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uparma / uparma-lib

Lookup library for all mappers. Format json
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Clean up params #74

Open StSchulze opened 2 years ago

StSchulze commented 2 years ago

Some of the parameters are not actual parameters of the specified engines, e.g.:


{
    "default_value": 1000,
    "description": "m/z value that is used as basis for the conversion from ppm to Da",
    "key_translations": {
      "deepnovo_style_1": "base_mz",
      "glycopeptide_fragmentor_style_1": "base_mz",
      "moda_style_1": "base_mz",
      "omssa_style_1": "base_mz",
      "pepnovo_style_1": "base_mz",
      "pipi_style_1": "base_mz",
      "ptmshepherd_style_1": "base_mz",
      "tag_graph_style_1": "base_mz",
      "ursgal_style_1": "base_mz"
    },
    "name": "base_mz",
    "tag": [
      "conversion"
    ],
    "triggers_rerun": true,
    "value_translations": {},
    "value_type": "int"
  },

base_mz is only used internally by Ursgal, not as a parameter within those engines (at least I'm very sure for most of them).

Similarly, there are inaccurate translations like this one: "omssa_style_1": "frag_mass_tolerance_unit", This should be either "-to_part2" (with "frag_mass_tolerance": "-to_part1") or should not be part of the parameters for omssa at all (which of course would be difficult for using it with anything else than Da).

fu commented 1 year ago

Is this still a thing?

StSchulze commented 1 year ago

To my knowledge that's still a thing, yes.

And here's a list of parameters that Greg had found that have only ursgal_style_1 translations and that we think are deprecated:

{ "default_value":"compomics_utilities_4_11_5", "description":"Defines the compomics version to use", "key_translations":{ "ucontroller_style_1":"compomics_version", "ursgal_style_1":"compomics_version" }, "name":"compomics_version", "tag":[ "node_versions" ], "triggers_rerun":true, "value_translations":{

}, "value_type":"str" } { "default_value":true, "description":"Compress raw search result to .gz: True or False", "key_translations":{ "ucontroller_style_1":"compress_raw_search_results_if_possible", "ursgal_style_1":"compress_raw_search_results_if_possible" }, "name":"compress_raw_search_results_if_possible", "tag":[ "conversion", "file_handling" ], "triggers_rerun":true, "value_translations":{ "ucontroller_style_1":[ [ "crux_2_1", false ], [ "deepnovo_0_0_1", false ], [ "deepnovo_pointnovo", false ], [ "kojak_1_5_3", false ], [ "mascot_2_5_1", true ], [ "mascot_2_6_2", true ], [ "moda_v1_51", false ], [ "moda_v1_61", false ], [ "moda_v1_62", false ], [ "msamanda_1_0_0_5242", false ], [ "msamanda_1_0_0_5243", false ], [ "msamanda_1_0_0_6299", false ], [ "msamanda_1_0_0_6300", false ], [ "msamanda_1_0_0_7503", false ], [ "msamanda_1_0_0_7504", false ], [ "msamanda_2_0_0_10695", false ], [ "msamanda_2_0_0_11219", false ], [ "msamanda_2_0_0_13723", false ], [ "msamanda_2_0_0_14665", false ], [ "msamanda_2_0_0_9695", false ], [ "msamanda_2_0_0_9706", false ], [ "msfragger_20170103", false ], [ "msfragger_20171106", false ], [ "msfragger_20190222", false ], [ "msfragger_20190628", false ], [ "msfragger_2_3", false ], [ "msfragger_3_0", false ], [ "msgfplus_v2016_09_16", true ], [ "msgfplus_v2017_01_27", true ], [ "msgfplus_v2018_01_30", true ], [ "msgfplus_v2018_06_28", true ], [ "msgfplus_v2018_09_12", true ], [ "msgfplus_v2019_01_22", true ], [ "msgfplus_v2019_04_18", true ], [ "msgfplus_v2019_07_03", true ], [ "msgfplus_v9979", true ], [ "myrimatch_2_1_138", true ], [ "myrimatch_2_2_140", true ], [ "novor_1_05", false ], [ "novor_1_1beta", false ], [ "omssa_2_1_9", false ], [ "pepnovo_3_1", false ], [ "pglyco_db_2_2_0", false ], [ "pglyco_db_2_2_2", false ], [ "pipi_1_4_5", false ], [ "pipi_1_4_6", false ], [ "xtandem_alanine", true ], [ "xtandem_cyclone_2010", true ], [ "xtandem_jackhammer", true ], [ "xtandem_piledriver", true ], [ "xtandem_sledgehammer", true ], [ "xtandem_vengeance", true ] ], "ursgal_style_1":[ [ "crux_2_1", "crux_2_1" ], [ "deepnovo_0_0_1", "deepnovo_0_0_1" ], [ "deepnovo_pointnovo", "deepnovo_pointnovo" ], [ "kojak_1_5_3", "kojak_1_5_3" ], [ "mascot_2_5_1", true ], [ "mascot_2_6_2", true ], [ "moda_v1_51", "moda_v1_51" ], [ "moda_v1_61", "moda_v1_61" ], [ "moda_v1_62", "moda_v1_62" ], [ "msamanda_1_0_0_5242", "msamanda_1_0_0_5242" ], [ "msamanda_1_0_0_5243", "msamanda_1_0_0_5243" ], [ "msamanda_1_0_0_6299", "msamanda_1_0_0_6299" ], [ "msamanda_1_0_0_6300", "msamanda_1_0_0_6300" ], [ "msamanda_1_0_0_7503", "msamanda_1_0_0_7503" ], [ "msamanda_1_0_0_7504", "msamanda_1_0_0_7504" ], [ "msamanda_2_0_0_10695", "msamanda_2_0_0_10695" ], [ "msamanda_2_0_0_11219", "msamanda_2_0_0_11219" ], [ "msamanda_2_0_0_13723", "msamanda_2_0_0_13723" ], [ "msamanda_2_0_0_14665", "msamanda_2_0_0_14665" ], [ "msamanda_2_0_0_9695", "msamanda_2_0_0_9695" ], [ "msamanda_2_0_0_9706", "msamanda_2_0_0_9706" ], [ "msfragger_20170103", "msfragger_20170103" ], [ "msfragger_20171106", "msfragger_20171106" ], [ "msfragger_20190222", "msfragger_20190222" ], [ "msfragger_20190628", "msfragger_20190628" ], [ "msfragger_2_3", "msfragger_2_3" ], [ "msfragger_3_0", "msfragger_3_0" ], [ "msgfplus_v2016_09_16", "msgfplus_v2016_09_16" ], [ "msgfplus_v2017_01_27", "msgfplus_v2017_01_27" ], [ "msgfplus_v2018_01_30", "msgfplus_v2018_01_30" ], [ "msgfplus_v2018_06_28", "msgfplus_v2018_06_28" ], [ "msgfplus_v2018_09_12", "msgfplus_v2018_09_12" ], [ "msgfplus_v2019_01_22", "msgfplus_v2019_01_22" ], [ "msgfplus_v2019_04_18", "msgfplus_v2019_04_18" ], [ "msgfplus_v2019_07_03", "msgfplus_v2019_07_03" ], [ "msgfplus_v9979", "msgfplus_v9979" ], [ "myrimatch_2_1_138", "myrimatch_2_1_138" ], [ "myrimatch_2_2_140", "myrimatch_2_2_140" ], [ "novor_1_05", "novor_1_05" ], [ "novor_1_1beta", "novor_1_1beta" ], [ "omssa_2_1_9", "omssa_2_1_9" ], [ "pepnovo_3_1", "pepnovo_3_1" ], [ "pglyco_db_2_2_0", "pglyco_db_2_2_0" ], [ "pglyco_db_2_2_2", "pglyco_db_2_2_2" ], [ "pipi_1_4_5", "pipi_1_4_5" ], [ "pipi_1_4_6", "pipi_1_4_6" ], [ "xtandem_alanine", "xtandem_alanine" ], [ "xtandem_cyclone_2010", "xtandem_cyclone_2010" ], [ "xtandem_jackhammer", "xtandem_jackhammer" ], [ "xtandem_piledriver", "xtandem_piledriver" ], [ "xtandem_sledgehammer", "xtandem_sledgehammer" ], [ "xtandem_vengeance", "xtandem_vengeance" ] ] }, "value_type":"bool" } { "default_value":[ "grouped_psms" ], "description":"List of parameters that are deleted before .json is dumped (to not overload the .json with unimportant informations)", "key_translations":{ "ucontroller_style_1":"del_from_params_before_json_dump", "ursgal_style_1":"del_from_params_before_json_dump" }, "name":"del_from_params_before_json_dump", "tag":[ "file_handling" ], "triggers_rerun":true, "value_translations":{

}, "value_type":"list" } { "default_value":true, "description":"Create folders for the output of engines that allow this option in their META_INFO ('create_own_folder' : True). True or False", "key_translations":{ "ucontroller_style_1":"engines_create_folders", "ursgal_style_1":"engines_create_folders" }, "name":"engines_create_folders", "tag":[ "file_handling" ], "triggers_rerun":true, "value_translations":{

}, "value_type":"bool" } { "default_value":".u.json", "description":"Exension for helper files", "key_translations":{ "ucontroller_style_1":"helper_extension", "ursgal_style_1":"helper_extension" }, "name":"helper_extension", "tag":[ "file_handling" ], "triggers_rerun":true, "value_translations":{

}, "value_type":"str" } { "default_value":".u.json", "description":"Exension for .json files", "key_translations":{ "ucontroller_style_1":"json_extension", "ursgal_style_1":"json_extension" }, "name":"json_extension", "tag":[ "file_handling" ], "triggers_rerun":true, "value_translations":{

}, "value_type":"str" } { "default_value":"None", "description":" Determines which msgfplus mzid conversion node should be used e.g. \"msgfplus2csv_v2017_07_04\"", "key_translations":{ "ucontroller_style_1":"msgfplus_mzid_converter_version", "ursgal_style_1":"msgfplus_mzid_converter_version" }, "name":"msgfplus_mzid_converter_version", "tag":[ "node_versions" ], "triggers_rerun":true, "value_translations":{ "ucontroller_style_1":[ [ "msgfplus_v2016_09_16", "msgfplus2csv_py_v1_0_0" ], [ "msgfplus_v2017_01_27", "msgfplus2csv_py_v1_0_0" ], [ "msgfplus_v2018_01_30", "msgfplus2csv_py_v1_0_0" ], [ "msgfplus_v2018_06_28", "msgfplus2csv_py_v1_0_0" ], [ "msgfplus_v2018_09_12", "msgfplus2csv_py_v1_0_0" ], [ "msgfplus_v2019_01_22", "msgfplus2csv_py_v1_0_0" ], [ "msgfplus_v2019_04_18", "msgfplus2csv_py_v1_0_0" ], [ "msgfplus_v2019_07_03", "msgfplus2csv_py_v1_0_0" ], [ "msgfplus_v9979", "msgfplus2csv_py_v1_0_0" ] ], "ursgal_style_1":[ [ "msgfplus_v2016_09_16", "msgfplus_v2016_09_16" ], [ "msgfplus_v2017_01_27", "msgfplus_v2017_01_27" ], [ "msgfplus_v2018_01_30", "msgfplus_v2018_01_30" ], [ "msgfplus_v2018_06_28", "msgfplus_v2018_06_28" ], [ "msgfplus_v2018_09_12", "msgfplus_v2018_09_12" ], [ "msgfplus_v2019_01_22", "msgfplus_v2019_01_22" ], [ "msgfplus_v2019_04_18", "msgfplus_v2019_04_18" ], [ "msgfplus_v2019_07_03", "msgfplus_v2019_07_03" ], [ "msgfplus_v9979", "msgfplus_v9979" ] ] }, "value_type":"str" } { "default_value":"mzidentml_lib_1_6_10", "description":"mzidentml converter version: version name", "key_translations":{ "ucontroller_style_1":"mzidentml_converter_version", "ursgal_style_1":"mzidentml_converter_version" }, "name":"mzidentml_converter_version", "tag":[ "node_versions" ], "triggers_rerun":true, "value_translations":{

}, "value_type":"str" } { "default_value":"mzml2mgf_2_0_0", "description":"mzml to mgf converter version: version name", "key_translations":{ "ucontroller_style_1":"mzml2mgf_converter_version", "ursgal_style_1":"mzml2mgf_converter_version" }, "name":"mzml2mgf_converter_version", "tag":[ "node_versions" ], "triggers_rerun":true, "value_translations":{

}, "value_type":"str" } { "default_value":"upeptide_mapper_1_0_0", "description":" determines which upeptide mapper node should be used", "key_translations":{ "ucontroller_style_1":"peptide_mapper_converter_version", "ursgal_style_1":"peptide_mapper_converter_version" }, "name":"peptide_mapper_converter_version", "tag":[ "node_versions" ], "triggers_rerun":true, "value_translations":{

}, "value_type":"str" } { "default_value":"", "description":"prefix to add in front of filenames", "key_translations":{ "ucontroller_style_1":"prefix", "ursgal_style_1":"prefix" }, "name":"prefix", "tag":[ "file_handling" ], "triggers_rerun":true, "value_translations":{

}, "value_type":"str" } { "default_value":{

}, "description":"Defines the column names which should have their different values merged into a single value when merging rows corresponding the same PSM Formatted as a dictionary with keys as the column names and values as a parameter to specify which one of the different values to take Available values: max_value\n min_value\n most_frequent\n avg_value", "key_translations":{ "ucontroller_style_1":"colnames_to_merge_multiple_values", "ursgal_style_1":"psm_colnames_to_merge_multiple_values" }, "name":"psm_colnames_to_merge_multiple_values", "tag":[ "conversion", "output" ], "triggers_rerun":true, "value_translations":{

}, "value_type":"dict" } { "default_value":".csv", "description":"CSV suffix of raw indentification: this is the conversion result after CSV conversion but before adding retention time", "key_translations":{ "ucontroller_style_1":"raw_ident_csv_suffix", "ursgal_style_1":"raw_ident_csv_suffix" }, "name":"raw_ident_csv_suffix", "tag":[ "file_handling" ], "triggers_rerun":true, "value_translations":{

}, "value_type":"str" } { "default_value":false, "description":"Show ursgal nodes that are in development: False or True", "key_translations":{ "ucontroller_style_1":"show_unodes_in_development", "ursgal_style_1":"show_unodes_in_development" }, "name":"show_unodes_in_development", "tag":[ "internal" ], "triggers_rerun":true, "value_translations":{

}, "value_type":"bool" } { "default_value":"https://www.sas.upenn.edu/~sschulze/ursgal_resources/", "description":"URL that is used to prepare and install resources via corresponding scripts (prepare_resources.py and install_resources.py)", "key_translations":{ "ucontroller_style_1":"ursgal_resource_url", "ursgal_style_1":"ursgal_resource_url" }, "name":"ursgal_resource_url", "tag":[ "download" ], "triggers_rerun":false, "value_translations":{

}, "value_type":"str" } { "default_value":"validated.csv", "description":"CSV suffix of validated identification files: string, CSV-file which contains PSMs validated with validation tools", "key_translations":{ "ucontroller_style_1":"validated_ident_csv_suffix", "ursgal_style_1":"validated_ident_csv_suffix" }, "name":"validated_ident_csv_suffix", "tag":[ "file_handling" ], "triggers_rerun":true, "value_translations":{

}, "value_type":"str" } { "default_value":"xtandem2csv_1_0_0", "description":" Determines which X!tandem conversion node should be used e.g. \"xtandem2csv_1_0_0\"", "key_translations":{ "ucontroller_style_1":"xtandem_converter_version", "ursgal_style_1":"xtandem_converter_version" }, "name":"xtandem_converter_version", "tag":[ "node_versions" ], "triggers_rerun":true, "value_translations":{

}, "value_type":"str" }

StSchulze commented 1 year ago

And then a few parameters that I think are XTandem parameters, but for some reason they don't have xtandem translation styles?

{ "default_value":{

}, "description":"Maximal number of modification sites per peptide for a specific modification, given as a dictionary: \n {unimod_name : number}", "key_translations":{ "ursgal_style_1":"max_num_per_mod_name_specific" }, "name":"max_num_per_mod_name_specific", "tag":[ "modifications" ], "triggers_rerun":true, "value_translations":{

}, "value_type":"dict" } { "default_value":[

], "description":"List of modifications (unimod name) that are not allowed to occur at the C-terminus of a peptide, e.g. ['GG']", "key_translations":{ "ursgal_style_1":"forbidden_cterm_mods" }, "name":"forbidden_cterm_mods", "tag":[ "modifications" ], "triggers_rerun":true, "value_translations":{

}, "value_type":"list" }