From e70d7ddb126fcd8f8398944479a0f8cc414afcb9 Mon Sep 17 00:00:00 2001 From: Christian Fufezan Date: Thu, 22 Sep 2022 15:57:58 +0200 Subject: [PATCH 1/7] Add 2 params --- jsons/parameters.json | 25 ++++++++++++++++++++++++- jsons/styles.json | 32 ++++++++++++++++++++------------ 2 files changed, 44 insertions(+), 13 deletions(-) diff --git a/jsons/parameters.json b/jsons/parameters.json index 382c97c..e62a744 100644 --- a/jsons/parameters.json +++ b/jsons/parameters.json @@ -3373,6 +3373,7 @@ "pnovo_style_1": "thread", "proteomics_qc_style_1": "n_cpus", "ptmshepherd_style_1": "threads", + "reporter_extract_style_1": "cpus", "ucontroller_style_1": "cpus", "ursgal_style_1": "cpus", "xtandem_style_1": "spectrum, threads" @@ -3467,6 +3468,12 @@ "max - 1" ] ], + "reporter_extract_style_1": [ + [ + -1, + -1 + ] + ], "ucontroller_style_1": [ [ -1, @@ -10980,6 +10987,7 @@ "mzml2mgf_style_1": "ms_level", "pipi_style_1": "ms_level", "pyqms_style_1": "ms_level", + "reporter_extract_style_1": "ms_level", "sugarpy_plot_style_1": "ms_level", "sugarpy_run_style_1": "ms_level", "ursgal_style_1": "ms_level" @@ -10990,7 +10998,7 @@ ], "triggers_rerun": true, "value_translations": {}, - "value_type": "int" + "value_type": "int or string of ints separated by ," }, { "default_value": false, @@ -14118,6 +14126,21 @@ "value_translations": {}, "value_type": "bool" }, + { + "default_value": "TMTpro", + "description": "Reporter Ion type", + "key_translations": { + "reporter_extract_style_1": "--quant_method", + "ursgal_style_1": "reporter_ion_type" + }, + "name": "reporter_ion_type", + "tag": [ + "quantification", + "MSn" + ], + "triggers_rerun": true, + "value_type": "float" + }, { "default_value": false, "description": "Require MS/MS match in condition to consider quantification", diff --git a/jsons/styles.json b/jsons/styles.json index ee09c1c..e353dcd 100644 --- a/jsons/styles.json +++ b/jsons/styles.json @@ -295,6 +295,14 @@ "1.0.0" ] }, + { + "name": "Reporter Extract Style 1", + "reference": "Mathieson T., Sweetman, G. and Fufezan, C. (2021)", + "style": "reporter_extract_style_1", + "versions": [ + "1.0.0" + ] + }, { "name": "Sanitize CSV", "reference": "Ursgal2 Team", @@ -572,17 +580,17 @@ ] }, { - "name": "mx_qc_style_1", + "name": "mx_gsk_style_1", "reference": "Ursgal2 Team", - "style": "mx_qc_style_1", + "style": "mx_gsk_style_1", "versions": [ "1.0.0" ] }, { - "name": "mx_gsk_style_1", + "name": "mx_qc_style_1", "reference": "Ursgal2 Team", - "style": "mx_gsk_style_1", + "style": "mx_qc_style_1", "versions": [ "1.0.0" ] @@ -687,6 +695,14 @@ "1.0.0" ] }, + { + "name": "spectrum_meta_data_style_1", + "reference": "Ursgal2 Team", + "style": "spectrum_meta_data_style_1", + "versions": [ + "1.0.0" + ] + }, { "name": "test_node_style_1", "reference": "Ursgal2 Team", @@ -718,13 +734,5 @@ "versions": [ "1.0.0" ] - }, - { - "name": "spectrum_meta_data_style_1", - "reference": "Ursgal2 Team", - "style": "spectrum_meta_data_style_1", - "versions": [ - "1.0.0" - ] } ] \ No newline at end of file From 0c206d46b2891f9404a100a91d18345945c612a4 Mon Sep 17 00:00:00 2001 From: ArtiVlasov <67375717+ArtiVlasov@users.noreply.github.com> Date: Thu, 22 Sep 2022 16:57:57 +0200 Subject: [PATCH 2/7] renamed quant_method param --- jsons/parameters.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/jsons/parameters.json b/jsons/parameters.json index e62a744..4400edf 100644 --- a/jsons/parameters.json +++ b/jsons/parameters.json @@ -14130,7 +14130,7 @@ "default_value": "TMTpro", "description": "Reporter Ion type", "key_translations": { - "reporter_extract_style_1": "--quant_method", + "reporter_extract_style_1": "quant_method", "ursgal_style_1": "reporter_ion_type" }, "name": "reporter_ion_type", From 4bfaa1e670a73fa53b4ebb4624dd7631a9c0838c Mon Sep 17 00:00:00 2001 From: ArtiVlasov <67375717+ArtiVlasov@users.noreply.github.com> Date: Thu, 22 Sep 2022 17:01:29 +0200 Subject: [PATCH 3/7] rmv typos --- jsons/parameters.json | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/jsons/parameters.json b/jsons/parameters.json index 4400edf..f260dc7 100644 --- a/jsons/parameters.json +++ b/jsons/parameters.json @@ -10998,7 +10998,7 @@ ], "triggers_rerun": true, "value_translations": {}, - "value_type": "int or string of ints separated by ," + "value_type": "int" }, { "default_value": false, @@ -14139,7 +14139,8 @@ "MSn" ], "triggers_rerun": true, - "value_type": "float" + "value_translations": {}, + "value_type": "str" }, { "default_value": false, From c85c1d3448456f7a448f68e5b9838b18bc8928cf Mon Sep 17 00:00:00 2001 From: ArtiVlasov <67375717+ArtiVlasov@users.noreply.github.com> Date: Fri, 23 Sep 2022 10:41:57 +0200 Subject: [PATCH 4/7] update param names --- jsons/parameters.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/jsons/parameters.json b/jsons/parameters.json index f260dc7..818700c 100644 --- a/jsons/parameters.json +++ b/jsons/parameters.json @@ -3373,7 +3373,7 @@ "pnovo_style_1": "thread", "proteomics_qc_style_1": "n_cpus", "ptmshepherd_style_1": "threads", - "reporter_extract_style_1": "cpus", + "reporter_extract_style_1": "--cpus", "ucontroller_style_1": "cpus", "ursgal_style_1": "cpus", "xtandem_style_1": "spectrum, threads" @@ -10987,7 +10987,7 @@ "mzml2mgf_style_1": "ms_level", "pipi_style_1": "ms_level", "pyqms_style_1": "ms_level", - "reporter_extract_style_1": "ms_level", + "reporter_extract_style_1": "--ms_level", "sugarpy_plot_style_1": "ms_level", "sugarpy_run_style_1": "ms_level", "ursgal_style_1": "ms_level" @@ -14130,7 +14130,7 @@ "default_value": "TMTpro", "description": "Reporter Ion type", "key_translations": { - "reporter_extract_style_1": "quant_method", + "reporter_extract_style_1": "--quant_method", "ursgal_style_1": "reporter_ion_type" }, "name": "reporter_ion_type", From 07ddb8c3a1372baff8562a062ff29498626bcb4e Mon Sep 17 00:00:00 2001 From: Christian Fufezan Date: Wed, 28 Sep 2022 16:11:47 +0200 Subject: [PATCH 5/7] Add percursor_window_scanner_style_1 as well --- jsons/parameters.json | 7 +++++++ jsons/styles.json | 8 ++++++++ 2 files changed, 15 insertions(+) diff --git a/jsons/parameters.json b/jsons/parameters.json index 818700c..efb4f5c 100644 --- a/jsons/parameters.json +++ b/jsons/parameters.json @@ -3368,6 +3368,7 @@ "omssa_style_1": "-nt", "percolator_style_1": "cpus", "percolator_style_2": "cpus", + "percursor_window_scanner_style_1": "--cpus", "pglyco_db_style_1": "process", "pipi_style_1": "thread_num", "pnovo_style_1": "thread", @@ -3450,6 +3451,12 @@ -1 ] ], + "percursor_window_scanner_style_1": [ + [ + -1, + -1 + ] + ], "pglyco_db_style_1": [ [ -1, diff --git a/jsons/styles.json b/jsons/styles.json index e353dcd..7bfc50e 100644 --- a/jsons/styles.json +++ b/jsons/styles.json @@ -271,6 +271,14 @@ "1.0.0" ] }, + { + "name": "Precursor Window Scanner Style 1", + "reference": "Mathieson T. and Sweetman, G. (2021)", + "style": "percursor_window_scanner_style_1", + "versions": [ + "1.0.0" + ] + }, { "name": "Proteomics Quality Control", "reference": "Ursgal2 Team", From 9d14ff53bdc1099b283ee40f2200eef5d96d61b8 Mon Sep 17 00:00:00 2001 From: ArtiVlasov <67375717+ArtiVlasov@users.noreply.github.com> Date: Thu, 29 Sep 2022 11:58:19 +0200 Subject: [PATCH 6/7] updated typo --- jsons/parameters.json | 4 ++-- jsons/styles.json | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/jsons/parameters.json b/jsons/parameters.json index efb4f5c..24b343c 100644 --- a/jsons/parameters.json +++ b/jsons/parameters.json @@ -3368,7 +3368,7 @@ "omssa_style_1": "-nt", "percolator_style_1": "cpus", "percolator_style_2": "cpus", - "percursor_window_scanner_style_1": "--cpus", + "precursor_window_scanner_style_1": "--cpus", "pglyco_db_style_1": "process", "pipi_style_1": "thread_num", "pnovo_style_1": "thread", @@ -3451,7 +3451,7 @@ -1 ] ], - "percursor_window_scanner_style_1": [ + "precursor_window_scanner_style_1": [ [ -1, -1 diff --git a/jsons/styles.json b/jsons/styles.json index 7bfc50e..6fdf0e4 100644 --- a/jsons/styles.json +++ b/jsons/styles.json @@ -274,7 +274,7 @@ { "name": "Precursor Window Scanner Style 1", "reference": "Mathieson T. and Sweetman, G. (2021)", - "style": "percursor_window_scanner_style_1", + "style": "precursor_window_scanner_style_1", "versions": [ "1.0.0" ] From 18bc6bcf91720746d73dc1258dcfa61c214aebd1 Mon Sep 17 00:00:00 2001 From: ArtiVlasov <67375717+ArtiVlasov@users.noreply.github.com> Date: Thu, 29 Sep 2022 14:04:47 +0200 Subject: [PATCH 7/7] sort the params --- jsons/parameters.json | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/jsons/parameters.json b/jsons/parameters.json index 24b343c..2b862f4 100644 --- a/jsons/parameters.json +++ b/jsons/parameters.json @@ -3368,10 +3368,10 @@ "omssa_style_1": "-nt", "percolator_style_1": "cpus", "percolator_style_2": "cpus", - "precursor_window_scanner_style_1": "--cpus", "pglyco_db_style_1": "process", "pipi_style_1": "thread_num", "pnovo_style_1": "thread", + "precursor_window_scanner_style_1": "--cpus", "proteomics_qc_style_1": "n_cpus", "ptmshepherd_style_1": "threads", "reporter_extract_style_1": "--cpus", @@ -3451,12 +3451,6 @@ -1 ] ], - "precursor_window_scanner_style_1": [ - [ - -1, - -1 - ] - ], "pglyco_db_style_1": [ [ -1, @@ -3475,6 +3469,12 @@ "max - 1" ] ], + "precursor_window_scanner_style_1": [ + [ + -1, + -1 + ] + ], "reporter_extract_style_1": [ [ -1,