Clean up params

[StSchulze]

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]

Is this still a thing?

[StSchulze]

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]

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"
}