Legend:
required parameter
advanced parameter
+ProteinResolverprotein inference
version1.10.0
Version of the tool that generated this parameters file.
++1Instance '1' section for 'ProteinResolver'
fasta
Input database fileinput file*.fasta
in
Input file holding experimental datainput file*.idXML,*.consensusXML
in_list[]
Input files holding the experimental data. Ignored if parameter 'in' is giveninput file*.idXML,*.consensusXML
in_path
Path to idXMLs or consensusXMLs files. Ignored if either 'in' or 'in_list' is given.
design
Text file containing the experimental design. See documentation for specific format requirementsinput file*.txt
protein_groups
output file. Contains all protein groupsoutput file*.csv
peptide_table
output file. Contains one peptide per line and all proteins which contain that peptideoutput file*.csv
protein_table
output file. Contains one protein per lineoutput file*.csv
additional_info
output file for additional infooutput file*.csv
log
Name of log file (created only when specified)
debug0
Sets the debug level
threads1
Sets the number of threads allowed to be used by the TOPP tool
no_progressfalse
Disables progress logging to command linetrue,false
testfalse
Enables the test mode (needed for internal use only)true,false
+++resolverAdditional options for algorithm
missed_cleavages2
Number of allowed missed cleavages0:∞
min_length6
Minimum length of peptide1:∞
enzymeTrypsin
Digestion enzymeTrypsin
+++designerAdditional options for quantitative experimental design
experimentExperimentalSetting
Identifier for the experimental design.
fileFile
Identifier for the file name.
separatortab
Separator, which should be used to split a row into columnstab,semi-colon,comma,whitespace