Repository revision
5:e8ddd32f450b

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

OpenPepXL tool metadata
Miscellaneous
OpenPepXL
Tool for protein-protein cross-linking identification using labeled linkers.
OpenPepXL
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openpepxl/OpenPepXL/2.5+galaxy0
2.5+galaxy0
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openpepxl/OpenPepXL/2.6+galaxy0
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openpepxl/OpenPepXL/2.5+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openpepxl/OpenPepXL/2.3.0
OpenPepXL
Requirements (dependencies defined in the <requirements> tag set)
name version type
openms 2.5 package
openms-thirdparty 2.5 package
blast 2.9.0 package
openjdk 8.0.192 package
ctdopts 1.4 package
Functional tests
name inputs outputs required files
Test-1 in: OpenPepXL_input.mzML
consensus: OpenPepXL_input.consensusXML
database: OpenPepXL_input.fasta
decoy_string: decoy
decoy_prefix: True
precursor|mass_tolerance: 10.0
precursor|mass_tolerance_unit: ppm
precursor|min_charge: 3
precursor|max_charge: 7
precursor|corrections: 2 1 0
fragment|mass_tolerance: 0.2
fragment|mass_tolerance_xlinks: 0.3
fragment|mass_tolerance_unit: Da
modifications|fixed:
modifications|variable:
modifications|variable_max_per_peptide: 2
peptide|min_size: 5
peptide|missed_cleavages: 2
peptide|enzyme: Trypsin
cross_linker|residue1: "K" "N-term"
cross_linker|residue2: "K" "N-term"
cross_linker|mass_light: 138.0680796
cross_linker|mass_iso_shift: 12.075321
cross_linker|mass_mono_link: 156.07864431 155.094628715
cross_linker|name: DSS
algorithm|number_top_hits: 5
algorithm|deisotope: auto
ions|b_ions: True
ions|y_ions: True
ions|a_ions: False
ions|x_ions: False
ions|c_ions: False
ions|z_ions: False
ions|neutral_losses: True
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_idXML_FLAG', 'out_mzIdentML_FLAG', 'out_xquestxml_FLAG', 'out_xquest_specxml_FLAG']
name: value
name: value
name: value
name: value
name: value
OpenPepXL_input.mzML
OpenPepXL_input.consensusXML
OpenPepXL_input.fasta
value