make-template: fix type error

Author: mr-c

cwltool/main.py

@@ -330,10 +330,10 @@ def generate_input_template(tool: Process) -> CWLObjectType:
     """Generate an example input object for the given CWL process."""
     template = ruamel.yaml.comments.CommentedMap()
     for inp in cast(
-        list[MutableMapping[str, str]],
+        list[CWLObjectType],
         realize_input_schema(tool.tool["inputs"], tool.schemaDefs),
     ):
-        name = shortname(inp["id"])
+        name = shortname(cast(str, inp["id"]))
         value, comment = generate_example_input(inp["type"], inp.get("default", None))
         template.insert(0, name, value, comment)
     return template

tests/CometAdapter.cwl

@@ -0,0 +1,228 @@
+# Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
+# SPDX-License-Identifier: Apache-2.0
+label: CometAdapter
+doc: Annotates MS/MS spectra using Comet.
+inputs:
+  in:
+    doc: Input file
+    type: File
+  out:
+    doc: Output file
+    type: string
+  database:
+    doc: FASTA file
+    type: File
+  comet_executable:
+    doc: The Comet executable. Provide a full or relative path, or make sure it can be found in your PATH environment.
+    type: File
+  pin_out:
+    doc: Output file - for Percolator input
+    type: string?
+  default_params_file:
+    doc: Default Comet params file. All parameters of this take precedence. A template file can be generated using 'comet.exe -p'
+    type: File?
+  precursor_mass_tolerance:
+    doc: "Precursor monoisotopic mass tolerance (Comet parameter: peptide_mass_tolerance).  See also precursor_error_units to set the unit."
+    type: double?
+  precursor_error_units:
+    doc: "Unit of precursor monoisotopic mass tolerance for parameter precursor_mass_tolerance (Comet parameter: peptide_mass_units)"
+    type: string?
+  isotope_error:
+    doc: This parameter controls whether the peptide_mass_tolerance takes into account possible isotope errors in the precursor mass measurement. Use -8/-4/0/4/8 only for SILAC.
+    type: string?
+  fragment_mass_tolerance:
+    doc: "This is half the bin size, which is used to segment the MS/MS spectrum. Thus, the value should be a bit higher than for other search engines, since the bin might not be centered around the peak apex (see 'fragment_bin_offset').CAUTION: Low tolerances have heavy impact on RAM usage (since Comet uses a lot of bins in this case). Consider using use_sparse_matrix and/or spectrum_batch_size."
+    type: double?
+  fragment_error_units:
+    doc: Fragment monoisotopic mass error units
+    type: string?
+  fragment_bin_offset:
+    doc: "Offset of fragment bins. Recommended by Comet: low-res: 0.4, high-res: 0.0"
+    type: double?
+  instrument:
+    doc: "Comets theoretical_fragment_ions parameter: theoretical fragment ion peak representation, high-res: sum of intensities plus flanking bins, ion trap (low-res) ms/ms: sum of intensities of central M bin only"
+    type: string?
+  use_A_ions:
+    doc: use A ions for PSM
+    type: boolean?
+  use_B_ions:
+    doc: use B ions for PSM
+    type: boolean?
+  use_C_ions:
+    doc: use C ions for PSM
+    type: boolean?
+  use_X_ions:
+    doc: use X ions for PSM
+    type: boolean?
+  use_Y_ions:
+    doc: use Y ions for PSM
+    type: boolean?
+  use_Z_ions:
+    doc: use Z ions for PSM
+    type: boolean?
+  use_NL_ions:
+    doc: use neutral loss (NH3, H2O) ions from b/y for PSM
+    type: boolean?
+  enzyme:
+    doc: The enzyme used for peptide digestion.
+    type: string?
+  second_enzyme:
+    doc: Additional enzyme used for peptide digestion.
+    type: string?
+  num_enzyme_termini:
+    doc: Specify the termini where the cleavage rule has to match
+    type: string?
+  missed_cleavages:
+    doc: Number of possible cleavage sites missed by the enzyme. It has no effect if enzyme is unspecific cleavage.
+    type: long?
+  min_peptide_length:
+    doc: Minimum peptide length to consider.
+    type: long?
+  max_peptide_length:
+    doc: Maximum peptide length to consider.
+    type: long?
+  num_hits:
+    doc: Number of peptide hits (PSMs) per spectrum in output file
+    type: long?
+  precursor_charge:
+    doc: "Precursor charge range to search (if spectrum is not annotated with a charge or if override_charge!=keep any known): 0:[num] == search all charges, 2:6 == from +2 to +6, 3:3 == +3"
+    type: string?
+  override_charge:
+    doc: "_keep any known_: keep any precursor charge state (from input), _ignore known_: ignore known precursor charge state and use precursor_charge parameter, _ignore outside range_: ignore precursor charges outside precursor_charge range, _keep known search unknown_: keep any known precursor charge state. For unknown charge states, search as singly charged if there is no signal above the precursor m/z or use the precursor_charge range"
+    type: string?
+  ms_level:
+    doc: MS level to analyze, valid are levels 2 (default) or 3
+    type: long?
+  activation_method:
+    doc: If not ALL, only searches spectra of the given method
+    type: string?
+  digest_mass_range:
+    doc: MH+ peptide mass range to analyze
+    type: string?
+  max_fragment_charge:
+    doc: Set maximum fragment charge state to analyze as long as still lower than precursor charge - 1. (Allowed max 5)
+    type: long?
+  max_precursor_charge:
+    doc: set maximum precursor charge state to analyze (allowed max 9)
+    type: long?
+  clip_nterm_methionine:
+    doc: If set to true, also considers the peptide sequence w/o N-term methionine separately and applies appropriate N-term mods to it
+    type: boolean?
+  spectrum_batch_size:
+    doc: max. number of spectra to search at a time; use 0 to search the entire scan range in one batch
+    type: long?
+  mass_offsets:
+    doc: One or more mass offsets to search (values subtracted from deconvoluted precursor mass). Has to include 0.0 if you want the default mass to be searched.
+    type: double[]?
+  minimum_peaks:
+    doc: Required minimum number of peaks in spectrum to search (default 10)
+    type: long?
+  minimum_intensity:
+    doc: Minimum intensity value to read in
+    type: double?
+  remove_precursor_peak:
+    doc: no = no removal, yes = remove all peaks around precursor m/z, charge_reduced = remove all charge reduced precursor peaks (for ETD/ECD). phosphate_loss = remove the HPO3 (-80) and H3PO4 (-98) precursor phosphate neutral loss peaks. See also remove_precursor_tolerance
+    type: string?
+  remove_precursor_tolerance:
+    doc: one-sided tolerance for precursor removal in Thompson
+    type: double?
+  clear_mz_range:
+    doc: for iTRAQ/TMT type data; will clear out all peaks in the specified m/z range, if not 0:0
+    type: string?
+  fixed_modifications:
+    doc: Fixed modifications, specified using Unimod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'
+    type: string[]?
+  variable_modifications:
+    doc: Variable modifications, specified using Unimod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'
+    type: string[]?
+  binary_modifications:
+    doc: "List of modification group indices. Indices correspond to the binary modification index used by comet to group individually searched lists of variable modifications.\nNote: if set, both variable_modifications and binary_modifications need to have the same number of entries as the N-th entry corresponds to the N-th variable_modification.\n      if left empty (default), all entries are internally set to 0 generating all permutations of modified and unmodified residues.\n      For a detailed explanation please see the parameter description in the Comet help."
+    type: long[]?
+  max_variable_mods_in_peptide:
+    doc: Set a maximum number of variable modifications per peptide
+    type: long?
+  require_variable_mod:
+    doc: If true, requires at least one variable modification per peptide
+    type: boolean?
+  reindex:
+    doc: Recalculate peptide to protein association using OpenMS. Annotates target-decoy information.
+    type: string?
+  log:
+    doc: Name of log file (created only when specified)
+    type: string?
+  debug:
+    doc: Sets the debug level
+    type: long?
+  threads:
+    doc: Sets the number of threads allowed to be used by the TOPP tool
+    type: long?
+  no_progress:
+    doc: Disables progress logging to command line
+    type: boolean?
+  force:
+    doc: Overrides tool-specific checks
+    type: boolean?
+  test:
+    doc: Enables the test mode (needed for internal use only)
+    type: boolean?
+  PeptideIndexing__decoy_string:
+    doc: String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins. If empty (default), it's determined automatically (checking for common terms, both as prefix and suffix).
+    type: string?
+  PeptideIndexing__decoy_string_position:
+    doc: Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession? (ignored if decoy_string is empty)
+    type: string?
+  PeptideIndexing__missing_decoy_action:
+    doc: "Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)"
+    type: string?
+  PeptideIndexing__write_protein_sequence:
+    doc: If set, the protein sequences are stored as well.
+    type: boolean?
+  PeptideIndexing__write_protein_description:
+    doc: If set, the protein description is stored as well.
+    type: boolean?
+  PeptideIndexing__keep_unreferenced_proteins:
+    doc: If set, protein hits which are not referenced by any peptide are kept.
+    type: boolean?
+  PeptideIndexing__unmatched_action:
+    doc: "If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit."
+    type: string?
+  PeptideIndexing__aaa_max:
+    doc: Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs. AAAs are 'B', 'J', 'Z' and 'X'.
+    type: long?
+  PeptideIndexing__mismatches_max:
+    doc: Maximal number of mismatched (mm) amino acids allowed when matching to a protein database. The required runtime is exponential in the number of mm's; apply with care. MM's are allowed in addition to AAA's.
+    type: long?
+  PeptideIndexing__IL_equivalent:
+    doc: Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable). Also occurrences of 'J' will be treated as 'I' thus avoiding ambiguous matching.
+    type: boolean?
+  PeptideIndexing__allow_nterm_protein_cleavage:
+    doc: Allow the protein N-terminus amino acid to clip.
+    type: string?
+  PeptideIndexing__enzyme__name:
+    doc: "Enzyme which determines valid cleavage sites - e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P). Default: deduce from input"
+    type: string?
+  PeptideIndexing__enzyme__specificity:
+    doc: "Specificity of the enzyme. Default: deduce from input.\n  'full': both internal cleavage sites must match.\n  'semi': one of two internal cleavage sites must match.\n  'none': allow all peptide hits no matter their context (enzyme is irrelevant)."
+    type: string?
+outputs:
+  out:
+    type: File
+    outputBinding:
+      glob: $(inputs.out)
+  pin_out:
+    type: File?
+    outputBinding:
+      glob: $(inputs.pin_out)
+cwlVersion: v1.2
+class: CommandLineTool
+baseCommand:
+  - CometAdapter
+requirements:
+  InlineJavascriptRequirement: {}
+  InitialWorkDirRequirement:
+    listing:
+      - entryname: cwl_inputs.json
+        entry: $(JSON.stringify(inputs))
+arguments:
+  - -ini
+  - cwl_inputs.json

tests/test_examples.py

@@ -1894,3 +1894,15 @@ def test_input_named_id() -> None:
         ]
     )
     assert exit_code == 0, stderr
+
+
+def test_make_template() -> None:
+    """End-to-end test of --make-template, especially for mypyc mode."""
+    exit_code, stdout, stderr = get_main_output(
+        [
+            "--make-template",
+            "--debug",
+            get_data("tests/CometAdapter.cwl"),
+        ]
+    )
+    assert exit_code == 0, stderr