| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openpepxllf/OpenPepXLLF/2.8+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openpepxllf/OpenPepXLLF/2.6+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openpepxllf/OpenPepXLLF/2.5+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openpepxllf/OpenPepXLLF/2.3.0 |
| OpenPepXLLF |
| 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: OpenPepXLLF_input.mzML database: OpenPepXLLF_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: 20.0 fragment|mass_tolerance_xlinks: 20.0 fragment|mass_tolerance_unit: ppm 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: 138.0680796 cross_linker|mass_mono_link: 156.07864431 155.094628715 cross_linker|name: DSS algorithm|number_top_hits: 5 algorithm|deisotope: auto algorithm|use_sequence_tags: False algorithm|sequence_tag_min_length: 2 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 |
OpenPepXLLF_input.mzML OpenPepXLLF_input.fasta value |
| Test-2 |
in: OpenPepXLLF_input2.mzML database: OpenPepXLLF_input2.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: 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: 1 peptide|min_size: 5 peptide|missed_cleavages: 1 peptide|enzyme: Trypsin cross_linker|residue1: "D" "E" "C-term" cross_linker|residue2: "K" "S" "T" "Y" "N-term" cross_linker|mass: -18.010595 cross_linker|mass_mono_link: cross_linker|name: DMTMM algorithm|number_top_hits: 1 algorithm|deisotope: auto algorithm|use_sequence_tags: False algorithm|sequence_tag_min_length: 2 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'] |
name: value name: value |
OpenPepXLLF_input2.mzML OpenPepXLLF_input2.fasta value |