| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openpepxl/OpenPepXL/3.1+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openpepxl/OpenPepXL/2.8+galaxy0 (this tool) |
| 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 |
| 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 | 2.8 | package |
| openms-thirdparty | 2.8 | package |
| omssa | 2.1.9 | package |
| blast | 2.13.0 | 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: 2 precursor|max_charge: 8 precursor|corrections: 4 3 2 1 0 fragment|mass_tolerance: 0.2 fragment|mass_tolerance_xlinks: 0.3 fragment|mass_tolerance_unit: Da modifications|fixed: Carbamidomethyl (C) modifications|variable: Oxidation (M) modifications|variable_max_per_peptide: 3 peptide|min_size: 5 peptide|missed_cleavages: 3 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|force: False adv_opts|test: true 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 |