From e85bae26f61daab5aa99f976176324e12f1c0573 Mon Sep 17 00:00:00 2001 From: Subina Mehta Date: Fri, 22 Nov 2024 10:39:16 -0500 Subject: [PATCH 01/21] WIP: clinicalmp_discovery --- .../clinicalmp-discovery/.dockstore.yml | 11 + .../clinicalmp-discovery/CHANGELOG.md | 4 + .../clinicalmp/clinicalmp-discovery/README.md | 25 + ...wc-clinicalmp-discovery-workflow-tests.yml | 87 ++ .../iwc-clinicalmp-discovery-workflow.ga | 1359 +++++++++++++++++ 5 files changed, 1486 insertions(+) create mode 100644 workflows/proteomics/clinicalmp/clinicalmp-discovery/.dockstore.yml create mode 100644 workflows/proteomics/clinicalmp/clinicalmp-discovery/CHANGELOG.md create mode 100644 workflows/proteomics/clinicalmp/clinicalmp-discovery/README.md create mode 100644 workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml create mode 100644 workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga diff --git a/workflows/proteomics/clinicalmp/clinicalmp-discovery/.dockstore.yml b/workflows/proteomics/clinicalmp/clinicalmp-discovery/.dockstore.yml new file mode 100644 index 000000000..1fe74f851 --- /dev/null +++ b/workflows/proteomics/clinicalmp/clinicalmp-discovery/.dockstore.yml @@ -0,0 +1,11 @@ +version: 1.2 +workflows: +- name: main + subclass: Galaxy + publish: true + primaryDescriptorPath: /iwc-clinicalmp-discovery-workflow.ga + testParameterFiles: + - /iwc-clinicalmp-discovery-workflow-tests.yml + authors: + - name: Subina Mehta + orcid: 0000-0001-9818-0537 diff --git a/workflows/proteomics/clinicalmp/clinicalmp-discovery/CHANGELOG.md b/workflows/proteomics/clinicalmp/clinicalmp-discovery/CHANGELOG.md new file mode 100644 index 000000000..8ec28ce1e --- /dev/null +++ b/workflows/proteomics/clinicalmp/clinicalmp-discovery/CHANGELOG.md @@ -0,0 +1,4 @@ +# Changelog + +## [0.1] 2024-11-18 +First release. diff --git a/workflows/proteomics/clinicalmp/clinicalmp-discovery/README.md b/workflows/proteomics/clinicalmp/clinicalmp-discovery/README.md new file mode 100644 index 000000000..6818fa7bd --- /dev/null +++ b/workflows/proteomics/clinicalmp/clinicalmp-discovery/README.md @@ -0,0 +1,25 @@ +# Clinical Metaproteomics 2: Discovery + +Discovery in clinical metaproteomics is greatly enhanced by using a well-curated database, particularly one generated with the **MetaNovo tool**. This tool creates a manageable and streamlined database by identifying proteins relevant to the dataset, reducing the complexity of downstream analysis. For optimal results, the MetaNovo-generated database can be merged with reviewed proteins from **Human SwissProt** and known contaminants from the **cRAP (common Repository of Adventitious Proteins)** database, resulting in a compact yet comprehensive database of approximately 21,200 protein sequences. This refined database serves as the foundation for peptide identification, where mass spectrometry (MS) data is matched against the database to identify relevant peptides efficiently and accurately. By reducing redundancy and focusing on clinically relevant sequences, this approach improves the discovery of biomarkers and key protein insights, allowing researchers to extract meaningful biological information with reduced noise and false positives. This streamlined process is particularly valuable in clinical studies, where precision and relevance are critical for advancing diagnostics and therapeutic research. + +In this current workflow, we perform Discovery using the SearchGUI and MaxQuant tools. A GTN has been developed for this workflow. +[https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.html](https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.html) + +## Inputs dataset + +- `MSMS datasets` in RAW dataset collection and MGF Dataset collection +- `Databases for discovery` in Fasta (protein sequences for database searching) +- `Experimental-Design Discovery MaxQuant` in Tabular Format + +## Inputs values + +For MaxQuant and SearchGUI/PeptideShaker +- Peptide Length +- Variable modifications +- Labeled element + + +## Processing + +- extract microbial proteins and peptides using text formating tools +- Grouping duplicates using the Group tool diff --git a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml new file mode 100644 index 000000000..93462ba23 --- /dev/null +++ b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml @@ -0,0 +1,87 @@ +- doc: Test outline for iwc-clinicalmp-discovery-workflow + job: + Human UniProt Microbial Proteins from MetaNovo and cRAP: + class: File + location: https://zenodo.org/records/14182981/files/Human-UniProt-Microbial-Proteins-(from-MetaNovo)-and-cRAP%20.fasta?download=1 + filetype: fasta + Experimental Design Discovery MaxQuant: + class: File + location: https://zenodo.org/records/14182981/files/Experimental-Design-Discovery-MaxQuant.tabular?download=1 + filetype: tabular + RAW files: + class: Collection + collection_type: list + elements: + - class: File + identifier: PTRC_Skubitz_Plex2_F10_9Aug19_Rage_Rep-19-06-08.raw + location: https://zenodo.org/records/14182981/files/PTRC_Skubitz_Plex2_F10_9Aug19_Rage_Rep-19-06-08.raw?download=1 + - class: File + identifier: PTRC_Skubitz_Plex2_F11_9Aug19_Rage_Rep-19-06-08.raw + location: https://zenodo.org/records/14182981/files/PTRC_Skubitz_Plex2_F11_9Aug19_Rage_Rep-19-06-08.raw?download=1 + - class: File + identifier: PTRC_Skubitz_Plex2_F13_9Aug19_Rage_Rep-19-06-08.raw + location: https://zenodo.org/records/14182981/files/PTRC_Skubitz_Plex2_F13_9Aug19_Rage_Rep-19-06-08.raw?download=1 + - class: File + identifier: PTRC_Skubitz_Plex2_F15_9Aug19_Rage_Rep-19-06-08.raw + location: https://zenodo.org/records/14182981/files/PTRC_Skubitz_Plex2_F15_9Aug19_Rage_Rep-19-06-08.raw?download=1 + outputs: + Human SwissProt: + asserts: + - that: has_text + text: ">sp|" + Human SwissProt+cRAP: + asserts: + - that: has_text + text: ">sp|" + Select microbial peptides MQ: + asserts: + - that: has_text + text: "Sequence" + Filtering Accesions: + asserts: + - has_n_columns: + n: 1 + MQ Peptide Sequences: + asserts: + - that: has_text + text: "Sequence" + Select microbial peptides SGPS: + asserts: + - that: has_text + text: "1" + Select microbial PSMs SGPS: + asserts: + - that: has_text + text: ">sp|" + Header removed MQ Peptides: + asserts: + - has_n_columns: + n: 1 + Filter confident microbial Peptides: + asserts: + - that: has_text + text: "1" + Filter confident microbial PSMs: + asserts: + - that: has_text + text: "1" + MQ Distinct Peptides: + asserts: + - has_n_columns: + n: 1 + Extracting peptides SGPS from PSM: + asserts: + - that: has_text + text: "id" + SGPS Peptides: + asserts: + - that: has_text + text: "Sequence" + SGPS Distinct Peptides: + asserts: + - has_n_columns: + n: 1 + SGPS MQ Peptides: + asserts: + - has_n_columns: + n: 1 \ No newline at end of file diff --git a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga new file mode 100644 index 000000000..345c33a64 --- /dev/null +++ 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\"operations\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.1.4", + "type": "tool", + "uuid": "b5462dd0-3af9-41d4-a011-65d4244525a9", + "when": null, + "workflow_outputs": [ + { + "label": "Distinct Peptides", + "output_name": "out_file1", + "uuid": "c283b145-a685-49c4-8787-6e2e70f262b4" + } + ] + } + }, + "tags": [ + "name:clinicalMP" + ], + "uuid": "94138387-134e-4622-96a9-fdaee428ee1b", + "version": 2 +} \ No newline at end of file From 6f0c3e4ba73213a72647e1672f6b1397bf5e1f4b Mon Sep 17 00:00:00 2001 From: Subina Mehta Date: Fri, 22 Nov 2024 10:51:15 -0500 Subject: [PATCH 02/21] Update iwc-clinicalmp-discovery-workflow.ga --- .../iwc-clinicalmp-discovery-workflow.ga | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga index 345c33a64..45dde73ac 100644 --- a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga +++ b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga @@ -11,7 +11,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "name": "Clinical Metaproteomics Discovery Workflow ", + "name": "Clinical Metaproteomics Discovery Workflow", "release": "0.1", "report": { "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" @@ -135,7 +135,7 @@ "post_job_actions": { "RenameDatasetActionoutput_database": { "action_arguments": { - "newname": "Human SwissProt " + "newname": "Human SwissProt" }, "action_type": "RenameDatasetAction", "output_name": "output_database" @@ -155,7 +155,7 @@ "when": null, "workflow_outputs": [ { - "label": "Human SwissProt ", + "label": "Human SwissProt", "output_name": "output_database", "uuid": "335f3fe6-c7fb-4fd6-b04e-9f5afb3fe5a6" } @@ -570,7 +570,7 @@ } }, "inputs": [], - "label": "Select microbial peptides MQ ", + "label": "Select microbial peptides MQ", "name": "Select", "outputs": [ { From d94771e283200a471680f2b4afb7ac62e8c9affa Mon Sep 17 00:00:00 2001 From: Subina Mehta Date: Fri, 22 Nov 2024 10:53:29 -0500 Subject: [PATCH 03/21] Update README.md --- workflows/proteomics/clinicalmp/clinicalmp-discovery/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/proteomics/clinicalmp/clinicalmp-discovery/README.md b/workflows/proteomics/clinicalmp/clinicalmp-discovery/README.md index 6818fa7bd..000ac21e4 100644 --- a/workflows/proteomics/clinicalmp/clinicalmp-discovery/README.md +++ b/workflows/proteomics/clinicalmp/clinicalmp-discovery/README.md @@ -7,7 +7,7 @@ In this current workflow, we perform Discovery using the SearchGUI and MaxQuant ## Inputs dataset -- `MSMS datasets` in RAW dataset collection and MGF Dataset collection +- `MSMS datasets` in RAW dataset collection - `Databases for discovery` in Fasta (protein sequences for database searching) - `Experimental-Design Discovery MaxQuant` in Tabular Format From de86d5d885f079060ea46ba6009920e9aa1a3fa6 Mon Sep 17 00:00:00 2001 From: Subina Mehta Date: Fri, 22 Nov 2024 11:14:06 -0500 Subject: [PATCH 04/21] Update iwc-clinicalmp-discovery-workflow-tests.yml --- ...wc-clinicalmp-discovery-workflow-tests.yml | 58 +------------------ 1 file changed, 1 insertion(+), 57 deletions(-) diff --git a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml index 93462ba23..b43ed088e 100644 --- a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml +++ b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml @@ -25,63 +25,7 @@ identifier: PTRC_Skubitz_Plex2_F15_9Aug19_Rage_Rep-19-06-08.raw location: https://zenodo.org/records/14182981/files/PTRC_Skubitz_Plex2_F15_9Aug19_Rage_Rep-19-06-08.raw?download=1 outputs: - Human SwissProt: - asserts: - - that: has_text - text: ">sp|" - Human SwissProt+cRAP: - asserts: - - that: has_text - text: ">sp|" - Select microbial peptides MQ: - asserts: - - that: has_text - text: "Sequence" - Filtering Accesions: - asserts: - - has_n_columns: - n: 1 - MQ Peptide Sequences: - asserts: - - that: has_text - text: "Sequence" - Select microbial peptides SGPS: - asserts: - - that: has_text - text: "1" - Select microbial PSMs SGPS: - asserts: - - that: has_text - text: ">sp|" - Header removed MQ Peptides: - asserts: - - has_n_columns: - n: 1 - Filter confident microbial Peptides: - asserts: - - that: has_text - text: "1" - Filter confident microbial PSMs: - asserts: - - that: has_text - text: "1" - MQ Distinct Peptides: - asserts: - - has_n_columns: - n: 1 - Extracting peptides SGPS from PSM: - asserts: - - that: has_text - text: "id" - SGPS Peptides: - asserts: - - that: has_text - text: "Sequence" - SGPS Distinct Peptides: - asserts: - - has_n_columns: - n: 1 SGPS MQ Peptides: asserts: - has_n_columns: - n: 1 \ No newline at end of file + n: 1 From fe34985c7ec36245fef4cb239746d6da5f80447d Mon Sep 17 00:00:00 2001 From: Subina Mehta Date: Fri, 22 Nov 2024 12:43:46 -0500 Subject: [PATCH 05/21] Update iwc-clinicalmp-discovery-workflow-tests.yml --- .../iwc-clinicalmp-discovery-workflow-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml index b43ed088e..a1c7354b9 100644 --- a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml +++ b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml @@ -2,7 +2,7 @@ job: Human UniProt Microbial Proteins from MetaNovo and cRAP: class: File - location: https://zenodo.org/records/14182981/files/Human-UniProt-Microbial-Proteins-(from-MetaNovo)-and-cRAP%20.fasta?download=1 + location: https://zenodo.org/records/10720030/files/Human_UniProt_Microbial_Proteins_(from_MetaNovo)_and_cRAP.fasta?download=1 filetype: fasta Experimental Design Discovery MaxQuant: class: File From c091be380777239100de1bb2110da18847e7e468 Mon Sep 17 00:00:00 2001 From: Subina Mehta Date: Fri, 22 Nov 2024 13:01:05 -0500 Subject: [PATCH 06/21] Update iwc-clinicalmp-discovery-workflow-tests.yml --- .../iwc-clinicalmp-discovery-workflow-tests.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml index a1c7354b9..43ab889a1 100644 --- a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml +++ b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml @@ -2,11 +2,11 @@ job: Human UniProt Microbial Proteins from MetaNovo and cRAP: class: File - location: https://zenodo.org/records/10720030/files/Human_UniProt_Microbial_Proteins_(from_MetaNovo)_and_cRAP.fasta?download=1 + location: https://zenodo.org/records/10720030/files/Human_UniProt_Microbial_Proteins_(from_MetaNovo)_and_cRAP.fasta filetype: fasta Experimental Design Discovery MaxQuant: class: File - location: https://zenodo.org/records/14182981/files/Experimental-Design-Discovery-MaxQuant.tabular?download=1 + location: https://zenodo.org/records/14182981/files/Experimental-Design-Discovery-MaxQuant.tabular filetype: tabular RAW files: class: Collection @@ -14,16 +14,16 @@ elements: - class: File identifier: PTRC_Skubitz_Plex2_F10_9Aug19_Rage_Rep-19-06-08.raw - location: https://zenodo.org/records/14182981/files/PTRC_Skubitz_Plex2_F10_9Aug19_Rage_Rep-19-06-08.raw?download=1 + location: https://zenodo.org/records/14182981/files/PTRC_Skubitz_Plex2_F10_9Aug19_Rage_Rep-19-06-08.raw - class: File identifier: PTRC_Skubitz_Plex2_F11_9Aug19_Rage_Rep-19-06-08.raw - location: https://zenodo.org/records/14182981/files/PTRC_Skubitz_Plex2_F11_9Aug19_Rage_Rep-19-06-08.raw?download=1 + location: https://zenodo.org/records/14182981/files/PTRC_Skubitz_Plex2_F11_9Aug19_Rage_Rep-19-06-08.raw - class: File identifier: PTRC_Skubitz_Plex2_F13_9Aug19_Rage_Rep-19-06-08.raw - location: https://zenodo.org/records/14182981/files/PTRC_Skubitz_Plex2_F13_9Aug19_Rage_Rep-19-06-08.raw?download=1 + location: https://zenodo.org/records/14182981/files/PTRC_Skubitz_Plex2_F13_9Aug19_Rage_Rep-19-06-08.raw - class: File identifier: PTRC_Skubitz_Plex2_F15_9Aug19_Rage_Rep-19-06-08.raw - location: https://zenodo.org/records/14182981/files/PTRC_Skubitz_Plex2_F15_9Aug19_Rage_Rep-19-06-08.raw?download=1 + location: https://zenodo.org/records/14182981/files/PTRC_Skubitz_Plex2_F15_9Aug19_Rage_Rep-19-06-08.raw outputs: SGPS MQ Peptides: asserts: From 493e50200e58d757ff880f175f989470a9de848f Mon Sep 17 00:00:00 2001 From: Subina Mehta Date: Fri, 22 Nov 2024 22:37:38 -0500 Subject: [PATCH 07/21] Update iwc-clinicalmp-discovery-workflow.ga --- .../iwc-clinicalmp-discovery-workflow.ga | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga index 45dde73ac..14191bd46 100644 --- a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga +++ b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga @@ -95,10 +95,10 @@ "inputs": [ { "description": "Input Raw files", - "name": "RAW files" + "name": "Tandem Mass Spectrometry MSMS files" } ], - "label": "RAW files", + "label": "Tandem Mass Spectrometry MSMS files", "name": "Input dataset collection", "outputs": [], "position": { @@ -715,7 +715,7 @@ "post_job_actions": { "RenameDatasetActionoutput": { "action_arguments": { - "newname": "Filtering Accesions" + "newname": "Filtering Accessions" }, "action_type": "RenameDatasetAction", "output_name": "output" @@ -735,7 +735,7 @@ "when": null, "workflow_outputs": [ { - "label": "Filtering Accesions", + "label": "Filtering Accessions", "output_name": "output", "uuid": "94f1a6b8-0f60-4ffc-ab90-31ba68d37cdc" } @@ -1356,4 +1356,4 @@ ], "uuid": "94138387-134e-4622-96a9-fdaee428ee1b", "version": 2 -} \ No newline at end of file +} From cf5b2cb6c7b3407dfc68b0d496e8806193990b65 Mon Sep 17 00:00:00 2001 From: Subina Mehta Date: Fri, 22 Nov 2024 22:37:44 -0500 Subject: [PATCH 08/21] Update iwc-clinicalmp-discovery-workflow-tests.yml --- .../iwc-clinicalmp-discovery-workflow-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml index 43ab889a1..ef491498a 100644 --- a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml +++ b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml @@ -8,7 +8,7 @@ class: File location: https://zenodo.org/records/14182981/files/Experimental-Design-Discovery-MaxQuant.tabular filetype: tabular - RAW files: + Tandem Mass Spectrometry MSMS files: class: Collection collection_type: list elements: From 67222b8fcaaba3c8d47799cf2fe642918ab1b8e4 Mon Sep 17 00:00:00 2001 From: Subina Mehta Date: Mon, 2 Dec 2024 11:07:21 -0500 Subject: [PATCH 09/21] Create readme.md --- .../clinicalmp/clinicalmp-discovery/test-data/readme.md | 1 + 1 file changed, 1 insertion(+) create mode 100644 workflows/proteomics/clinicalmp/clinicalmp-discovery/test-data/readme.md diff --git a/workflows/proteomics/clinicalmp/clinicalmp-discovery/test-data/readme.md b/workflows/proteomics/clinicalmp/clinicalmp-discovery/test-data/readme.md new file mode 100644 index 000000000..14312539f --- /dev/null +++ b/workflows/proteomics/clinicalmp/clinicalmp-discovery/test-data/readme.md @@ -0,0 +1 @@ +dsfsfsd From 22aff08bbf26c9e2dfbd1a1989bd1f6f48f4df96 Mon Sep 17 00:00:00 2001 From: Subina Mehta Date: Mon, 2 Dec 2024 11:07:53 -0500 Subject: [PATCH 10/21] Add files via upload --- .../test-data/Experimental Design Discovery MaxQuant.tabular | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 workflows/proteomics/clinicalmp/clinicalmp-discovery/test-data/Experimental Design Discovery MaxQuant.tabular diff --git a/workflows/proteomics/clinicalmp/clinicalmp-discovery/test-data/Experimental Design Discovery MaxQuant.tabular b/workflows/proteomics/clinicalmp/clinicalmp-discovery/test-data/Experimental Design Discovery MaxQuant.tabular new file mode 100644 index 000000000..9734eddf3 --- /dev/null +++ b/workflows/proteomics/clinicalmp/clinicalmp-discovery/test-data/Experimental Design Discovery MaxQuant.tabular @@ -0,0 +1,3 @@ +Name Fraction Experiment PTM +PTRC_Skubitz_Plex2_F10_9Aug19_Rage_Rep-19-06-08.raw 1 1 FALSE +PTRC_Skubitz_Plex2_F11_9Aug19_Rage_Rep-19-06-08.raw 2 1 FALSE \ No newline at end of file From f5356fdf8bfd13e20e1ebba01d4ecc51c9853a82 Mon Sep 17 00:00:00 2001 From: Subina Mehta Date: Mon, 2 Dec 2024 11:08:11 -0500 Subject: [PATCH 11/21] Delete workflows/proteomics/clinicalmp/clinicalmp-discovery/test-data/readme.md --- .../clinicalmp/clinicalmp-discovery/test-data/readme.md | 1 - 1 file changed, 1 deletion(-) delete mode 100644 workflows/proteomics/clinicalmp/clinicalmp-discovery/test-data/readme.md diff --git a/workflows/proteomics/clinicalmp/clinicalmp-discovery/test-data/readme.md b/workflows/proteomics/clinicalmp/clinicalmp-discovery/test-data/readme.md deleted file mode 100644 index 14312539f..000000000 --- a/workflows/proteomics/clinicalmp/clinicalmp-discovery/test-data/readme.md +++ /dev/null @@ -1 +0,0 @@ -dsfsfsd From 00c62e2a4480d1d637b0d2e33e53841091d48c00 Mon Sep 17 00:00:00 2001 From: Subina Mehta Date: Mon, 2 Dec 2024 11:10:12 -0500 Subject: [PATCH 12/21] Update iwc-clinicalmp-discovery-workflow-tests.yml --- .../iwc-clinicalmp-discovery-workflow-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml index ef491498a..9467dc714 100644 --- a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml +++ b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml @@ -6,7 +6,7 @@ filetype: fasta Experimental Design Discovery MaxQuant: class: File - location: https://zenodo.org/records/14182981/files/Experimental-Design-Discovery-MaxQuant.tabular + path: test-data/Experimental Design Discovery MaxQuant.tabular filetype: tabular Tandem Mass Spectrometry MSMS files: class: Collection From cc5ef4122f380262c9af9859842003432569cd92 Mon Sep 17 00:00:00 2001 From: Subina Mehta Date: Mon, 2 Dec 2024 11:10:45 -0500 Subject: [PATCH 13/21] Update iwc-clinicalmp-discovery-workflow-tests.yml --- .../iwc-clinicalmp-discovery-workflow-tests.yml | 6 ------ 1 file changed, 6 deletions(-) diff --git a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml index 9467dc714..f15a725ec 100644 --- a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml +++ b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml @@ -18,12 +18,6 @@ - class: File identifier: PTRC_Skubitz_Plex2_F11_9Aug19_Rage_Rep-19-06-08.raw location: https://zenodo.org/records/14182981/files/PTRC_Skubitz_Plex2_F11_9Aug19_Rage_Rep-19-06-08.raw - - class: File - identifier: PTRC_Skubitz_Plex2_F13_9Aug19_Rage_Rep-19-06-08.raw - location: https://zenodo.org/records/14182981/files/PTRC_Skubitz_Plex2_F13_9Aug19_Rage_Rep-19-06-08.raw - - class: File - identifier: PTRC_Skubitz_Plex2_F15_9Aug19_Rage_Rep-19-06-08.raw - location: https://zenodo.org/records/14182981/files/PTRC_Skubitz_Plex2_F15_9Aug19_Rage_Rep-19-06-08.raw outputs: SGPS MQ Peptides: asserts: From 11afb04e04c138cac53b636152e64425c1382f9f Mon Sep 17 00:00:00 2001 From: Subina Mehta Date: Mon, 2 Dec 2024 11:52:39 -0500 Subject: [PATCH 14/21] raw file deletion --- .../iwc-clinicalmp-discovery-workflow-tests.yml | 5 +---- .../test-data/Experimental Design Discovery MaxQuant.tabular | 3 +-- 2 files changed, 2 insertions(+), 6 deletions(-) diff --git a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml index f15a725ec..bc445df8c 100644 --- a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml +++ b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml @@ -15,11 +15,8 @@ - class: File identifier: PTRC_Skubitz_Plex2_F10_9Aug19_Rage_Rep-19-06-08.raw location: https://zenodo.org/records/14182981/files/PTRC_Skubitz_Plex2_F10_9Aug19_Rage_Rep-19-06-08.raw - - class: File - identifier: PTRC_Skubitz_Plex2_F11_9Aug19_Rage_Rep-19-06-08.raw - location: https://zenodo.org/records/14182981/files/PTRC_Skubitz_Plex2_F11_9Aug19_Rage_Rep-19-06-08.raw outputs: SGPS MQ Peptides: asserts: - has_n_columns: - n: 1 + n: 1 \ No newline at end of file diff --git a/workflows/proteomics/clinicalmp/clinicalmp-discovery/test-data/Experimental Design Discovery MaxQuant.tabular b/workflows/proteomics/clinicalmp/clinicalmp-discovery/test-data/Experimental Design Discovery MaxQuant.tabular index 9734eddf3..92f9fa3a8 100644 --- a/workflows/proteomics/clinicalmp/clinicalmp-discovery/test-data/Experimental Design Discovery MaxQuant.tabular +++ b/workflows/proteomics/clinicalmp/clinicalmp-discovery/test-data/Experimental Design Discovery MaxQuant.tabular @@ -1,3 +1,2 @@ Name Fraction Experiment PTM -PTRC_Skubitz_Plex2_F10_9Aug19_Rage_Rep-19-06-08.raw 1 1 FALSE -PTRC_Skubitz_Plex2_F11_9Aug19_Rage_Rep-19-06-08.raw 2 1 FALSE \ No newline at end of file +PTRC_Skubitz_Plex2_F10_9Aug19_Rage_Rep-19-06-08.raw 1 1 FALSE \ No newline at end of file From acee887e6155e24e4fc78b1f6ef1ea93f05e2d5a Mon Sep 17 00:00:00 2001 From: Subina Mehta Date: Thu, 5 Dec 2024 10:58:54 -0500 Subject: [PATCH 15/21] Update workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga Co-authored-by: Marius van den Beek --- .../iwc-clinicalmp-discovery-workflow.ga | 7 ------- 1 file changed, 7 deletions(-) diff --git a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga index 14191bd46..7d69ed610 100644 --- a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga +++ b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga @@ -1215,13 +1215,6 @@ "top": 329.70161173161625 }, "post_job_actions": { - "EmailActionout_file1": { - "action_arguments": { - "host": "usegalaxy.eu" - }, - "action_type": "EmailAction", - "output_name": "out_file1" - }, "RenameDatasetActionout_file1": { "action_arguments": { "newname": "SGPS Distinct Peptides" From 3bf3f31c94357d1ea02540f3412e853b5d8cb6f9 Mon Sep 17 00:00:00 2001 From: Subina Mehta Date: Thu, 5 Dec 2024 10:59:03 -0500 Subject: [PATCH 16/21] Update workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga Co-authored-by: Marius van den Beek --- .../iwc-clinicalmp-discovery-workflow.ga | 7 ------- 1 file changed, 7 deletions(-) diff --git a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga index 7d69ed610..8577c87bf 100644 --- a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga +++ b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga @@ -1048,13 +1048,6 @@ "top": 524.4947117996797 }, "post_job_actions": { - "EmailActionout_file1": { - "action_arguments": { - "host": "usegalaxy.eu" - }, - "action_type": "EmailAction", - "output_name": "out_file1" - }, "RenameDatasetActionout_file1": { "action_arguments": { "newname": "MQ Distinct Peptides" From 0ef4e56da78b9df54b658b883f24a9556c53b9fb Mon Sep 17 00:00:00 2001 From: Subina Mehta Date: Thu, 5 Dec 2024 11:34:55 -0500 Subject: [PATCH 17/21] Update iwc-clinicalmp-discovery-workflow.ga --- .../clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga index 8577c87bf..ffffaadaa 100644 --- a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga +++ b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga @@ -25,7 +25,7 @@ "input_connections": {}, "inputs": [ { - "description": "FastaCLI: MetaNovo Human SwissProt cRAP with decoys on data 1 (MetaNovo Human SwissProt cRAP_concatenated_target_decoy) (49,076 sequences)", + "description": "Adding decoys to MetaNovo Human SwissProt cRAP to improve FDR", "name": "Human UniProt Microbial Proteins from MetaNovo and cRAP" } ], From 7aeca24bef7046eef8d023da4e4ee29155bdb157 Mon Sep 17 00:00:00 2001 From: Subina Mehta Date: Thu, 5 Dec 2024 12:37:47 -0500 Subject: [PATCH 18/21] Update iwc-clinicalmp-discovery-workflow-tests.yml --- .../iwc-clinicalmp-discovery-workflow-tests.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml index bc445df8c..f9c55dacf 100644 --- a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml +++ b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow-tests.yml @@ -19,4 +19,6 @@ SGPS MQ Peptides: asserts: - has_n_columns: - n: 1 \ No newline at end of file + n: 1 + - has_text: + text: "AAFPNVTAMNITTNNGK" From 10a853c999d2e26895a9cf316bafce33cffbb146 Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Fri, 6 Dec 2024 17:01:51 +0100 Subject: [PATCH 19/21] Remove odd annotation --- .../clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga index ffffaadaa..bdceb8d62 100644 --- a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga +++ b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga @@ -18,7 +18,7 @@ }, "steps": { "0": { - "annotation": "FastaCLI: MetaNovo Human SwissProt cRAP with decoys on data 1 (MetaNovo Human SwissProt cRAP_concatenated_target_decoy) (49,076 sequences)", + "annotation": "", "content_id": null, "errors": null, "id": 0, From 2b83ec3bb17c047cc303f7b2f6d5ea7b05d562fa Mon Sep 17 00:00:00 2001 From: Subina Mehta Date: Fri, 6 Dec 2024 11:09:24 -0500 Subject: [PATCH 20/21] Update iwc-clinicalmp-discovery-workflow.ga --- .../clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga index bdceb8d62..7acfd3e09 100644 --- a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga +++ b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga @@ -203,7 +203,7 @@ "input_connections": {}, "inputs": [ { - "description": "Experimental Design Discovery MaxQuant", + "description": "Experimental Design manually created for MaxQuant", "name": "Experimental Design Discovery MaxQuant" } ], From d66c8c4586d2f59eb2f7afe66db4ea50acf10097 Mon Sep 17 00:00:00 2001 From: Subina Mehta Date: Mon, 9 Dec 2024 10:55:12 -0500 Subject: [PATCH 21/21] Update iwc-clinicalmp-discovery-workflow.ga --- .../clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga index 7acfd3e09..c7ada0e47 100644 --- a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga +++ b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga @@ -196,7 +196,7 @@ "workflow_outputs": [] }, "5": { - "annotation": "Experimental Design Discovery MaxQuant", + "annotation": "File for experimental design containing Name, Fraction, Experiment, and PTM, where the name refers to the dataset filename, with each dataset listed on a separate line.", "content_id": null, "errors": null, "id": 5,