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Revision: 9:37d669de2828

Repository 'maxquant'

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant

MaxQuant tool metadata

Miscellaneous

Name: MaxQuant

Description:

Id: maxquant

Guid: toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy3

Version: 1.6.10.43+galaxy3

Version command string: None

Display in tool panel: True

Version lineage of this tool (guids ordered most recent to oldest)

toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy4

toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy3 (this tool)

toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy2

toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy1

toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43

toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.3.4+galaxy1

toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.3.4

toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/0.1.0

maxquant

Requirements (dependencies defined in the <requirements> tag set)

Requirements:

name

version

type

maxquant

1.6.10.43

package

python

3.7

package

pyyaml

5.1.2

package

r-ptxqc

0.92.6

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: ^>.*\|(.*)\|.*$
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-4

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