I will.
But in the meantime, what I found out was;
the OpenMS XTandemAdapter calls the separately installed xTandem
tandem.exe executable (so one can still manage one's installs) but has a
Linux command line tool to run the adapter.
I've worked with OpenMS CLI tools before, and they're pretty good about
being garbage-in, garbage-out...meaning you don't have to run them
through a TOPPAS or Knime pipeline. You can just call them at the
command line in total isolation (or via script, like the subprocess
module in Python) with the file you want searched, and all the CLI
parameters.
Here's the help :)
=====
Usage:
XTandemAdapter <options>
Options (mandatory options marked with '*'):
-in <file>* Input file (valid formats: 'mzML')
-out <file>* Output file (valid formats:
'idXML')
-database <file>* FASTA file or pro file.
Non-existing relative file-names are looked up via'OpenMS.ini
:id_db_dir' (valid formats:
'FASTA')
-xtandem_executable <executable>* X! Tandem executable of the
installation e.g. 'tandem.exe'
-default_config_file <file> Default parameters input file,
defaulting to the ones in the OpenMS/share folder.All
parameters of this adapter
take precedence over this file! Use it for parameters not
available here! (valid
formats: 'xml')
-ignore_adapter_param The config given in
'default_config_file' is used exclusively! No matter what other
parameters (apart from
-in,-out,-database,-xtandem_executable) are saying.
-precursor_mass_tolerance <tolerance> Precursor mass tolerance
(default: '10')
-fragment_mass_tolerance <tolerance> Fragment mass error (default:
'0.3')
-precursor_error_units <unit> Parent monoisotopic mass error
units (default: 'ppm' valid: 'ppm', 'Da')
-fragment_error_units <unit> Fragment monoisotopic mass
error units (default: 'Da' valid: 'ppm', 'Da')
-min_precursor_charge <charge> Minimum precursor charge
(default: '2')
-max_precursor_charge <charge> Maximum precursor charge
(default: '4')
-allow_isotope_error <error> If set, misassignment to the
first and second isotopic 13C peak are also considered.
(default: 'yes' valid: 'yes',
'no')
-fixed_modifications <mods> Fixed modifications, specified
using UniMod (www.unimod.org) terms, e.g. 'Carbamidome
thyl (C)' or 'Oxidation (M)'
(valid: '15N-oxobutanoic (N-term C)', '2-dimethylsucciny
l (C)', '2-monomethylsuccinyl
(C)', '2-nitrobenzyl (Y)', '2-succinyl (C)', '2HPG (R)'
, '3-deoxyglucosone (R)',
'3-phosphoglyceryl (K)', '3sulfo (N-term)', '4-ONE (C)',
'4-ONE (H)', '4-ONE (K)',
'4-ONE+Delta:H(-2)O(-1) (C)', '4-ONE+Delta:H(-2)O(-1) (H)',
'4-ONE+Delta:H(-2)O(-1) (K)',
'4AcAllylGal (C)', 'ADP-Ribosyl (C)', 'ADP-Ribosyl
(D)', 'ADP-Ribosyl (E)',
'ADP-Ribosyl (K)', 'ADP-Ribosyl (N)', 'ADP-Ribosyl (R)',
'ADP-Ribosyl (S)',
'ADP-Ribosyl (T)', 'AEBS (H)', 'AEBS (K)', 'AEBS (S)', 'AEBS (Y)',
...
'thioacylPA (K)', 'trifluoro (L)')
-variable_modifications <mods> Variable modifications,
specified using UniMod (www.unimod.org) terms, e.g. 'Carbamid
omethyl (C)' or 'Oxidation
(M)' (valid: '15N-oxobutanoic (N-term C)', '2-dimethylsucc
inyl (C)',
'2-monomethylsuccinyl (C)', '2-nitrobenzyl (Y)', '2-succinyl (C)', '2HPG
(R)', '3-deoxyglucosone (R)',
'3-phosphoglyceryl (K)', '3sulfo (N-term)', '4-ONE (C)'
, '4-ONE (H)', '4-ONE (K)',
'4-ONE+Delta:H(-2)O(-1) (C)', '4-ONE+Delta:H(-2)O(-1)
(H)', '4-ONE+Delta:H(-2)O(-1)
(K)', '4AcAllylGal (C)', 'ADP-Ribosyl (C)', 'ADP-Ribosy
l (D)', 'ADP-Ribosyl (E)',
'ADP-Ribosyl (K)', 'ADP-Ribosyl (N)', 'ADP-Ribosyl (R)',
'ADP-Ribosyl (S)',
'ADP-Ribosyl (T)', 'AEBS (H)', 'AEBS (K)', 'AEBS (S)', 'AEBS (Y)',
...
'thioacylPA (K)', 'trifluoro (L)')
-missed_cleavages <num> Number of possible cleavage
sites missed by the enzyme (default: '1')
-minimum_fragment_mz <num> Minimum fragment mz (default:
'150')
-cleavage_site <cleavage site> The enzyme used for peptide
digestion. (default: 'Trypsin' valid: 'Trypsin/P', '2-iod
obenzoate', 'CNBr',
'Formic_acid', 'Asp-N_ambic', 'unspecific cleavage', 'Chymotrypsi
n', 'TrypChymo', 'PepsinA',
'V8-DE', 'Lys-C/P', 'glutamyl endopeptidase', 'Trypsin',
'Asp-N', 'Arg-C', 'Lys-C',
'leukocyte elastase', 'V8-E')
-output_results <result reporting> Which hits should be reported.
All, valid ones (passing the E-Value threshold), or
stochastic (failing the
threshold) (default: 'all' valid: 'all', 'valid', 'stochastic
')
-max_valid_expect <E-Value> Maximal E-Value of a hit to be
reported (only evaluated if 'output_result' is 'valid'
or 'stochastic' (default: '0.1')
-refinement Enable the refinement. For
most applications (especially when using FDR, PEP approach
es) it is NOT recommended to
set this flag.
-use_noise_suppression Enable the use of the noise
suppression routines.
-semi_cleavage If set, both termini must NOT
follow the cutting rule. For most applications it is
NOT recommended to set this flag.
Common TOPP options:
-ini <file> Use the given TOPP INI file
-log <file> Name of log file (created only
when specified)
-instance <n> Instance number for the TOPP
INI file (default: '1')
-debug <n> Sets the debug level (default:
'0')
-threads <n> Sets the number of threads
allowed to be used by the TOPP tool (default: '1')
-write_ini <file> Writes the default
configuration file
-write_ctd <out_dir> Writes the common tool
description file(s) (Toolname(s).ctd) to <out_dir>
-write_wsdl <file> Writes the default WSDL file
-no_progress Disables progress logging to
command line
-force Overwrite tool specific checks.
-test Enables the test mode (needed
for internal use only)
--help Shows options
--helphelp Shows all options (including
advanced)
Eric Deutsch wrote:
Hi Mike, great, since this is a question that comes up fairly often,
would you post your solution once you get it working?
--
*Michael Rightmire*
B.Sci. Molecular Biotechnology
MCSE,MCP+I,HPUXCA,CompTIA,VDE, SIAM,ISCB
Skype:RightmireM
+49-721-1320-2562 (DE)
+1-408-890-2121 (USA)
Biocom Biotechnology and Software
BiocomSoftware.Com <Http://biocomsoftware.com>
BiocomSoftware.De <http://Biocomsoftware.de>
//
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