Skip to content

Commit

Permalink
update cutadapt
Browse files Browse the repository at this point in the history
  • Loading branch information
Delphine-L committed Apr 23, 2024
1 parent 3f711cf commit 73da790
Show file tree
Hide file tree
Showing 2 changed files with 38 additions and 71 deletions.
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@
],
"format-version": "0.1",
"license": "CC-BY-4.0",
"release": "0.1.4",
"release": "0.1.5",
"name": "Assembly-Hifi-only-VGP3",
"steps": {
"0": {
Expand All @@ -34,7 +34,7 @@
"name": "Input dataset collection",
"outputs": [],
"position": {
"left": 0.0,
"left": 0,
"top": 549.7803459425681
},
"tool_id": null,
Expand Down Expand Up @@ -124,13 +124,7 @@
"type": "parameter_input",
"uuid": "3ce6ecc2-3262-4695-b4ef-1a58f52a48bd",
"when": null,
"workflow_outputs": [
{
"label": null,
"output_name": "output",
"uuid": "eb6539b5-84f1-4a55-906a-e1dada745409"
}
]
"workflow_outputs": []
},
"4": {
"annotation": "If empty, read coverage will be estimated from the Genomescope parameters. ",
Expand All @@ -157,13 +151,7 @@
"type": "parameter_input",
"uuid": "1e16198c-a515-4b6d-9a72-d1de93974d2b",
"when": null,
"workflow_outputs": [
{
"label": null,
"output_name": "output",
"uuid": "48ba5562-b3eb-4e8f-82f3-83f6436da6a9"
}
]
"workflow_outputs": []
},
"5": {
"annotation": "GenomeScope model parameters generated by K-mer profiling workflow",
Expand Down Expand Up @@ -217,13 +205,7 @@
"type": "parameter_input",
"uuid": "df030d72-fca9-4b7e-b58b-dcd27c453543",
"when": null,
"workflow_outputs": [
{
"label": null,
"output_name": "output",
"uuid": "9a6c9fbe-757b-4a7e-8b69-896e4a35b6d6"
}
]
"workflow_outputs": []
},
"7": {
"annotation": "",
Expand All @@ -250,13 +232,7 @@
"type": "data_input",
"uuid": "b7958e14-2495-4d38-8da1-ea583f5ae8e2",
"when": null,
"workflow_outputs": [
{
"label": null,
"output_name": "output",
"uuid": "70dc3f0f-18af-4dad-9e5b-96d9669af408"
}
]
"workflow_outputs": []
},
"8": {
"annotation": "",
Expand All @@ -283,13 +259,7 @@
"type": "parameter_input",
"uuid": "163c033f-85ce-46e5-b00a-3b3904dea278",
"when": null,
"workflow_outputs": [
{
"label": null,
"output_name": "output",
"uuid": "95517f19-9c34-4374-8439-3273b414dd88"
}
]
"workflow_outputs": []
},
"9": {
"annotation": "",
Expand All @@ -316,17 +286,11 @@
"type": "parameter_input",
"uuid": "88e40054-8605-4746-b91b-38ff85c70fd6",
"when": null,
"workflow_outputs": [
{
"label": null,
"output_name": "output",
"uuid": "e15697b0-756e-4b6f-a52a-a8eece196e37"
}
]
"workflow_outputs": []
},
"10": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.7+galaxy0",
"content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.8+galaxy0",
"errors": null,
"id": 10,
"input_connections": {
Expand Down Expand Up @@ -357,6 +321,11 @@
"top": 992.890625
},
"post_job_actions": {
"HideDatasetActionjson_stats": {
"action_arguments": {},
"action_type": "HideDatasetAction",
"output_name": "json_stats"
},
"TagDatasetActionout1": {
"action_arguments": {
"tags": "trimmed_"
Expand All @@ -365,15 +334,15 @@
"output_name": "out1"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.7+galaxy0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.8+galaxy0",
"tool_shed_repository": {
"changeset_revision": "944ae523bacb",
"changeset_revision": "b1c926deaa2d",
"name": "cutadapt",
"owner": "lparsons",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"adapter_options\": {\"action\": \"trim\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"35\", \"match_read_wildcards\": false, \"no_match_adapter_wildcards\": true, \"revcomp\": true}, \"filter_options\": {\"discard_trimmed\": true, \"discard_untrimmed\": false, \"minimum_length\": null, \"maximum_length\": null, \"max_n\": null, \"pair_filter\": \"any\", \"max_expected_errors\": null, \"max_average_error_rate\": null, \"discard_cassava\": false}, \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [], \"front_adapters\": [], \"anywhere_adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"\", \"adapter\": \"ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT\"}, \"single_noindels\": false}, {\"__index__\": 1, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"\", \"adapter\": \"ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT\"}, \"single_noindels\": false}]}}, \"output_selector\": [\"report\", \"json_stats\"], \"read_mod_options\": {\"cut\": \"0\", \"quality_cutoff\": \"0\", \"nextseq_trim\": \"0\", \"trim_n\": false, \"poly_a\": false, \"strip_suffix\": \"\", \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "4.7+galaxy0",
"tool_state": "{\"adapter_options\": {\"action\": \"trim\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"35\", \"match_read_wildcards\": false, \"no_match_adapter_wildcards\": true, \"revcomp\": true}, \"filter_options\": {\"discard_trimmed\": true, \"discard_untrimmed\": false, \"minimum_length\": null, \"maximum_length\": null, \"max_n\": null, \"pair_filter\": \"any\", \"max_expected_errors\": null, \"max_average_error_rate\": null, \"discard_cassava\": false}, \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"RuntimeValue\"}, \"r1\": {\"adapters\": [], \"front_adapters\": [], \"anywhere_adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"\", \"adapter\": \"ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT\"}, \"single_noindels\": false}, {\"__index__\": 1, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"\", \"adapter\": \"ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT\"}, \"single_noindels\": false}]}}, \"output_selector\": [\"report\", \"json_stats\"], \"read_mod_options\": {\"cut\": \"0\", \"quality_cutoff\": \"0\", \"nextseq_trim\": \"0\", \"trim_n\": false, \"poly_a\": false, \"strip_suffix\": \"\", \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "4.8+galaxy0",
"type": "tool",
"uuid": "f679b5eb-cc26-4005-9499-3ad2eb4698d4",
"when": null,
Expand Down Expand Up @@ -501,7 +470,7 @@
"owner": "devteam",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"avoid_scientific_notation\": false, \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": \"c3*2\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_state": "{\"avoid_scientific_notation\": false, \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": \"c3*2\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.0",
"type": "tool",
"uuid": "0203b86a-9457-48fc-87af-e251b24bad2b",
Expand Down Expand Up @@ -639,7 +608,7 @@
}
},
"tool_id": "Cut1",
"tool_state": "{\"columnList\": \"c7\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_state": "{\"columnList\": \"c7\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.0.2",
"type": "tool",
"uuid": "fb6d8a81-7921-4b8b-be3c-e6f37772caa9",
Expand Down Expand Up @@ -719,7 +688,7 @@
}
},
"tool_id": "param_value_from_file",
"tool_state": "{\"input1\": {\"__class__\": \"RuntimeValue\"}, \"param_type\": \"integer\", \"remove_newlines\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"param_type\": \"integer\", \"remove_newlines\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "0.1.0",
"type": "tool",
"uuid": "65b07e97-c8ea-4fbb-b37e-aab4c93c61fa",
Expand Down Expand Up @@ -966,7 +935,7 @@
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"advanced_options\": {\"advanced_selector\": \"set\", \"__current_case__\": 1, \"hifiasm_kmer_length\": \"51\", \"window_size\": \"51\", \"drop_kmers\": \"5.0\", \"max_overlaps\": \"100\", \"correction_rounds\": \"3\", \"min_hist_cnt\": null, \"max_kocc\": \"20000\", \"hg_size\": \"\"}, \"assembly_options\": {\"assembly_selector\": \"set\", \"__current_case__\": 1, \"cleaning_rounds\": \"4\", \"adapter_length\": \"0\", \"pop_contigs\": \"10000000\", \"pop_unitigs\": \"100000\", \"remove_tips\": \"3\", \"max_overlap\": \"0.8\", \"min_overlap\": \"0.2\", \"disable_post_join\": false, \"ignore_error_corrected\": false, \"hom_cov\": {\"__class__\": \"ConnectedValue\"}}, \"bins_out\": false, \"filter_bits\": {\"__class__\": \"ConnectedValue\"}, \"hic_partition\": {\"hic_partition_selector\": \"blank\", \"__current_case__\": 0}, \"log_out\": true, \"mode\": {\"mode_selector\": \"standard\", \"__current_case__\": 0, \"reads\": {\"__class__\": \"RuntimeValue\"}}, \"ont_integration\": {\"ont_integration_selector\": \"blank\", \"__current_case__\": 0}, \"purge_options\": {\"purge_selector\": \"set\", \"__current_case__\": 1, \"purge_level\": \"0\", \"similarity_threshold\": \"0.75\", \"minimum_overlap\": \"1\", \"purge_max\": null, \"n_hap\": null}, \"scaffolding_options\": {\"scaffold_selector\": \"blank\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_state": "{\"advanced_options\": {\"advanced_selector\": \"set\", \"__current_case__\": 1, \"hifiasm_kmer_length\": \"51\", \"window_size\": \"51\", \"drop_kmers\": \"5.0\", \"max_overlaps\": \"100\", \"correction_rounds\": \"3\", \"min_hist_cnt\": null, \"max_kocc\": \"20000\", \"hg_size\": \"\"}, \"assembly_options\": {\"assembly_selector\": \"set\", \"__current_case__\": 1, \"cleaning_rounds\": \"4\", \"adapter_length\": \"0\", \"pop_contigs\": \"10000000\", \"pop_unitigs\": \"100000\", \"remove_tips\": \"3\", \"max_overlap\": \"0.8\", \"min_overlap\": \"0.2\", \"disable_post_join\": false, \"ignore_error_corrected\": false, \"hom_cov\": {\"__class__\": \"ConnectedValue\"}}, \"bins_out\": false, \"filter_bits\": {\"__class__\": \"ConnectedValue\"}, \"hic_partition\": {\"hic_partition_selector\": \"blank\", \"__current_case__\": 0}, \"log_out\": true, \"mode\": {\"mode_selector\": \"standard\", \"__current_case__\": 0, \"reads\": {\"__class__\": \"ConnectedValue\"}}, \"ont_integration\": {\"ont_integration_selector\": \"blank\", \"__current_case__\": 0}, \"purge_options\": {\"purge_selector\": \"set\", \"__current_case__\": 1, \"purge_level\": \"0\", \"similarity_threshold\": \"0.75\", \"minimum_overlap\": \"1\", \"purge_max\": null, \"n_hap\": null}, \"scaffolding_options\": {\"scaffold_selector\": \"blank\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "0.19.8+galaxy1",
"type": "tool",
"uuid": "cecbcd76-97f0-4e7a-9c90-061d3e5be432",
Expand Down Expand Up @@ -1560,7 +1529,7 @@
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"miniprot\": false, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"lineage_conditional\": {\"selector\": \"download\", \"__current_case__\": 1}, \"outputs\": [\"short_summary\", \"missing\", \"image\", \"gff\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"miniprot\": false, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"lineage_conditional\": {\"selector\": \"download\", \"__current_case__\": 1}, \"outputs\": [\"short_summary\", \"missing\", \"image\", \"gff\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "5.5.0+galaxy0",
"type": "tool",
"uuid": "1cd23635-275c-411f-b91d-f53f2bb229cb",
Expand Down Expand Up @@ -1690,11 +1659,6 @@
"uuid": "da32529d-f84c-4af6-b443-eddfc1705d78",
"when": null,
"workflow_outputs": [
{
"label": "Merqury completeness stats",
"output_name": "stats_files",
"uuid": "640107ca-7175-4624-9851-33911c197b18"
},
{
"label": "Merqury png",
"output_name": "png_files",
Expand All @@ -1704,6 +1668,11 @@
"label": "Merqury Histograms",
"output_name": "hist_files",
"uuid": "9bb427f1-2afd-4e63-b7a1-2c9b54c6bee0"
},
{
"label": "Merqury completeness stats",
"output_name": "stats_files",
"uuid": "640107ca-7175-4624-9851-33911c197b18"
}
]
},
Expand Down Expand Up @@ -3149,21 +3118,11 @@
"uuid": "08a613ce-a4c1-46df-930c-153b491114d2",
"when": null,
"workflow_outputs": [
{
"label": null,
"output_name": "3:output",
"uuid": "4dcd2aff-fbe3-4471-9913-1495e27a19cf"
},
{
"label": "Nx Plot",
"output_name": "Nx Plot",
"uuid": "e34782d2-17d1-4598-92d1-93ca3d7ec7dc"
},
{
"label": null,
"output_name": "2:output",
"uuid": "9366eaf9-0b1d-4a64-8cb8-75e10f47d8b3"
},
{
"label": "Size Plot",
"output_name": "Size Plot",
Expand All @@ -3176,6 +3135,6 @@
"VGP",
"Reviewed"
],
"uuid": "7a7986c0-d9d5-42cf-b7a8-4049c943d68c",
"version": 0
"uuid": "f6f4cac5-6900-440b-8f1d-52420f635420",
"version": 1
}
Original file line number Diff line number Diff line change
@@ -1,5 +1,13 @@
# Changelog


## [0.1.5] 2024-04-23

### Manual update

- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.7+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.8+galaxy0`


## [0.1.4] 2024-04-19

### Manual Updates
Expand Down

0 comments on commit 73da790

Please sign in to comment.