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Repository revision

Revision: 11:0f97ea098da0

Repository 'openms_rnpxlsearch'

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

RNPxlSearch tool metadata

Miscellaneous

Name: RNPxlSearch

Description: Annotate RNA/DNA-peptide cross-links in MS/MS spectra.

Id: RNPxlSearch

Guid: toolshed.g2.bx.psu.edu/repos/galaxyp/openms_rnpxlsearch/RNPxlSearch/2.8+galaxy0

Version: 2.8+galaxy0

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/openms_rnpxlsearch/RNPxlSearch/3.1+galaxy0

toolshed.g2.bx.psu.edu/repos/galaxyp/openms_rnpxlsearch/RNPxlSearch/2.8+galaxy0 (this tool)

toolshed.g2.bx.psu.edu/repos/galaxyp/openms_rnpxlsearch/RNPxlSearch/2.6+galaxy0

toolshed.g2.bx.psu.edu/repos/galaxyp/openms_rnpxlsearch/RNPxlSearch/2.5+galaxy0

toolshed.g2.bx.psu.edu/repos/galaxyp/openms_rnpxlsearch/RNPxlSearch/2.3.0

toolshed.g2.bx.psu.edu/repos/galaxyp/openms_rnpxlsearch/RNPxlSearch/2.2.0

RNPxlSearch

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

Requirements:

name

version

type

openms

2.8

package

openms-thirdparty

2.8

package

omssa

2.1.9

package

blast

2.13.0

package

ctdopts

1.4

package

Functional tests

name

inputs

outputs

required files

Test-1

in: RNPxlSearch_1_input.mzML
database: RNPxlSearch_1_input.fasta
precursor|mass_tolerance: 20.0
precursor|mass_tolerance_unit: ppm
precursor|min_charge: 2
precursor|max_charge: 5
precursor|isotopes: 0 1
fragment|mass_tolerance: 20.0
fragment|mass_tolerance_unit: ppm
modifications|fixed: None
modifications|variable: Oxidation (M)
modifications|variable_max_per_peptide: 2
peptide|min_size: 6
peptide|max_size: 1000000
peptide|missed_cleavages: 1
peptide|enzyme: Trypsin
report|top_hits: 1
RNPxl|length: 2
RNPxl|sequence: GUA
RNPxl|target_nucleotides: "A=C10H14N5O7P" "C=C9H14N3O8P" "G=C10H14N5O8P" "U=C9H13N2O9P"
RNPxl|nt_groups:
RNPxl|mapping: "A->A" "C->C" "G->G" "U->U"
RNPxl|can_cross_link: U
RNPxl|fragment_adducts: "U:C9H10N2O5;U-H3PO4" "U:C4H4N2O2;U'" "U:C4H2N2O1;U'-H2O" "U:C3O;C3O" "U:C9H13N2O9P1;U" "U:C9H11N2O8P1;U-H2O" "U:C9H12N2O6;U-HPO3"
RNPxl|modifications: "U:" "U:-H2O" "U:-H2O-HPO3" "U:-HPO3"
RNPxl|scoring: fast
RNPxl|decoys: False
RNPxl|CysteineAdduct: False
RNPxl|filter_fractional_mass: False
RNPxl|carbon_labeled_fragments: False
RNPxl|only_xl: False
RNPxl|filter_small_peptide_mass: 600.0
RNPxl|marker_ions_tolerance: 0.05
adv_opts|force: False
adv_opts|test: true
OPTIONAL_OUTPUTS: ctd_out_FLAG

name: value
name: value

RNPxlSearch_1_input.mzML
RNPxlSearch_1_input.fasta
value

Test-2

in: RNPxlSearch_1_input.mzML
database: RNPxlSearch_1_input.fasta
precursor|mass_tolerance: 20.0
precursor|mass_tolerance_unit: ppm
precursor|min_charge: 2
precursor|max_charge: 5
precursor|isotopes: 0 1
fragment|mass_tolerance: 20.0
fragment|mass_tolerance_unit: ppm
modifications|fixed: None
modifications|variable: Oxidation (M)
modifications|variable_max_per_peptide: 2
peptide|min_size: 6
peptide|max_size: 1000000
peptide|missed_cleavages: 1
peptide|enzyme: Trypsin
report|top_hits: 1
RNPxl|length: 2
RNPxl|sequence: GUA
RNPxl|target_nucleotides: "A=C10H14N5O7P" "C=C9H14N3O8P" "G=C10H14N5O8P" "U=C9H13N2O9P"
RNPxl|nt_groups:
RNPxl|mapping: "A->A" "C->C" "G->G" "U->U"
RNPxl|can_cross_link: U
RNPxl|fragment_adducts: "U:C9H10N2O5;U-H3PO4" "U:C4H4N2O2;U'" "U:C4H2N2O1;U'-H2O" "U:C3O;C3O" "U:C9H13N2O9P1;U" "U:C9H11N2O8P1;U-H2O" "U:C9H12N2O6;U-HPO3"
RNPxl|modifications: "U:" "U:-H2O" "U:-H2O-HPO3" "U:-HPO3"
RNPxl|scoring: fast
RNPxl|decoys: True
RNPxl|CysteineAdduct: False
RNPxl|filter_fractional_mass: False
RNPxl|carbon_labeled_fragments: False
RNPxl|only_xl: False
RNPxl|filter_small_peptide_mass: 600.0
RNPxl|marker_ions_tolerance: 0.05
adv_opts|force: False
adv_opts|test: true
OPTIONAL_OUTPUTS: ctd_out_FLAG

name: value
name: value

RNPxlSearch_1_input.mzML
RNPxlSearch_1_input.fasta
value

Test-3

in: RNPxlSearch_1_input.mzML
database: RNPxlSearch_1_input.fasta
precursor|mass_tolerance: 10.0
precursor|mass_tolerance_unit: ppm
precursor|min_charge: 2
precursor|max_charge: 5
precursor|isotopes: 0 1
fragment|mass_tolerance: 10.0
fragment|mass_tolerance_unit: ppm
modifications|fixed: None
modifications|variable: None
modifications|variable_max_per_peptide: 2
peptide|min_size: 6
peptide|max_size: 1000000
peptide|missed_cleavages: 1
peptide|enzyme: Trypsin
report|top_hits: 3
RNPxl|length: 2
RNPxl|sequence:
RNPxl|target_nucleotides: "A=C10H14N5O7P" "C=C9H14N3O8P" "G=C10H14N5O8P" "U=C9H13N2O9P"
RNPxl|nt_groups:
RNPxl|mapping: "A->A" "C->C" "G->G" "U->U"
RNPxl|can_cross_link: U
RNPxl|fragment_adducts: "U:C9H10N2O5;U-H3PO4" "U:C4H4N2O2;U'" "U:C4H2N2O1;U'-H2O" "U:C3O;C3O" "U:C9H13N2O9P1;U" "U:C9H11N2O8P1;U-H2O" "U:C9H12N2O6;U-HPO3"
RNPxl|modifications: "U:" "U:-H2O" "U:-H2O-HPO3" "U:-HPO3"
RNPxl|scoring: fast
RNPxl|decoys: False
RNPxl|CysteineAdduct: False
RNPxl|filter_fractional_mass: False
RNPxl|carbon_labeled_fragments: False
RNPxl|only_xl: False
RNPxl|filter_small_peptide_mass: 600.0
RNPxl|marker_ions_tolerance: 0.05
adv_opts|force: False
adv_opts|test: true
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_tsv_FLAG']

name: value
name: value
name: value

RNPxlSearch_1_input.mzML
RNPxlSearch_1_input.fasta
value

Test-4

in: RNPxlSearch_1_input.mzML
database: RNPxlSearch_1_input.fasta
precursor|mass_tolerance: 10.0
precursor|mass_tolerance_unit: ppm
precursor|min_charge: 2
precursor|max_charge: 5
precursor|isotopes: 0 1
fragment|mass_tolerance: 10.0
fragment|mass_tolerance_unit: ppm
modifications|fixed: None
modifications|variable: None
modifications|variable_max_per_peptide: 2
peptide|min_size: 6
peptide|max_size: 1000000
peptide|missed_cleavages: 1
peptide|enzyme: Trypsin
report|top_hits: 2
RNPxl|length: 2
RNPxl|sequence:
RNPxl|target_nucleotides: "A=C10H14N5O7P" "C=C9H14N3O8P" "G=C10H14N5O8P" "U=C9H13N2O9P"
RNPxl|nt_groups:
RNPxl|mapping: "A->A" "C->C" "G->G" "U->U"
RNPxl|can_cross_link: U
RNPxl|fragment_adducts: "U:C9H10N2O5;U-H3PO4" "U:C4H4N2O2;U'" "U:C4H2N2O1;U'-H2O" "U:C3O;C3O" "U:C9H13N2O9P1;U" "U:C9H11N2O8P1;U-H2O" "U:C9H12N2O6;U-HPO3"
RNPxl|modifications: "U:" "U:-H2O" "U:-H2O-HPO3" "U:-HPO3"
RNPxl|scoring: fast
RNPxl|decoys: True
RNPxl|CysteineAdduct: False
RNPxl|filter_fractional_mass: False
RNPxl|carbon_labeled_fragments: False
RNPxl|only_xl: False
RNPxl|filter_small_peptide_mass: 600.0
RNPxl|marker_ions_tolerance: 0.05
adv_opts|force: False
adv_opts|test: true
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_tsv_FLAG']

name: value
name: value
name: value

RNPxlSearch_1_input.mzML
RNPxlSearch_1_input.fasta
value