Repository revision
12:16026cdb1330

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

ProteinQuantifier tool metadata
Miscellaneous
Compute peptide and protein abundances
ProteinQuantifier
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_proteinquantifier/ProteinQuantifier/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_proteinquantifier/ProteinQuantifier/2.8+galaxy0
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_proteinquantifier/ProteinQuantifier/2.6+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_proteinquantifier/ProteinQuantifier/2.5+galaxy0
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_proteinquantifier/ProteinQuantifier/2.2.0
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_proteinquantifier/ProteinQuantifier/2.1.0
ProteinQuantifier
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: ProteinQuantifier_input.featureXML
top: 3
average: median
include_all: False
best_charge_and_fraction: False
greedy_group_resolution: False
ratios: False
ratiosSILAC: False
consensus|normalize: False
consensus|fix_peptides: False
format|separator:
format|quoting: double
format|replacement: _
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG', 'peptide_out_FLAG']
name: value
name: value
name: value
ProteinQuantifier_input.featureXML
value
Test-2 in: ProteinQuantifier_input.featureXML
top: 2
average: sum
include_all: True
best_charge_and_fraction: True
greedy_group_resolution: False
ratios: False
ratiosSILAC: False
consensus|normalize: False
consensus|fix_peptides: False
format|separator:
format|quoting: double
format|replacement: _
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG', 'peptide_out_FLAG']
name: value
name: value
name: value
ProteinQuantifier_input.featureXML
value
Test-3 in: ProteinQuantifier_3_input.featureXML
top: 2
average: mean
include_all: True
best_charge_and_fraction: False
greedy_group_resolution: False
ratios: False
ratiosSILAC: False
consensus|normalize: False
consensus|fix_peptides: False
format|separator:
format|quoting: double
format|replacement: _
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG', 'peptide_out_FLAG']
name: value
name: value
name: value
ProteinQuantifier_3_input.featureXML
value
Test-4 in: ProteinQuantifier_input.consensusXML
top: 0
average: sum
include_all: False
best_charge_and_fraction: False
greedy_group_resolution: False
ratios: False
ratiosSILAC: False
consensus|normalize: False
consensus|fix_peptides: False
format|separator:
format|quoting: double
format|replacement: _
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
ProteinQuantifier_input.consensusXML
value
Test-5 in: ProteinQuantifier_input.consensusXML
top: 3
average: sum
include_all: False
best_charge_and_fraction: False
greedy_group_resolution: False
ratios: False
ratiosSILAC: False
consensus|normalize: False
consensus|fix_peptides: False
format|separator:
format|quoting: double
format|replacement: _
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
ProteinQuantifier_input.consensusXML
value
Test-6 in: ProteinQuantifier_input.consensusXML
top: 3
average: sum
include_all: True
best_charge_and_fraction: False
greedy_group_resolution: False
ratios: False
ratiosSILAC: False
consensus|normalize: False
consensus|fix_peptides: False
format|separator:
format|quoting: double
format|replacement: _
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
ProteinQuantifier_input.consensusXML
value
Test-7 in: ProteinQuantifier_input.consensusXML
top: 0
average: sum
include_all: False
best_charge_and_fraction: False
greedy_group_resolution: False
ratios: False
ratiosSILAC: False
consensus|normalize: False
consensus|fix_peptides: True
format|separator:
format|quoting: double
format|replacement: _
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
ProteinQuantifier_input.consensusXML
value
Test-8 in: ProteinQuantifier_input.consensusXML
top: 3
average: sum
include_all: False
best_charge_and_fraction: False
greedy_group_resolution: False
ratios: False
ratiosSILAC: False
consensus|normalize: False
consensus|fix_peptides: True
format|separator:
format|quoting: double
format|replacement: _
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
ProteinQuantifier_input.consensusXML
value
Test-9 in: ProteinQuantifier_input.consensusXML
top: 3
average: sum
include_all: True
best_charge_and_fraction: False
greedy_group_resolution: False
ratios: False
ratiosSILAC: False
consensus|normalize: False
consensus|fix_peptides: True
format|separator:
format|quoting: double
format|replacement: _
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG', 'mztab_FLAG']
name: value
name: value
name: value
ProteinQuantifier_input.consensusXML
value
Test-10 in: ProteinQuantifier_input.consensusXML
top: 3
average: sum
include_all: True
best_charge_and_fraction: False
greedy_group_resolution: False
ratios: True
ratiosSILAC: False
consensus|normalize: False
consensus|fix_peptides: True
format|separator:
format|quoting: double
format|replacement: _
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
ProteinQuantifier_input.consensusXML
value
Test-11 in: ProteinQuantifier_input.consensusXML
top: 3
average: sum
include_all: True
best_charge_and_fraction: False
greedy_group_resolution: False
ratios: False
ratiosSILAC: True
consensus|normalize: False
consensus|fix_peptides: True
format|separator:
format|quoting: double
format|replacement: _
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
ProteinQuantifier_input.consensusXML
value
Test-12 in: ProteinQuantifier_input.idXML
top: 0
average: sum
include_all: False
best_charge_and_fraction: False
greedy_group_resolution: False
ratios: False
ratiosSILAC: False
consensus|normalize: False
consensus|fix_peptides: False
format|separator:
format|quoting: double
format|replacement: _
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG', 'peptide_out_FLAG']
name: value
name: value
name: value
ProteinQuantifier_input.idXML
value