| Previous changeset 6:5e67ea368004 (2025-04-15) |
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Commit message:
planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/dorado commit 97793e41864a750b1c18c80b858c118e43ae8d97 |
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modified:
dorado.xml macros.xml |
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added:
test-data/corrected_reads.fasta test-data/corrected_reads_paf.fasta test-data/overlaps.paf test-data/reads.fq.gz |
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| diff -r 5e67ea368004 -r 34e128a6a6ed dorado.xml --- a/dorado.xml Tue Apr 15 07:04:29 2025 +0000 +++ b/dorado.xml Mon Jun 23 03:09:42 2025 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="dorado" name="Dorado" version="@VERSION@+galaxy0" python_template_version="3.5" profile="24.1"> +<tool id="dorado" name="Dorado" version="@VERSION@+galaxy1" python_template_version="3.5" profile="24.1"> <description>basecaller for raw Oxford Nanopore data</description> <macros> <import>macros.xml</import> @@ -29,12 +29,7 @@ ]]></command> <inputs> <param name="pod5_file" type="data" format="pod5" label="Raw pod5 file" help="Only pod5 is supported. You can convert fast5 to pod5 with the fast5 to pod5 tool."/> - <param name="model" type="select" label="Basecalling model. See the Help section for info on model names."> - <options from_data_table="dorado_models"> - <!-- only allow models that shipped in this container --> - <filter type="static_value" column="1" value="@CONTAINER_HASH@"/> - </options> - </param> + <expand macro="model_param"/> <param type="select" argument="--trim" label="DNA adapter and primer trimming" help="Detect and remove any adapter and/or primer sequences from the beginning and end of DNA reads. Note that if you intend to demultiplex the reads, trimming adapters and primers could interfere with correct demultiplexing."> <option value="all" selected="true">Any. Trim any detected adapters or primers.</option> <option value="primers"> Primers. Trim any detected adapters or primers, but if barcoding is enabled the barcode sequences will not be trimmed.</option> @@ -43,7 +38,7 @@ </param> <!-- dev note: the barcode kits are hardcoded in https://github.com/nanoporetech/dorado/blob/release-v0.9/dorado/utils/barcode_kits.cpp --> <param type="select" argument="--kit-name" optional="true" label="Enable barcoding with the selected kit name." help="Reads are classified into their barcode groups during basecalling. The classification will be reflected in the read group name as well as in the BC tag of the output record."> - <expand macro="barcode_kits" /> + <expand macro="barcode_kits"/> </param> </inputs> <outputs> |
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| diff -r 5e67ea368004 -r 34e128a6a6ed macros.xml --- a/macros.xml Tue Apr 15 07:04:29 2025 +0000 +++ b/macros.xml Mon Jun 23 03:09:42 2025 +0000 |
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| @@ -25,6 +25,14 @@ </citation> </citations> </xml> + <xml name="model_param"> + <param name="model" type="select" label="Basecalling model. See the Help section for info on model names."> + <options from_data_table="dorado_models"> + <!-- only allow models that shipped in this container --> + <filter type="static_value" column="1" value="@CONTAINER_HASH@"/> + </options> + </param> + </xml> <xml name="barcode_kits"> <option value="EXP-NBD103">EXP-NBD103</option> <option value="EXP-NBD104">EXP-NBD104</option> |
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| diff -r 5e67ea368004 -r 34e128a6a6ed test-data/corrected_reads.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/corrected_reads.fasta Mon Jun 23 03:09:42 2025 +0000 |
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| b'@@ -0,0 +1,12 @@\n+>3855985e-bb9b-4df4-9825-cc08f373342b\n+CCCCTTGCTCTCTGTATTATTTCCTTCTGTTAGGGGGTTGGGGAGAGACATCTAGGATCCTTGGCGAAAAGAGGTGTTGAAAGGCAGAGGGGAGAGAATGGGGATAGGAGAGGGGAATAATTCACAGAAGATACACAAATAGCCAATATGAAAATTAAACCAAGCTCAATATCATTAGATTTAAGAAGTGCAAAATTCTTAAAGATACCTTCCTTGATTAGTTGTGCAAAAATAAAAACTTTGGACAACATCCAGTGTTAGTGGAGTAGAGAAATGAATATTCCCAATCACTCTTGATAGGAGTGTAAATTGGTGCAATCTCCCAGAAGGCAATTTCACTTTCACAGTTTTATATGTGCTTCCTCTTTGGCCCAGCAGTTTCACTTATAGGAATCTGTCCTACAGAAACATTAAACAAGCATATACAAATACAAGAACAAGAATGTTTATTAAAGCATTGTTGCATTAGAGTAAAAACAAAAACAATTACAATGCCTATCAATAAGGGGCCAGATAAGTCATTTGTGATTTATGTATACTATGGACTACTAGGCCCATGTTGCACTGAATACACATTCTGACATCAAAAAGATTAAGTTGAAAGGCAAGAGCTGCAGTGATGATCCCATCCATGTTTATTTTTTAAAAACTATATATGTTTATATACACATATTAAGTCTAGAAGGATCTAGTGGTGATCTTGGTGGGGAGGGGAGCAGGGAATTAAGAGGAGACAGGTATATTTTCCTTCTAATTTCATATACTTTTGTTGATTTTTAAAAATAGCAAACGGCCGGGTGCAGTGGCTCACACCTGTAATCCCAACACCTTGGGAGGCAGAGGAGGGCAGATCACTTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAATATGGTGAAATGTTGTCTACTAAAAATACAAAAATTAGCCAGCCATGGTGGTGGGCACCTGTAATCCCAGCTACTCGGGGAGGCTGAGGCATGAGAATCACTTGAACCCGGAAGGTGGAGGTTGCAGTGAGCTGAGATCGCGCCACTGCACTCCAGCCTGGTCAACAGAATGAGACTCAGTCTTAAAAACAAAAACAAAAACACATAGAAAACATAAAAATAAAAATAGCAAACAGGTATTACTTCTATAATTAAGAAATGAGTAAAAACTGAAAAGAACAAAGGGAAACAGCACGTATAGAAGGCAAGCTCGCCCCAATTCACCTTGCATGTCCCTTGGCCCTGGCTCCCATCTAACCACAGAGAAGGGGTCAGAGACTCCAGTGCTGATGGGTTTTTTGCAGGGCATTGTAGCCCTAGAATATTTATGAGGCCTCCAGCAGCAATGAGTCCACGAAGGTTGCTGTGAGGATTAAATGAGATAATGTATTAAAGGCACTAGGAAAGTGGCTGGCTGGTGGTAAGCCCTCAATACTAACAGCTTTTCATTATTATTGTTATTATTTAAAAGCATCCTGTAGCCCAGTTCTGCAGGGTGCTCCTCTACTTTCCAGATCCCACTCACTGGCACAGATTTTAAGCATTCATGGCAGGTGTACAAATGCTTAGTTTCATGTCAGGGCTATAACTGCACTTAATTGCTAACAAAACCACTTCAAAAGAGCTGTTCACCTAAGGGATGCTTGTGCAGTTGGAAACCATGGCTACGTGGCTCTACTCAGCTTCAGAAGAGCATTACTTCCTTACCCATTAATGAATATATAAATAAATAATGATCACCATGCAAATGGCATATCTAAGCTTTTTGCAAATTTAAAGCAAAAATGGTTATTGGTCGCCCCTTTCATGTAAAAAAAAAAAGTTTTCAAAGTAGGTGGAAATAAGAAAGGGAATAAGTCTACGTTTTCTCCTCACCCCACCCCCTTGGAGAAGTCGGCCTCCTGCTGCCTCCGAATCCTTCCACTGAAGGTCGCCAGCATGGAGTTCATGGCTGTGCAATCAAATGAAACTCATGATGCAAATATATTGGGAAAAGAGAGAGAATTAAGTCTAGAGAGCCCTCATTTTATTATAAAATTATTGCTTTCTCTACCAAGGAGACTGAATAGAATAAAATTACAGGTACATGTGTACAATTGTACCTGTGGACCAAAAAAAAAAAAGGGGAGGGATTATTTGTATGCTAGAATGCATGCACAAAAAATAAACCAGATGGAAGAAATGATAAAGAAGGAGTTGCCTTTCAGGAACGACAGCTGCTTACAGCTGTGGGAGTTCCTGCAACAGTTTATATTGGCCATTTTGTTTCCTGGCTAAACTGATTGCATTATATCACGATTTTTTTTGACAACTTGAAAATCAGATTTTATTTCTCTCTCATAAACTCTTTTAATACCATTCTTAATAAGGAAGAAAAATGTTGCATGTTGTGACTGATAAATGGAAAACCTCATTTAGGATTTGGTTTACATATTCCAAATGGTAAAAGCTCAGTAACATGAAGATCGTGTGTACTCAGGCCAAGAAGATCACAGGATTGACAAATAACATACAGTCCTGGGCGCCCATTTGTGATTGTGCAAGATTTTCATTTTTGCTTTGTGATTAACACTGCCTCTGAACTGAGGAGTTACCATGCTAGCAAATCATTTGTCTATCACATCATCCACCTTCCCTCTCCTACAGAATTAACTCTCTTGATGGAACTGTAGGCATTGGGGACAAGTCCGCAGGGAAGCTATTTCTGAACAGGGATTCTCAAGTAGGTGGCTGTCGACTCATATGTCTCCCCTTCTCACACACTAACTAGTGTGGGTTTGTGTTTAAAAACAGACACCCACAGACACATAGATTTTCTCTTTCTCTCTCCATTTATTTTGAGCTAATCCCAAGGGAACTGTATCCTATTTATCTTTGTTCACCAAGTGCCTGGCCATCGAGGTTCAATAAATATTTGTTGAATGAATAAAAAGAAATCTGTTCTCTACTTCCTGGGGAAAGGAGTGAGCCTTAATCATGAGTAGAGTCTTTGTAATGTGAAGCCTTGGAAAAGCCATTTTTTTTTTTTTTTGGCCTGGGAGGGAAGCAAAGAAGGGAGTCAATGAAATTTGGAAACAGAACCTGTCCATCCACTTATCAATTTATTCAGCAAATAGTTATACACCGTCCTTGTTTTCATGGAATTCACAGTCTACTGGAGAGATGGATAAGAAGTAGAAGTCAGAAACAGAATGACAAATTATAAGTGCTATAAGGGAAGTAACTGGTTGTTGGAACAGACATTAATAGACAGGTTGACCAGAGAATCTCTTTAAGTAGACATCTGAGCTGAAACCTAAAGGATGAGAAGGTCAAGGAAGCAAGGAGCTAAGGAAGCAAGGAGCTTGATGTCATTAAGAATACCAAAAGCAAGTCAGTGGGGCCTAGCAGAGTGAGCAAGGAGAGAATGGTGTGCTAGAAGATGAAGGCTGGATGGGCCATGGTGAGGAATCTGGATTTTTATTCTGAGTTAAACTTCTTTATGAAAATGGAAAATTGAACTCTATAATTCTCAATATGGAACTTAGAACAGTACTTGACATGTAGCAAGTGATCAATAAATGTTAGCCATTATTTTACATGTATAGTACCCAAGTAAATTGGCAAGCCTTCGTCATAGTAATTGGAAAAAAATGATTAAAACTTTAGCAGTGAAAAAGATGGTCATTTACTTGATAAACATAGTTTTTATTTAGCAACTTTTCTTGTTTCTTTTTTTTTTTTTGGTATTTTTTTGTAGAGATGGGATTTCACCTTGTTGCTCAGGCTGGTCTTAAACTCCTGGGCTCAAGAGATCCACCCACCTAGGCCTCCCAAAGTGCTAGGATTACAGGCGTGTCCAGCCTATTTAGGAACCTTTTCCATACAACCAGTCAAATTCCAGACAAAGCTGGTCAGATTCCACTTACAAAAGGGAACACTCATTTCTTACTGATCCACTGATACTCAGTTTTC'..b'GCTATTTGGGAGGCTGAGGTGGGAGAATCACCTGACCCCAGGAGGTTGAGGCTGCAGTTAGCCATGATCACACCACCGCACTCCCGCCTAGGCAACAGGAGTGAGACCCTGTCTTAAAAAAAAGGAAAATCTTCGAGATTAGGGACGAGTGATCATCCAGCCATCACAAAGTATAAGACCTCACAAGAAGAAGGAGTGGCCGGGTGCGGTGGCTCACATCTGTAATCCCAGCACTGTGGGAGGCCGAGGCAGGTGGATCACGAGGTGAAGAGATCGAGACCATCCTGGCCAACATGGGGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCTGGGTGTGGTAGTGGGCACCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGGGTGAACCTGGGAGGCGGAGCTTGCAGTGAGCTGAGATCGCACCACTGCACTCCAGCCTGGGCAACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAGAGGAAGGAGAGAACAATGTTGCAAACAACTTACGCAATTCTTCTGGCAAATTGCTTGTTTTTAGAGTTCCTCTGGCTGGAGGGTTGCTAGGGGGTCTAGGCACAGCAGCTGGGGACGGAGGCTGGGGAACCTGTGGTCTCAGCTCTGCAGGGCACTCCAAGGACTCCCCAGGAGCACCAGCTCTATTAGGTGGCTGGTGATGTGGCTGGTCCCTAGAAAGGAATACATTTACAGTCAATTTTCATTCTTTACAAAGGCAAACCTTCAGGGACAGAAAGACTTTTAGAACTATGGGAAGATCCCAGTGGGCTCTCTCTCCTCTGCCTCTATTTCTTAACTGAGACAGAAGGAAGAGGGGAGCTCCATGGAGTTGTAGTCAATAAGCGTTTCAGCTGGCTGCCACATGTGAGGGCCTGTGCTCTGACTCCAAAGAGGGAAGCAGGATTTGATTTCTCTATTCAAGATTTGTTTAATTGGAAAAACAAGTCTCATGCACAGGGCAGACAAGGTCACCAACAAAACAAAGTAGTATGACAGGTGACACAGATGGTTGATGTTATAGGCATTCAGATAAAAAGACATGACTTTTAGCTCATAATAGGTAACATTTAATTATGTATCAAAAGGTAAAGAGGGCCATGTAGATTTAGAAGTATTTGTACTGTTGACATATAAATGGAAATCTGATTTTGAAGACCCTTTAAAGAAGTTGCTACCATATTAGATAGCATCTTTATTATTTTCGTTGCCAGTATTCCCACGAGCATTCTGCTGAGATGAACAATCAGATGACCTCGTGTGAGATTTGGAGGAGAGAAGGAAATGGAGAGCATGCTTCTGCCGCTTCTGTGGTTTCTGTCGGTAAGCACAGTGATGAGGTGCTGAGTTTTCCCCAGAAGGCCTCCCAGTGTCCTATTACCAGCTTCACAAGCGTCGAGGGCAGGGCATGGGCATCTATTGTTCACCAGTGGAGATCTATCTGGCACAGAACCGATCCAACCATTGCAGTGGTCACAGCGGTGTTGGCTTTCTGATTCTCGACCTTCCTGACCACCAGAGGAGACAGCCTCTTTGGTGGCCCTGTTCTGTGGTATTGTGCTAACCGGTGGTGGGACTAAAACTGTCTCTATAATGTTTTATTTCTTAAAAAAAAATTCTGAAGCAAATGTGACAATATGTTAACATTCTTAAAATCTGGGTAGTGGGAACATGGATGTTGTTATTTGTGGTGTGTTTGAAATTGTGTCATATTATAAATTTAAAAAAAATGTTTTGACTACAAAATCTCTATGTATATGCCCAGTTTTTGTAGATTGTTGCTTACGCTTTTCATATTTTTACCCAAGGAGTAATCAGGAATTCTAAAAGTCTTATGTAACAGGATTTAAAATAAAATTACACAGAATCTCAACTGTACTATATTTTGAAAATATGAATGATTAAGATTATTTTTTATATTTTTATTAATATAGAGAAAATAATTTCTATAAAATATGCTTTCAGCTAATGGGGGATCCCATTCCATATTTTTTTCTTTTTCTTTTTTTTTTTATTTCTCCAAGAAAAACTCATTCCAGTTCTTTTGCATTAAATTCTCTTATACCAAAAAAATTGTTTCAAAAGTTGCTTAGTTGTTATAGAAGATGATTGCTTATATGATAAAGAAATGTTAAGGCCTTGATAATATTCAAAAGCTTCTGTATAAAAACAATACCATGGAAATTAATGACAGAGTAAACTTTCTGAATTAAAGTTCTCTTTCAAACTATGAGTAAGAGGAGAATTAGCTGGCTTCTTTTTTCTTTTTTTTGAGGCAGGGTCTTGCTCTGTCACCCAGGCTCAATCACAGCTCACTGCAGCCTTGACCTCCTGGGCTCAGGTGATTTTCCCACCTTAGCCTCCTGAGTAGCTGGGACCACAGGCATGAGCCACCACACCTGGCTAATTTTTGTATTATTTTGGTAGAGATGGGATTTCGCCATGTTGCCCAAGCTGGTCACAAACTTCCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTATGCCCAACCTCAGTTGGATGGGTTTGTGTGTATGTGTGTGTGTGTTTTGTTTGTTTTTTAGTTTTTGAGACAGAGTCTCACTCTGTCACCCAGGCTGGAGTGCAGTGGCACAATCACGGCTCACTGCAGCCATGACCTCTTGTGCTCAGGCAGTTCTCCTGCCTCAGCCTCCTTAGTAGCTGGAACCACAGGTATGTGCCACCACACCCGGCTAATTTTTGTATTTTTTTGTAGAGATGGGTTTTCGCTATGTTGCCCAGGCTGGTCTCAAATTCCTGGGCTCAAACAATCCACCCACCTCTGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACCAAGCCCAGCCTAGCTCCTCTACCTGAACTTATTTTTCATTATCCTAAAGTGATAAAATAGATCAAGAAGATCAGAACAGGCTTAAATTGATGCTATAAAACCAATTACTCTGTATTATCTTTGCAACTCTTTTGTAAGTCTAAAATTGTTTGAAAATAAAAGTTTATTTTAAAAATTACTATTCTCTTTCCTATTCAACACAAAACTTATTTCATAAAGATGCTTACATTTTGTTTATTTCCCTGGAATTTTAGATATTTCTTCTGTTAGAGTGCCTATCCTGCTATAAAATCACATTTTACCTAATTCCATTGTTTAAACTCCATGTATTTATGGTTTAGAAAAATAAGGGATCTGGCCCAGCACGGTGGCTAACACCCGTAATCCCAGCACTTTGGGAGGCTGATGTGGGTGGATCACTTGAGGCCAGGAGTTTGAAACCAGCCTGGGCAACAAAGTGAGACCCCTTCTCTGCAAAAAATAAAAAAATTAGCTGGGTGTGGTAGCGGGCGTCTGTAGTTCCAGCTACTCTTGGGAGGCTGAGGTTGGAAGATGGCTTGAGTGCAGGAGGCGAAGGTTTCAGTGAGTCGAGATCTCGCCACTGCACTCCACCCTAAGTGACAGAGTCAGATCCTGTCCCAAAAGAAAGAGAGAAAAAAAGAGATCTGTCTTGAAAGAAAATATGAGGGTTTGTGGGCTTCTGAGCAAAAGAGAAAGCAGGCATGTGCCTCTTCACCATTGTTAATAAAGTGGGCTTTTTTTCTTTCCATGAAATGTTCAAACTAATTACCGCTTTCTGTATTTCTGAAAAATCCACTCTAATAGGAACTTCATATTTTACTCTATGCTGTAAAAACAGAATCTAGTTTTACAGTGGTATATAAAAGTTGCTTTTGAGCAAAAGTAAACATTTAATCTACTTTCTTCCAAATATTGTCATAAATGAGGAAGCTCCATTTACATGAGTTTTACCTATATATTTTAGATCCATAAATTAAGAGAAAAGGAAAGTCCAAAGAGAATAAGGGAAAAAAAATGATTAAAGAGGCAGGGCACAGTGGCTCATGCCTGCAATCCCAGCACTTTGGGAGGCCGAGGCGAGACGATG\n' 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| diff -r 5e67ea368004 -r 34e128a6a6ed test-data/corrected_reads_paf.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/corrected_reads_paf.fasta Mon Jun 23 03:09:42 2025 +0000 |
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| @@ -0,0 +1,3 @@ +[2025-05-09 07:19:50.605] [[32minfo[m] Running: "correct" "test-data/reads.fq" "--from-paf" "overlaps.paf" +[2025-05-09 07:19:50.606] [[32minfo[m] Failed to load NVML +[2025-05-09 07:19:50.606] [[31m[1merror[m] Input reads file test-data/reads.fq does not exist! |
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| diff -r 5e67ea368004 -r 34e128a6a6ed test-data/overlaps.paf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/overlaps.paf Mon Jun 23 03:09:42 2025 +0000 |
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| @@ -0,0 +1,3 @@ +[2025-05-09 07:19:09.954] [[32minfo[m] Running: "correct" "test-data/reads.fq" "--to-paf" +[2025-05-09 07:19:09.962] [[32minfo[m] Failed to load NVML +[2025-05-09 07:19:09.965] [[31m[1merror[m] Input reads file test-data/reads.fq does not exist! |
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| diff -r 5e67ea368004 -r 34e128a6a6ed test-data/reads.fq.gz |
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| Binary file test-data/reads.fq.gz has changed |