IDFileConverter

Converts identification engine file formats.

Web Documentation for IDFileConverter

Options

version
Version of the tool that generated this parameters file.
mz_name
[pepXML only] Experiment filename/path (extension will be removed) to match in the pepXML file ('base_name' attribute). Only necessary if different from 'mz_file'.
peptideprophet_analyzed
[pepXML output only] Write output in the format of a PeptideProphet analysis result. By default a 'raw' pepXML is produced that contains only search engine results.
score_type
[Percolator only] Which of the Percolator scores to report as 'the' score for a peptide hit
ignore_proteins_per_peptide
[Sequest only] Workaround to deal with .out files that contain e.g. "+1" in references column, but do not list extra references in subsequent lines (try -debug 3 or 4)
scan_regex
[Mascot, pepXML, Percolator only] Regular expression used to extract the scan number or retention time. See documentation for details.
no_spectra_data_override
[+mz_file only] Avoid overriding 'spectra_data' in protein identifications if 'mz_file' is given and 'spectrum_reference's are added/updated. Use only if you are sure it is absolutely the same 'mz_file' as used for identification.
no_spectra_references_override
[+mz_file only] Avoid overriding 'spectrum_reference' in peptide identifications if 'mz_file' is given and a 'spectrum_reference' is already present.
add_ionmatch_annotation
[+mz_file only] Annotate the identifications with ion matches from spectra in 'mz_file' using the given tolerance (in Da). This will take quite some time.
concatenate_peptides
[FASTA output only] Will concatenate the top peptide hits to one peptide sequence, rather than write a new peptide for each hit.
number_of_hits
[FASTA output only] Controls how many peptide hits will be exported. A value of 0 or less exports all hits.
log
Name of log file (created only when specified)
debug
Sets the debug level
threads
Sets the number of threads allowed to be used by the TOPP tool
no_progress
Disables progress logging to command line
force
Overrides tool-specific checks
test
Enables the test mode (needed for internal use only)
isotope_model
Model to use for isotopic peaks ('none' means no isotopic peaks are added, 'coarse' adds isotopic peaks in unit mass distance, 'fine' uses the hyperfine isotopic generator to add accurate isotopic peaks. Note that adding isotopic peaks is very slow.
max_isotope
Defines the maximal isotopic peak which is added if 'isotope_model' is 'coarse'
max_isotope_probability
Defines the maximal isotopic probability to cover if 'isotope_model' is 'fine'
add_metainfo
Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++
add_losses
Adds common losses to those ion expect to have them, only water and ammonia loss is considered
sort_by_position
Sort output by position
add_precursor_peaks
Adds peaks of the unfragmented precursor ion to the spectrum
add_all_precursor_charges
Adds precursor peaks with all charges in the given range
add_abundant_immonium_ions
Add most abundant immonium ions (for Proline, Cystein, Iso/Leucine, Histidin, Phenylalanin, Tyrosine, Tryptophan)
add_first_prefix_ion
If set to true e.g. b1 ions are added
add_y_ions
Add peaks of y-ions to the spectrum
add_b_ions
Add peaks of b-ions to the spectrum
add_a_ions
Add peaks of a-ions to the spectrum
add_c_ions
Add peaks of c-ions to the spectrum
add_x_ions
Add peaks of x-ions to the spectrum
add_z_ions
Add peaks of z-ions to the spectrum
y_intensity
Intensity of the y-ions
b_intensity
Intensity of the b-ions
a_intensity
Intensity of the a-ions
c_intensity
Intensity of the c-ions
x_intensity
Intensity of the x-ions
z_intensity
Intensity of the z-ions
relative_loss_intensity
Intensity of loss ions, in relation to the intact ion intensity
precursor_intensity
Intensity of the precursor peak
precursor_H2O_intensity
Intensity of the H2O loss peak of the precursor
precursor_NH3_intensity
Intensity of the NH3 loss peak of the precursor
enzyme
Enzym used to digest the fasta proteins
missed_cleavages
Number of allowed missed cleavages while digesting the fasta proteins
min_charge
Minimum charge
max_charge
Maximum charge
precursor_charge
Manually set precursor charge. (default: 0, meaning max_charge + 1 will be used as precursor charge)

Input Ports

Icon
Input file or directory containing the data to convert. This may be:#br#- a single file in OpenMS database format (.oms),#br#- a single file in a multi-purpose XML format (.idXML, .mzid, .pepXML, .protXML),#br#- a single file in a search engine-specific format (Mascot: .mascotXML, OMSSA: .omssaXML, X! Tandem: .xml, Percolator: .psms, xQuest: .xquest.xml),#br#- a single file in fasta format (can only be used to generate a theoretical mzML),#br#- a single text file (tab separated) with one line for all peptide sequences matching a spectrum (top N hits),#br#- for Sequest results, a directory containing .out files.#br# [oms,idXML,mzid,fasta,pepXML,protXML,mascotXML,omssaXML,xml,psms,tsv,xquest.xml]
Icon
[pepXML, Sequest, Mascot, X! Tandem, mzid, Percolator only] Retention times and native spectrum ids (spectrum_references) will be looked up in this file [mzML,mzXML,mzData,opt.]

Output Ports

Icon
Output file [oms,idXML,mzid,pepXML,fasta,xquest.xml,mzML]

Views

IDFileConverter Std Output
The text sent to standard out during the execution of IDFileConverter.
IDFileConverter Error Output
The text sent to standard error during the execution of IDFileConverter. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Workflows

  • No workflows found

Links

Developers

You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.