Repository revision
1:528bcf03e561

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/1.6.0.0
1.6.0.0
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+galaxy0
toolshed.g2.bx.psu.edu/repos/galaxyp/pepquery/pepquery/1.6.0.0 (this tool)
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 1.6.0 package
Functional tests
name inputs outputs required files
Test-1 req_inputs|input_type|input_type_selector: peptide
req_inputs|spectrum_file: iTRAQ_f4.mgf
ms_params|search|min_peaks: 10
req_inputs|db_file: Uniprot.fasta
ms_params|digestion|enzyme: 0
modifications|aa: True
ms_params|tolerance_params|precursor_unit: ppm
ms_params|tolerance_params|tolerance: 0.6
req_inputs|input_type|multiple|input: ELGSSDLTAR
modifications|fixed_mod: ['6', '103', '157']
modifications|max_mods: 3
modifications|unmodified: False
ms_params|search|max_charge: 3
ms_params|search|frag_method: 1
ms_params|search|max_length: 45
ms_params|search|min_score: 12
req_inputs|input_type|multiple|peptide_input_selector: single
ms_params|digestion|max_missed_cleavages: 2
ms_params|search|num_random_peptides: 1000
ms_params|search|scoring_method: 1
modifications|var_mod: 117
report_spectrum_file: True
ms_params|search|min_charge: 2
ms_params|tolerance_params|precursor_tolerance: 10
attributes: name
Uniprot.fasta
iTRAQ_f4.mgf
name
Test-2 req_inputs|input_type|input_type_selector: peptide
req_inputs|spectrum_file: iTRAQ_f4.mgf
ms_params|search|min_peaks: 10
req_inputs|db_file: Uniprot.fasta
ms_params|digestion|enzyme: 0
modifications|aa: True
ms_params|tolerance_params|precursor_unit: ppm
ms_params|tolerance_params|tolerance: 0.6
req_inputs|input_type|multiple|input: novel_peptides
modifications|fixed_mod: ['6', '103', '157']
modifications|max_mods: 3
modifications|unmodified: False
ms_params|search|max_charge: 3
ms_params|search|frag_method: 1
ms_params|search|max_length: 45
ms_params|search|min_score: 12
req_inputs|input_type|multiple|peptide_input_selector: multiple
ms_params|digestion|max_missed_cleavages: 2
ms_params|search|num_random_peptides: 1000
ms_params|search|scoring_method: 1
modifications|var_mod: 117
report_spectrum_file: True
ms_params|search|min_charge: 2
ms_params|tolerance_params|precursor_tolerance: 10
attributes: name
novel_peptides
Uniprot.fasta
iTRAQ_f4.mgf
name
Test-3 req_inputs|input_type|input_type_selector: 1
req_inputs|spectrum_file: iTRAQ_f4.mgf
ms_params|search|min_peaks: 10
req_inputs|db_file: Uniprot.fasta
req_inputs|input_type|multiple|protein_input_selector: multiple
ms_params|digestion|enzyme: 0
modifications|aa: True
ms_params|tolerance_params|precursor_unit: ppm
ms_params|tolerance_params|tolerance: 0.6
req_inputs|input_type|multiple|input: novel_proteins.fa
modifications|fixed_mod: ['6', '103', '157']
modifications|max_mods: 3
modifications|unmodified: False
ms_params|search|max_charge: 3
ms_params|search|frag_method: 1
ms_params|search|max_length: 45
ms_params|search|min_score: 12
ms_params|digestion|max_missed_cleavages: 2
ms_params|search|num_random_peptides: 1000
ms_params|search|scoring_method: 1
modifications|var_mod: 117
report_spectrum_file: True
ms_params|search|min_charge: 2
ms_params|tolerance_params|precursor_tolerance: 10
attributes: name
novel_proteins.fa
Uniprot.fasta
iTRAQ_f4.mgf
name
Test-4 req_inputs|input_type|input_type_selector: 2
req_inputs|spectrum_file: iTRAQ_f4.mgf
ms_params|search|min_peaks: 10
req_inputs|db_file: Uniprot.fasta
ms_params|digestion|enzyme: 0
modifications|aa: True
ms_params|tolerance_params|precursor_unit: ppm
ms_params|tolerance_params|tolerance: 0.6
modifications|fixed_mod: ['6', '103', '157']
modifications|max_mods: 3
modifications|unmodified: False
ms_params|search|max_charge: 3
ms_params|search|frag_method: 1
ms_params|search|max_length: 45
ms_params|search|min_score: 12
req_inputs|input_type|input: gaactgggcagcagcgatctgaccgcgcgcagcccgtatcgcgaatttaccgatcatctggtgaaa
ms_params|digestion|max_missed_cleavages: 2
ms_params|search|num_random_peptides: 1000
ms_params|search|scoring_method: 1
modifications|var_mod: 117
report_spectrum_file: True
ms_params|search|min_charge: 2
ms_params|tolerance_params|precursor_tolerance: 10
attributes: name
Uniprot.fasta
iTRAQ_f4.mgf
name