Mercurial > repos > tduigou > sculpt_sequences

annotate test-data/test_json_workflow2.json @ 1:a0cd867780ec draft default tip

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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
author tduigou
date Thu, 17 Jul 2025 13:24:49 +0000
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a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents:
diff changeset
1 {
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
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2 "DnaOptimizationProblemClass":"DnaOptimizationProblem",
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
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3 "avoid_patterns": "BsaI_site\nNotI_site\nXbaI_site\nClaI_site\n8x1mer",
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents:
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4 "hairpin_constraints": "stem_size=20, hairpin_window=200\nstem_size=10, hairpin_window=100",
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents:
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5 "gc_constraints": "mini=0.1, maxi=0.9\nmini=0.3, maxi=0.7, window=50",
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents:
diff changeset
6 "kmer_size": "15",
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents:
diff changeset
7 "methylation_protection":"methylation_protection",
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
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8 "allow_edits":"True",
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents:
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9 "assembly_plan_name": "Type2sRestrictionAssembly",
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
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10 "topology": "circular",
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
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11 "enzyme": "auto",
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents:
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12 "execution": "true",
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
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13 "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
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14 "table": "sample",
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
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15 "fragment_column": "fragment",
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
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16 "sequence_column": "sequence",
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
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17 "annotation_column": "annotation"
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
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18 }