Skip to content

Commit

Permalink
Merge pull request #376 from planemo-autoupdate/workflows/VGP-assembl…
Browse files Browse the repository at this point in the history
…y-v2/Assembly-decontamination-VGP9

Updating workflows/VGP-assembly-v2/Assembly-decontamination-VGP9 from 0.1.4 to 0.1.5
  • Loading branch information
Delphine-L authored Apr 23, 2024
2 parents 3f711cf + 6b75b04 commit b8d6636
Show file tree
Hide file tree
Showing 2 changed files with 48 additions and 38 deletions.
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@
],
"format-version": "0.1",
"license": "BSD-3-Clause",
"release": "0.1.4",
"release": "0.1.5",
"name": "Assembly-decontamination-VGP9",
"steps": {
"0": {
Expand Down Expand Up @@ -76,7 +76,7 @@
},
"2": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1",
"errors": null,
"id": 2,
"input_connections": {
Expand Down Expand Up @@ -107,23 +107,23 @@
"output_name": "output"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "ddf54b12c295",
"changeset_revision": "fbf99087e067",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"code\": \"s/.*/\\\\U&/\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.1.1",
"tool_version": "9.3+galaxy1",
"type": "tool",
"uuid": "b9b3d9b9-1716-486d-b65c-b0fb196cbc01",
"when": null,
"workflow_outputs": []
},
"3": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/2.14.1+galaxy1",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/2.14.1+galaxy2",
"errors": null,
"id": 3,
"input_connections": {
Expand All @@ -146,23 +146,23 @@
"top": 176.06640625
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/2.14.1+galaxy1",
"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/2.14.1+galaxy2",
"tool_shed_repository": {
"changeset_revision": "d999e774072a",
"changeset_revision": "cbf3f518b668",
"name": "ncbi_blast_plus",
"owner": "devteam",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"db_opts\": {\"db_opts_selector\": \"file\", \"__current_case__\": 2, \"database\": \"\", \"histdb\": \"\", \"subject\": {\"__class__\": \"ConnectedValue\"}}, \"level\": \"40\", \"linker\": \"1\", \"outformat\": \"fasta\", \"window\": \"64\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.14.1+galaxy1",
"tool_version": "2.14.1+galaxy2",
"type": "tool",
"uuid": "903a13af-2be0-48a9-8355-1e2486d857cf",
"when": null,
"workflow_outputs": []
},
"4": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1",
"errors": null,
"id": 4,
"input_connections": {
Expand Down Expand Up @@ -193,15 +193,15 @@
"output_name": "output"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "ddf54b12c295",
"changeset_revision": "fbf99087e067",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"code\": \"s/[a-z]/N/g\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.1.1",
"tool_version": "9.3+galaxy1",
"type": "tool",
"uuid": "5089350b-c1a9-498a-9786-9864d484f77a",
"when": null,
Expand Down Expand Up @@ -272,7 +272,7 @@
},
"6": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.14.1+galaxy1",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.14.1+galaxy2",
"errors": null,
"id": 6,
"input_connections": {
Expand All @@ -295,23 +295,23 @@
"top": 392.03515625
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.14.1+galaxy1",
"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.14.1+galaxy2",
"tool_shed_repository": {
"changeset_revision": "d999e774072a",
"changeset_revision": "cbf3f518b668",
"name": "ncbi_blast_plus",
"owner": "devteam",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"blast_type\": \"blastn\", \"db_opts\": {\"db_opts_selector\": \"db\", \"__current_case__\": 0, \"database\": [\"refseq_mitochondrion\"], \"histdb\": \"\", \"subject\": \"\"}, \"evalue_cutoff\": \"0.001\", \"output\": {\"out_format\": \"cols\", \"__current_case__\": 2, \"std_cols\": [\"qseqid\", \"sseqid\", \"length\", \"qstart\", \"qend\", \"evalue\"], \"ext_cols\": [\"qlen\"], \"ids_cols\": null, \"misc_cols\": [\"qcovs\", \"qcovhsp\"], \"tax_cols\": null}, \"query\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.14.1+galaxy1",
"tool_version": "2.14.1+galaxy2",
"type": "tool",
"uuid": "1737bad0-48d9-489e-9a45-d6f3d3fcb900",
"when": null,
"workflow_outputs": []
},
"7": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1",
"errors": null,
"id": 7,
"input_connections": {
Expand All @@ -334,15 +334,15 @@
"top": 57.37109375
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "ddf54b12c295",
"changeset_revision": "fbf99087e067",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"case_sensitive\": \"-i\", \"color\": \"NOCOLOR\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"\", \"lines_after\": \"0\", \"lines_before\": \"0\", \"regex_type\": \"-G\", \"url_paste\": \"scaffold\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.1.1",
"tool_version": "9.3+galaxy1",
"type": "tool",
"uuid": "372a2507-7844-43e7-9be0-7add6d5f6def",
"when": null,
Expand Down Expand Up @@ -393,7 +393,7 @@
},
"9": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1",
"errors": null,
"id": 9,
"input_connections": {
Expand Down Expand Up @@ -424,23 +424,23 @@
"output_name": "output"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "ddf54b12c295",
"changeset_revision": "fbf99087e067",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"code\": \"s/>//g\\ns/[A-Z]/\\\\L&/g\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.1.1",
"tool_version": "9.3+galaxy1",
"type": "tool",
"uuid": "f11170d4-82b0-4582-902e-133de9c17218",
"when": null,
"workflow_outputs": []
},
"10": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1",
"errors": null,
"id": 10,
"input_connections": {
Expand All @@ -463,23 +463,23 @@
"top": 370.75390625
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "ddf54b12c295",
"changeset_revision": "fbf99087e067",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"code\": \"s/[A-Z]/\\\\L&/g\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.1.1",
"tool_version": "9.3+galaxy1",
"type": "tool",
"uuid": "0c4be94e-a0a5-46e7-a586-e45ce92411d2",
"when": null,
"workflow_outputs": []
},
"11": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1",
"errors": null,
"id": 11,
"input_connections": {
Expand All @@ -502,23 +502,23 @@
"top": 195.1875
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4",
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "d698c222f354",
"changeset_revision": "fbf99087e067",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"caseinsensitive\": \"false\", \"find_and_replace\": [], \"find_pattern\": \"kraken:taxid\\\\|[0-9]+\", \"global\": \"true\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"is_regex\": \"true\", \"replace_pattern\": \"\", \"searchwhere\": {\"__current_case__\": 0, \"searchwhere_select\": \"line\"}, \"skip_first_line\": \"false\", \"wholewords\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.1.4",
"tool_version": "9.3+galaxy1",
"type": "tool",
"uuid": "c37db543-a966-4ed2-88b9-87b317465144",
"when": null,
"workflow_outputs": []
},
"12": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1",
"errors": null,
"id": 12,
"input_connections": {
Expand Down Expand Up @@ -547,15 +547,15 @@
"top": 276.36328125
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "d698c222f354",
"changeset_revision": "fbf99087e067",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"inputs\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "0.1.1",
"tool_version": "9.3+galaxy1",
"type": "tool",
"uuid": "5b7e33a0-0ec4-4539-bb91-0c862597df69",
"when": null,
Expand Down Expand Up @@ -622,4 +622,4 @@
],
"uuid": "f6d8df21-f1dc-493c-bfab-e2cbecb8873d",
"version": 1
}
}
Original file line number Diff line number Diff line change
@@ -1,5 +1,15 @@
# Changelog

## [0.1.5] 2024-04-01

### Automatic update
- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1`
- `toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/2.14.1+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/2.14.1+galaxy2`
- `toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.14.1+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.14.1+galaxy2`
- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1`
- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1`
- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1`


## [0.1.4] 2024-03-11

Expand Down

0 comments on commit b8d6636

Please sign in to comment.