Repository revision
13:7f6a1f27553e

Repository 'openms_xtandemadapter'
hg clone https://toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter

XTandemAdapter tool metadata
Miscellaneous
Annotates MS/MS spectra using X! Tandem.
XTandemAdapter
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.6+galaxy0
2.6+galaxy0
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.8+galaxy0
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.6+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.5+galaxy0
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.3.0
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.2.0.1
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.2.0
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.1.0
XTandemAdapter
Requirements (dependencies defined in the <requirements> tag set)
name version type
openms 2.6 package
openms-thirdparty 2.6 package
blast 2.9.0 package
ctdopts 1.4 package
Functional tests
name inputs outputs required files
Test-1 in: spectra.mzML
database: proteins.fasta
default_config_file: CHEMISTRY/XTandem_default_input.xml
ignore_adapter_param: False
precursor_mass_tolerance: 5.0
fragment_mass_tolerance: 0.3
precursor_error_units: ppm
fragment_error_units: Da
max_precursor_charge: 0
no_isotope_error: False
fixed_modifications:
variable_modifications: Oxidation (M)
minimum_fragment_mz: 150.0
enzyme: Trypsin
missed_cleavages: 1
semi_cleavage: False
output_results: all
max_valid_expect: 0.1
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG']
name: value
name: value
spectra.mzML
proteins.fasta
CHEMISTRY/XTandem_default_input.xml
value
Test-2 in: spectra.mzML
database: proteins.fasta
default_config_file: CHEMISTRY/XTandem_default_input.xml
ignore_adapter_param: False
precursor_mass_tolerance: 5.0
fragment_mass_tolerance: 0.3
precursor_error_units: ppm
fragment_error_units: Da
max_precursor_charge: 0
no_isotope_error: False
fixed_modifications:
variable_modifications: Oxidation (M)
minimum_fragment_mz: 150.0
enzyme: Trypsin
missed_cleavages: 1
semi_cleavage: False
output_results: valid
max_valid_expect: 1e-14
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG']
name: value
name: value
spectra.mzML
proteins.fasta
CHEMISTRY/XTandem_default_input.xml
value
Test-3 in: spectra.mzML
database: proteinslong.fasta
default_config_file: CHEMISTRY/XTandem_default_input.xml
ignore_adapter_param: False
precursor_mass_tolerance: 5.0
fragment_mass_tolerance: 0.3
precursor_error_units: ppm
fragment_error_units: Da
max_precursor_charge: 0
no_isotope_error: False
fixed_modifications:
variable_modifications: Oxidation (M)
minimum_fragment_mz: 150.0
enzyme: Trypsin
missed_cleavages: 1
semi_cleavage: False
output_results: all
max_valid_expect: 0.1
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG']
name: value
name: value
spectra.mzML
proteinslong.fasta
CHEMISTRY/XTandem_default_input.xml
value