                  'filename(s)': ['/tmp/tmpj3aqa6lu/files/9/6/4/dataset_9649367d-27ab-42b3-8f51-56f81f942d9c.dat'],
+                                  'filename(s)': ['/tmp/tmp1yi7ks0w/files/1/b/7/dataset_1b7d7582-03af-4303-8f60-ef2c3c433521.dat'],
                                   'method': 'blast'}}}
--- a/test-data/test_2/data_test2.json	Thu Mar 02 14:57:54 2023 +0000
+++ b/test-data/test_2/data_test2.json	Tue Feb 10 17:52:55 2026 +0000
@@ -1,1 +1,1 @@
-{"plasmidfinder": {"user_input": {"filename(s)": ["/tmp/tmpj3aqa6lu/files/3/2/3/dataset_32342c91-595d-40c3-b39a-60aa67724edc.dat"], "method": "kma", "file_format": "fastq"}, "run_info": {"date": "09.09.2022", "time": "08:53:07"}, "results": {"Gram Positive": {"Inc18": "No hit found", "Rep3": "No hit found", "Rep_trans": "No hit found"}}}}
\ No newline at end of file
+{"plasmidfinder": {"user_input": {"filename(s)": ["/tmp/tmp1yi7ks0w/files/0/e/3/dataset_0e36e86f-0bbd-4a32-940e-8e30997c8d02.dat"], "method": "kma", "file_format": "fastq"}, "run_info": {"date": "10.02.2026", "time": "15:20:44"}, "results": {"Gram Positive": {"Inc18": {"rep14a_2_ORF1(pKQ10)_EFU01917": {"plasmid": "rep14a", "identity": 99.5, "HSP_length": 402, "template_length": 402, "position_in_ref": "1..403", "contig_name": "NA", "positions_in_contig": "NA..NA", "note": "ORF1(pKQ10)", "accession": "EFU01917", "coverage": 100.0, "hit_id": "rep14a_2_ORF1(pKQ10)_EFU01917"}}, "Rep3": "No hit found", "Rep_trans": {"rep14a_2_ORF1(pKQ10)_EFU01917": {"plasmid": "rep14a", "identity": 99.5, "HSP_length": 402, "template_length": 402, "position_in_ref": "1..403", "contig_name": "NA", "positions_in_contig": "NA..NA", "note": "ORF1(pKQ10)", "accession": "EFU01917", "coverage": 100.0, "hit_id": "rep14a_2_ORF1(pKQ10)_EFU01917"}}}}}}
\ No newline at end of file
--- a/test-data/test_2/logfile_test2.log	Thu Mar 02 14:57:54 2023 +0000
+++ b/test-data/test_2/logfile_test2.log	Tue Feb 10 17:52:55 2026 +0000
@@ -1,7 +1,27 @@
-{'plasmidfinder': {'results': {'Gram Positive': {'Inc18': 'No hit found',
+{'plasmidfinder': {'results': {'Gram Positive': {'Inc18': {'rep14a_2_ORF1(pKQ10)_EFU01917': {'HSP_length': 402,
+                                                                                             'accession': 'EFU01917',
+                                                                                             'contig_name': 'NA',
+                                                                                             'coverage': 100.0,
+                                                                                             'hit_id': 'rep14a_2_ORF1(pKQ10)_EFU01917',
+                                                                                             'identity': 99.5,
+                                                                                             'note': 'ORF1(pKQ10)',
+                                                                                             'plasmid': 'rep14a',
+                                                                                             'position_in_ref': '1..403',
+                                                                                             'positions_in_contig': 'NA..NA',
+                                                                                             'template_length': 402}},
                                                  'Rep3': 'No hit found',
-                                                 'Rep_trans': 'No hit found'}},
-                   'run_info': {'date': '09.09.2022', 'time': '08:53:07'},
+                                                 'Rep_trans': {'rep14a_2_ORF1(pKQ10)_EFU01917': {'HSP_length': 402,
+                                                                                                 'accession': 'EFU01917',
+                                                                                                 'contig_name': 'NA',
+                                                                                                 'coverage': 100.0,
+                                                                                                 'hit_id': 'rep14a_2_ORF1(pKQ10)_EFU01917',
+                                                                                                 'identity': 99.5,
+                                                                                                 'note': 'ORF1(pKQ10)',
+                                                                                                 'plasmid': 'rep14a',
+                                                                                                 'position_in_ref': '1..403',
+                                                                                                 'positions_in_contig': 'NA..NA',
+                                                                                                 'template_length': 402}}}},
+                   'run_info': {'date': '10.02.2026', 'time': '15:20:44'},
                    'user_input': {'file_format': 'fastq',
-                                  'filename(s)': ['/tmp/tmpj3aqa6lu/files/3/2/3/dataset_32342c91-595d-40c3-b39a-60aa67724edc.dat'],
+                                  'filename(s)': ['/tmp/tmp1yi7ks0w/files/0/e/3/dataset_0e36e86f-0bbd-4a32-940e-8e30997c8d02.dat'],
                                   'method': 'kma'}}}
--- a/test-data/test_2/results_tab_test2.tsv	Thu Mar 02 14:57:54 2023 +0000
+++ b/test-data/test_2/results_tab_test2.tsv	Tue Feb 10 17:52:55 2026 +0000
@@ -1,1 +1,3 @@
 Database	Plasmid	Identity	Query / Template length	Contig	Position in contig	Note	Accession number
+Inc18	rep14a	99.5	402 / 402	NA	NA..NA	ORF1(pKQ10)	EFU01917
+Rep_trans	rep14a	99.5	402 / 402	NA	NA..NA	ORF1(pKQ10)	EFU01917
--- a/test-data/test_2/results_test2.txt	Thu Mar 02 14:57:54 2023 +0000
+++ b/test-data/test_2/results_test2.txt	Tue Feb 10 17:52:55 2026 +0000
@@ -4,11 +4,11 @@
 
 ****************************************************************************************
 Inc18
-****************************************************************************************************************
-Plasmid    Identity    Query / Template length    Contig        Position in contig    Note    Accession number
-****************************************************************************************************************
--          -           -                          No hit found  -                     -       -
-================================================================================================================
+*****************************************************************************************************************
+Plasmid      Identity  Query / Template length    Contig    Position in contig    Note         Accession number
+*****************************************************************************************************************
+rep14a           99.5  402 / 402                  NA        NA..NA                ORF1(pKQ10)  EFU01917
+=================================================================================================================
 
 ****************************************************************************************
 Rep3
@@ -20,14 +20,72 @@
 
 ****************************************************************************************
 Rep_trans
-****************************************************************************************************************
-Plasmid    Identity    Query / Template length    Contig        Position in contig    Note    Accession number
-****************************************************************************************************************
--          -           -                          No hit found  -                     -       -
-================================================================================================================
+*****************************************************************************************************************
+Plasmid      Identity  Query / Template length    Contig    Position in contig    Note         Accession number
+*****************************************************************************************************************
+rep14a           99.5  402 / 402                  NA        NA..NA                ORF1(pKQ10)  EFU01917
+=================================================================================================================
 
 
 
 
 Extended Output:
 
+# rep14a_EFU01917
+template: 	GTGCGACTGTACAACAAAAAGCTAGAGCAGGAACGAAAAAAAGTAATCGTGCCAAAAGAA
+          	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+query:    	GTGCGACTGTACAACAAAAAGCTAGAGCAGGAACGAAAAAAAGTAATCGTGCCAAAAGAA
+
+template: 	ATCGATACGTGGTGGCGGTTAGAAATGCAGCTAAGACGTGGCAAAGCAACGGATTGGCAT
+          	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+query:    	ATCGATACGTGGTGGCGGTTAGAAATGCAGCTAAGACGTGGCAAAGCAACGGATTGGCAT
+
+template: 	GCGATGGTTCAGGAAAGCTTAGATAGTTTTGCAAGCCCGCATTTTTTGCCGATTGATATA
+          	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+query:    	GCGATGGTTCAGGAAAGCTTAGATAGTTTTGCAAGCCCGCATTTTTTGCCGATTGATATA
+
+template: 	AAACCTATTGATAAAATAGTTATTGAAGGTTTGATAGCTGAGCCTTCTAATTGGTCGATA
+          	||||||||||||||||||||||||||_|||||||||||||||||||||||||||||||||
+query:    	AAACCTATTGATAAAATAGTTATTGATGGTTTGATAGCTGAGCCTTCTAATTGGTCGATA
+
+template: 	ATTGCTAGACATACAAAATATAAATATCGGAATTTGCTGAAGCAAGAAAGTCAAAATGAT
+          	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+query:    	ATTGCTAGACATACAAAATATAAATATCGGAATTTGCTGAAGCAAGAAAGTCAAAATGAT
+
+template: 	GAGTTAACGAACCATTTACGAGAGACTTTTAAGGAATCTGCAGACGAATTAAAAAAAGAA
+          	|||||||||||_||||||||||||||||||||||||||||||||||||||||||||||||
+query:    	GAGTTAACGAATCATTTACGAGAGACTTTTAAGGAATCTGCAGACGAATTAAAAAAAGAA
+
+template: 	TTGGATACGTGGCTTTTGGGGTTGGATGTGACAGAGAAGTGA
+          	||||||||||||||||||||||||||||||||||||||||||
+query:    	TTGGATACGTGGCTTTTGGGGTTGGATGTGACAGAGAAGTGA
+
+# rep14a_EFU01917
+template: 	GTGCGACTGTACAACAAAAAGCTAGAGCAGGAACGAAAAAAAGTAATCGTGCCAAAAGAA
+          	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+query:    	GTGCGACTGTACAACAAAAAGCTAGAGCAGGAACGAAAAAAAGTAATCGTGCCAAAAGAA
+
+template: 	ATCGATACGTGGTGGCGGTTAGAAATGCAGCTAAGACGTGGCAAAGCAACGGATTGGCAT
+          	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+query:    	ATCGATACGTGGTGGCGGTTAGAAATGCAGCTAAGACGTGGCAAAGCAACGGATTGGCAT
+
+template: 	GCGATGGTTCAGGAAAGCTTAGATAGTTTTGCAAGCCCGCATTTTTTGCCGATTGATATA
+          	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+query:    	GCGATGGTTCAGGAAAGCTTAGATAGTTTTGCAAGCCCGCATTTTTTGCCGATTGATATA
+
+template: 	AAACCTATTGATAAAATAGTTATTGAAGGTTTGATAGCTGAGCCTTCTAATTGGTCGATA
+          	||||||||||||||||||||||||||_|||||||||||||||||||||||||||||||||
+query:    	AAACCTATTGATAAAATAGTTATTGATGGTTTGATAGCTGAGCCTTCTAATTGGTCGATA
+
+template: 	ATTGCTAGACATACAAAATATAAATATCGGAATTTGCTGAAGCAAGAAAGTCAAAATGAT
+          	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+query:    	ATTGCTAGACATACAAAATATAAATATCGGAATTTGCTGAAGCAAGAAAGTCAAAATGAT
+
+template: 	GAGTTAACGAACCATTTACGAGAGACTTTTAAGGAATCTGCAGACGAATTAAAAAAAGAA
+          	|||||||||||_||||||||||||||||||||||||||||||||||||||||||||||||
+query:    	GAGTTAACGAATCATTTACGAGAGACTTTTAAGGAATCTGCAGACGAATTAAAAAAAGAA
+
+template: 	TTGGATACGTGGCTTTTGGGGTTGGATGTGACAGAGAAGTGA
+          	||||||||||||||||||||||||||||||||||||||||||
+query:    	TTGGATACGTGGCTTTTGGGGTTGGATGTGACAGAGAAGTGA
+