Repository revision
3:962599ac5406

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

PepQuery tool metadata
Miscellaneous
PepQuery
Peptide-centric search engine for novel peptide identification and validation.
pepquery
toolshed.g2.bx.psu.edu/repos/galaxyp/pepquery/pepquery/1.6.2+galaxy1
1.6.2+galaxy1
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/galaxyp/pepquery/pepquery/1.6.2+galaxy1 (this tool)
toolshed.g2.bx.psu.edu/repos/galaxyp/pepquery/pepquery/1.6.2+galaxy0
toolshed.g2.bx.psu.edu/repos/galaxyp/pepquery/pepquery/1.6.0.0
toolshed.g2.bx.psu.edu/repos/galaxyp/pepquery/pepquery/1.3.0.0
pepquery
Requirements (dependencies defined in the <requirements> tag set)
name version type
pepquery 1.6.2 package
Functional tests
name inputs outputs required files
Test-1 req_inputs|input_type|multiple|input: ELGSSDLTAR
req_inputs|input_type|multiple|peptide_input_selector: single
req_inputs|input_type|input_type_selector: peptide
req_inputs|db_file: Uniprot.fasta
req_inputs|spectrum_file: iTRAQ_f4.mgf
modifications|fixed_mod: ['6', '103', '157']
modifications|var_mod: 117
modifications|max_mods: 3
modifications|unmodified: False
modifications|aa: True
ms_params|tolerance_params|precursor_tolerance: 10
ms_params|tolerance_params|precursor_unit: ppm
ms_params|tolerance_params|tolerance: 0.6
ms_params|digestion|enzyme: 0
ms_params|digestion|max_missed_cleavages: 2
ms_params|search|frag_method: 1
ms_params|search|scoring_method: 1
ms_params|search|max_charge: 3
ms_params|search|min_charge: 2
ms_params|search|min_peaks: 10
ms_params|search|min_score: 12
ms_params|search|max_length: 45
ms_params|search|num_random_peptides: 1000
report_spectrum_file: True
 name: value
 Uniprot.fasta
iTRAQ_f4.mgf
value
Test-2 req_inputs|input_type|multiple|input: novel_peptides
req_inputs|input_type|multiple|peptide_input_selector: multiple
req_inputs|input_type|input_type_selector: peptide
req_inputs|db_file: Uniprot.fasta
req_inputs|spectrum_file: iTRAQ_f4.mgf
modifications|fixed_mod: ['6', '103', '157']
modifications|var_mod: 117
modifications|max_mods: 3
modifications|unmodified: False
modifications|aa: True
ms_params|tolerance_params|precursor_tolerance: 10
ms_params|tolerance_params|precursor_unit: ppm
ms_params|tolerance_params|tolerance: 0.6
ms_params|digestion|enzyme: 0
ms_params|digestion|max_missed_cleavages: 2
ms_params|search|frag_method: 1
ms_params|search|scoring_method: 1
ms_params|search|max_charge: 3
ms_params|search|min_charge: 2
ms_params|search|min_peaks: 10
ms_params|search|min_score: 12
ms_params|search|max_length: 45
ms_params|search|num_random_peptides: 1000
report_spectrum_file: True
 name: value
 novel_peptides
Uniprot.fasta
iTRAQ_f4.mgf
value
Test-3 req_inputs|input_type|multiple|input: novel_peptides
req_inputs|input_type|multiple|peptide_input_selector: multiple
req_inputs|input_type|input_type_selector: peptide
req_inputs|db_file: Uniprot.fasta
req_inputs|spectrum_file: iTRAQ_f4.mgf
modifications|fixed_mod: ['6', '103', '157']
modifications|var_mod: 117
modifications|max_mods: 3
modifications|unmodified: True
modifications|aa: True
ms_params|tolerance_params|precursor_tolerance: 10
ms_params|tolerance_params|precursor_unit: ppm
ms_params|tolerance_params|tolerance: 0.6
ms_params|digestion|enzyme: 0
ms_params|digestion|max_missed_cleavages: 1
ms_params|search|frag_method: 1
ms_params|search|scoring_method: 1
ms_params|search|max_charge: 3
ms_params|search|min_charge: 2
ms_params|search|min_peaks: 7
ms_params|search|min_score: 10
ms_params|search|max_length: 45
ms_params|search|num_random_peptides: 1000
report_spectrum_file: False
 name: value
 novel_peptides
Uniprot.fasta
iTRAQ_f4.mgf
value
Test-4 req_inputs|input_type|multiple|input: novel_proteins.fa
req_inputs|input_type|multiple|protein_input_selector: multiple
req_inputs|input_type|input_type_selector: 1
req_inputs|db_file: Uniprot.fasta
req_inputs|spectrum_file: iTRAQ_f4.mgf
modifications|fixed_mod: ['6', '103', '157']
modifications|var_mod: 117
modifications|max_mods: 3
modifications|unmodified: False
modifications|aa: True
ms_params|tolerance_params|precursor_tolerance: 10
ms_params|tolerance_params|precursor_unit: ppm
ms_params|tolerance_params|tolerance: 0.6
ms_params|digestion|enzyme: 0
ms_params|digestion|max_missed_cleavages: 2
ms_params|search|frag_method: 1
ms_params|search|scoring_method: 1
ms_params|search|max_charge: 3
ms_params|search|min_charge: 2
ms_params|search|min_peaks: 10
ms_params|search|min_score: 12
ms_params|search|max_length: 45
ms_params|search|num_random_peptides: 1000
report_spectrum_file: True
 name: value
 novel_proteins.fa
Uniprot.fasta
iTRAQ_f4.mgf
value
Test-5 req_inputs|input_type|input: gaactgggcagcagcgatctgaccgcgcgcagcccgtatcgcgaatttaccgatcatctggtgaaa
req_inputs|input_type|input_type_selector: 2
req_inputs|db_file: Uniprot.fasta
req_inputs|spectrum_file: iTRAQ_f4.mgf
modifications|fixed_mod: ['6', '103', '157']
modifications|var_mod: 117
modifications|max_mods: 3
modifications|unmodified: False
modifications|aa: True
ms_params|tolerance_params|precursor_tolerance: 10
ms_params|tolerance_params|precursor_unit: ppm
ms_params|tolerance_params|tolerance: 0.6
ms_params|digestion|enzyme: 0
ms_params|digestion|max_missed_cleavages: 2
ms_params|search|frag_method: 1
ms_params|search|scoring_method: 1
ms_params|search|max_charge: 3
ms_params|search|min_charge: 2
ms_params|search|min_peaks: 10
ms_params|search|min_score: 12
ms_params|search|max_length: 45
ms_params|search|num_random_peptides: 1000
report_spectrum_file: True
 name: value
 Uniprot.fasta
iTRAQ_f4.mgf
value
Test-6 req_inputs|input_type|multiple|input: novel_peptides
req_inputs|input_type|multiple|peptide_input_selector: multiple
req_inputs|input_type|input_type_selector: peptide
req_inputs|db_file: Uniprot.fasta
req_inputs|spectrum_file: immunopeptidomics.mgf
req_inputs|indexType: 2
req_inputs|tags|tag_file: test.tags
req_inputs|tags|tagIndexType: 2
req_inputs|tags|tagType: PepQuery
modifications|fixed_mod:
modifications|var_mod: ['117', '114', '118', '128']
modifications|max_mods: 3
modifications|unmodified: True
modifications|aa: True
ms_params|tolerance_params|precursor_tolerance: 20
ms_params|tolerance_params|precursor_unit: ppm
ms_params|tolerance_params|tolerance: 0.02
ms_params|digestion|enzyme: 0
ms_params|digestion|max_missed_cleavages: 0
ms_params|search|frag_method: 1
ms_params|search|scoring_method: 1
ms_params|search|max_charge: 3
ms_params|search|min_charge: 2
ms_params|search|min_peaks: 10
ms_params|search|min_score: 12
ms_params|search|max_length: 25
ms_params|search|num_random_peptides: 1000
report_spectrum_file: True
 name: value
 novel_peptides
Uniprot.fasta
immunopeptidomics.mgf
test.tags
value
Test-7 req_inputs|input_type|multiple|input: novel_peptides
req_inputs|input_type|multiple|peptide_input_selector: multiple
req_inputs|input_type|input_type_selector: peptide
req_inputs|db_file: Uniprot.fasta
req_inputs|spectrum_file: immunopeptidomics.mgf
req_inputs|indexType: 2
req_inputs|tags|qry_res: pFind.qry.res
req_inputs|tags|tagType: pFind
modifications|fixed_mod:
modifications|var_mod: ['117', '114', '118', '128']
modifications|max_mods: 3
modifications|unmodified: True
modifications|aa: True
ms_params|tolerance_params|precursor_tolerance: 20
ms_params|tolerance_params|precursor_unit: ppm
ms_params|tolerance_params|tolerance: 0.02
ms_params|digestion|enzyme: 0
ms_params|digestion|max_missed_cleavages: 0
ms_params|search|frag_method: 1
ms_params|search|scoring_method: 1
ms_params|search|max_charge: 3
ms_params|search|min_charge: 2
ms_params|search|min_peaks: 10
ms_params|search|min_score: 12
ms_params|search|max_length: 25
ms_params|search|num_random_peptides: 1000
report_spectrum_file: True
 name: value
name: value
 novel_peptides
Uniprot.fasta
immunopeptidomics.mgf
pFind.qry.res
value