Repository revision
3:55290cddb679

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

NucleicAcidSearchEngine tool metadata
Miscellaneous
Annotate nucleic acid identifications to MS/MS spectra.
NucleicAcidSearchEngine
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_nucleicacidsearchengine/NucleicAcidSearchEngine/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_nucleicacidsearchengine/NucleicAcidSearchEngine/2.8+galaxy0
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_nucleicacidsearchengine/NucleicAcidSearchEngine/2.6+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_nucleicacidsearchengine/NucleicAcidSearchEngine/2.5+galaxy0
NucleicAcidSearchEngine
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: NucleicAcidSearchEngine_1.mzML
database: NucleicAcidSearchEngine_1.fasta
precursor|mass_tolerance: 5.0
precursor|mass_tolerance_unit: ppm
precursor|min_charge: -2
precursor|max_charge: -14
precursor|include_unknown_charge: True
precursor|use_avg_mass: False
precursor|use_adducts: False
precursor|potential_adducts: "K:+" "Na:+" "Na2:++" "K2:++" "NaK:++" "K3:+++" "Na3:+++" "NaK2:+++" "Na2K:+++"
precursor|isotopes: 0 1 2
fragment|mass_tolerance: 5.0
fragment|mass_tolerance_unit: ppm
fragment|ions: ['a-B', 'c', 'w', 'y']
modifications|variable:
modifications|variable_max_per_oligo: 2
modifications|resolve_ambiguities: False
oligo|min_size: 5
oligo|max_size: 0
oligo|missed_cleavages: 22
oligo|enzyme: no cleavage
report|top_hits: 1
fdr|decoy_pattern: DECOY_
fdr|cutoff: 0.05
fdr|remove_decoys: True
adv_opts_cond|decharge_ms2: False
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'id_out_FLAG']
name: value
name: value
name: value
NucleicAcidSearchEngine_1.mzML
NucleicAcidSearchEngine_1.fasta
value