| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.17.0+galaxy7 (this tool) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/0.1.0 |
| maxquant |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| maxquant | 1.6.17.0 | package |
| python | 3.7 | package |
| pyyaml | 5.1.2 | package |
| r-ptxqc | 1.0.10 | package |
| tar | 1.32 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input_opts|ftype: .mzxml input_opts|fasta_files: bsa.fasta input_opts|identifier_parse_rule: >([^\s]*) input_opts|description_parse_rule: >(.*) paramGroups_0|files: BSA_min_23.mzXML paramGroups_0|maxMissedCleavages: 1 paramGroups_0|fixedModifications: Carbamidomethyl (C) paramGroups_0|variableModifications: Oxidation (M) paramGroups_0|enzymes: Trypsin/P output_opts|output: ['evidence', 'msms', 'allPeptides', 'msmsScans', 'mzTab', 'mzRange', 'parameters', 'peptides', 'peptideSection', 'proteinGroups', 'summary', 'modificationSpecificPeptides', 'output_all', 'config', 'mqpar'] |
name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value |
bsa.fasta BSA_min_23.mzXML value |
| Test-2 |
input_opts|ftype: .mzxml input_opts|fasta_files: bsa.fasta input_opts|identifier_parse_rule: >([^\s]*) input_opts|description_parse_rule: >(.*) search_opts|incl_contaminants: False search_opts|decoy_mode: randomize search_opts|psm_fdr: 0.5 search_opts|protein_fdr: 0.4 search_opts|min_pep_length: 7 search_opts|max_pep_length: 24 protein_quant|peptides_for_quantification: 0 protein_quant|only_unmod_prot|mods_used_prot_quant: ['Pro5', 'Pro6'] protein_quant|only_unmod_prot|unmod_prot: True paramGroups_0|files: BSA_min_23.mzXML paramGroups_0|fixedModifications: paramGroups_0|variableModifications: Oxidation (M) paramGroups_0|quant_method|iso_labels|iso_label_0|internallabel: TMT2plex-Lys126 paramGroups_0|quant_method|iso_labels|iso_label_0|terminallabel: TMT2plex-Nter126 paramGroups_0|quant_method|iso_labels|iso_label_0|cp1: 6.7 paramGroups_0|quant_method|iso_labels|iso_label_0|cp2: 3 paramGroups_0|quant_method|iso_labels|iso_label_0|tmtlike: True paramGroups_0|quant_method|iso_labels|iso_label_1|internallabel: TMT2plex-Lys127 paramGroups_0|quant_method|iso_labels|iso_label_1|terminallabel: TMT2plex-Nter127 paramGroups_0|quant_method|iso_labels|iso_label_1|tmtlike: True paramGroups_0|quant_method|iso_labels|labeling: custom paramGroups_0|quant_method|filter_by_pif|filter_pif: False paramGroups_0|quant_method|select_quant_method: reporter_ion_ms2 paramGroups_1|files: BSA_min_22 paramGroups_1|fixedModifications: paramGroups_1|variableModifications: paramGroups_1|enzymes: paramGroups_1|quant_method|iso_labels|labeling: itraq4plex paramGroups_1|quant_method|filter_by_pif|reporter_pif: 0.8 paramGroups_1|quant_method|filter_by_pif|filter_pif: True paramGroups_1|quant_method|select_quant_method: reporter_ion_ms2 output_opts|dry_run: True output_opts|output: ['config', 'mqpar', 'mzTab'] |
name: value name: value |
bsa.fasta BSA_min_23.mzXML BSA_min_22 value |
| Test-3 |
input_opts|ftype: .mzxml input_opts|fasta_files: bsa.fasta input_opts|identifier_parse_rule: >([^\s]*) input_opts|description_parse_rule: >(.*) search_opts|incl_contaminants: False search_opts|decoy_mode: randomize search_opts|psm_fdr: 0.5 search_opts|protein_fdr: 0.4 search_opts|min_pep_length: 7 search_opts|max_pep_length: 24 protein_quant|peptides_for_quantification: 0 protein_quant|only_unmod_prot|mods_used_prot_quant: ['Pro5', 'Pro6'] protein_quant|only_unmod_prot|unmod_prot: True paramGroups_0|files: BSA_min_23.mzXML paramGroups_0|fixedModifications: paramGroups_0|variableModifications: Oxidation (M) paramGroups_0|quant_method|iso_labels|iso_label_0|internallabel: TMT2plex-Lys126 paramGroups_0|quant_method|iso_labels|iso_label_0|terminallabel: TMT2plex-Nter126 paramGroups_0|quant_method|iso_labels|iso_label_0|cp1: 6.7 paramGroups_0|quant_method|iso_labels|iso_label_0|cp2: 3 paramGroups_0|quant_method|iso_labels|iso_label_0|tmtlike: True paramGroups_0|quant_method|iso_labels|iso_label_1|internallabel: TMT2plex-Lys127 paramGroups_0|quant_method|iso_labels|iso_label_1|terminallabel: TMT2plex-Nter127 paramGroups_0|quant_method|iso_labels|iso_label_1|tmtlike: True paramGroups_0|quant_method|iso_labels|labeling: custom paramGroups_0|quant_method|filter_by_pif|filter_pif: False paramGroups_0|quant_method|select_quant_method: reporter_ion_ms3 paramGroups_1|files: BSA_min_22 paramGroups_1|fixedModifications: paramGroups_1|variableModifications: paramGroups_1|enzymes: paramGroups_1|quant_method|iso_labels|labeling: itraq4plex paramGroups_1|quant_method|filter_by_pif|reporter_pif: 0.8 paramGroups_1|quant_method|filter_by_pif|filter_pif: True paramGroups_1|quant_method|select_quant_method: reporter_ion_ms3 output_opts|dry_run: True output_opts|output: ['config', 'mqpar', 'mzTab'] |
name: value name: value |
bsa.fasta BSA_min_23.mzXML BSA_min_22 value |
| Test-4 |
input_opts|ftype: .mzxml input_opts|fasta_files: bsa.fasta input_opts|identifier_parse_rule: ^>.*\|(.*)\|.*$ input_opts|description_parse_rule: ^>.*\|.*\|[^ ]+ (.*) OS.*$ search_opts|min_unique_pep: 1 protein_quant|lfq_opts|do_ibaq|ibaqLogFit: False protein_quant|lfq_opts|do_ibaq|ibaq: True paramGroups_0|files: BSA_min_22 paramGroups_0|maxMissedCleavages: 1 paramGroups_0|variableModifications: Oxidation (M) paramGroups_0|quant_method|select_quant_method: lfq output_opts|dry_run: True output_opts|output: ['config', 'mqpar'] |
name: value name: value |
bsa.fasta BSA_min_22 value |
| Test-5 |
input_opts|ftype: .mzxml input_opts|fasta_files: bsa.fasta input_opts|identifier_parse_rule: ^>.*\|(.*)\|.*$ input_opts|description_parse_rule: ^>.*\|.*\|[^ ]+ (.*) OS.*$ search_opts|min_unique_pep: 1 search_opts|mbr|match_between_runs: True protein_quant|lfq_opts|do_ibaq|ibaqLogFit: False protein_quant|lfq_opts|do_ibaq|ibaq: True paramGroups_0|files: BSA_min_22 paramGroups_0|maxMissedCleavages: 1 paramGroups_0|variableModifications: Oxidation (M) paramGroups_0|quant_method|select_quant_method: lfq output_opts|dry_run: True output_opts|output: ['config', 'mqpar'] |
name: value name: value |
bsa.fasta BSA_min_22 value |
| Test-6 |
input_opts|ftype: .mzxml input_opts|fasta_files: bsa.fasta input_opts|identifier_parse_rule: >([^\s]*) input_opts|description_parse_rule: >(.*) search_opts|template: 04/exp_design paramGroups_0|files: ['BSA_min_23.mzXML', 'BSA_min_22'] paramGroups_0|fixedModifications: Carbamidomethyl (C) paramGroups_0|variableModifications: Oxidation (M) paramGroups_0|enzymes: Trypsin/P paramGroups_0|quant_method|light_labels: ['Arg6', 'Lys4'] paramGroups_0|quant_method|heavy_labels: ['Arg10', 'DimethLys8'] paramGroups_0|quant_method|select_quant_method: silac output_opts|dry_run: True output_opts|output: ['config', 'mqpar'] |
name: value name: value |
bsa.fasta 04/exp_design BSA_min_23.mzXML BSA_min_22 value |
| Test-7 |
input_opts|ftype: .mzxml input_opts|fasta_files: tmt_data.fasta input_opts|identifier_parse_rule: >([^\s]*) input_opts|description_parse_rule: >(.*) paramGroups_0|files: tmt_data.mzXML paramGroups_0|fixedModifications: paramGroups_0|variableModifications: Oxidation (M) paramGroups_0|quant_method|iso_labels|labeling: tmt10plex paramGroups_0|quant_method|select_quant_method: reporter_ion_ms2 qc|do_it: True output_opts|output: ['config', 'mqpar'] |
name: value name: value name: value |
tmt_data.fasta tmt_data.mzXML value |
| Test-8 |
input_opts|ftype: .mzxml input_opts|fasta_files: tmt_data_16.fasta input_opts|identifier_parse_rule: >([^\s]*) input_opts|description_parse_rule: >(.*) paramGroups_0|files: tmt_data.mzXML paramGroups_0|fixedModifications: paramGroups_0|variableModifications: Oxidation (M) paramGroups_0|quant_method|iso_labels|labeling: tmtpro16plex paramGroups_0|quant_method|select_quant_method: reporter_ion_ms2 qc|do_it: False output_opts|output: ['config', 'mqpar', 'proteinGroups'] |
name: value name: value name: value |
tmt_data_16.fasta tmt_data.mzXML value |
| Test-9 |
input_opts|ftype: .mzxml input_opts|fasta_files: tmt_data_18.fasta input_opts|identifier_parse_rule: >([^\s]*) input_opts|description_parse_rule: >(.*) paramGroups_0|files: tmt_data_18.mzXML paramGroups_0|fixedModifications: paramGroups_0|variableModifications: Oxidation (M) paramGroups_0|quant_method|iso_labels|labeling: tmtpro18plex paramGroups_0|quant_method|select_quant_method: reporter_ion_ms2 qc|do_it: False output_opts|output: msmsScans |
name: value |
tmt_data_18.fasta tmt_data_18.mzXML value |
| Test-10 |
input_opts|ftype: .thermo.raw input_opts|fasta_files: bsa.fasta input_opts|identifier_parse_rule: ^>.*\|(.*)\|.*$ input_opts|description_parse_rule: ^>.*\|.*\|[^ ]+ (.*) OS.*$ search_opts|min_unique_pep: 1 paramGroups_0|files: thermo.raw paramGroups_0|maxMissedCleavages: 1 paramGroups_0|variableModifications: Oxidation (M) paramGroups_0|quant_method|select_quant_method: lfq output_opts|output: ['config', 'mqpar'] |
name: value name: value |
bsa.fasta thermo.raw value |