| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.8+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.6+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.5+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.3.0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.2.0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.1.0 |
| PeptideIndexer |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| openms | 2.6 | package |
| openms-thirdparty | 2.6 | package |
| blast | 2.9.0 | package |
| ctdopts | 1.4 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
in: PeptideIndexer_1.idXML fasta: PeptideIndexer_1.fasta decoy_string: decoy_string_position: prefix missing_decoy_action: error write_protein_sequence: False write_protein_description: False keep_unreferenced_proteins: False unmatched_action: warn aaa_max: 4 mismatches_max: 0 IL_equivalent: False enzyme|name: auto enzyme|specificity: none adv_opts_cond|force: False adv_opts_cond|test: true adv_opts_cond|adv_opts_selector: advanced OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
PeptideIndexer_1.idXML PeptideIndexer_1.fasta value |
| Test-2 |
in: PeptideIndexer_1.idXML fasta: PeptideIndexer_1.fasta decoy_string: decoy_string_position: prefix missing_decoy_action: error write_protein_sequence: True write_protein_description: False keep_unreferenced_proteins: False unmatched_action: warn aaa_max: 4 mismatches_max: 0 IL_equivalent: False enzyme|name: auto enzyme|specificity: none adv_opts_cond|force: False adv_opts_cond|test: true adv_opts_cond|adv_opts_selector: advanced OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
PeptideIndexer_1.idXML PeptideIndexer_1.fasta value |
| Test-3 |
in: PeptideIndexer_1.idXML fasta: PeptideIndexer_1.fasta decoy_string: decoy_string_position: prefix missing_decoy_action: error write_protein_sequence: False write_protein_description: False keep_unreferenced_proteins: True unmatched_action: warn aaa_max: 4 mismatches_max: 0 IL_equivalent: False enzyme|name: auto enzyme|specificity: none adv_opts_cond|force: False adv_opts_cond|test: true adv_opts_cond|adv_opts_selector: advanced OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
PeptideIndexer_1.idXML PeptideIndexer_1.fasta value |
| Test-4 |
in: PeptideIndexer_1.idXML fasta: PeptideIndexer_1.fasta decoy_string: decoy_string_position: prefix missing_decoy_action: error write_protein_sequence: True write_protein_description: False keep_unreferenced_proteins: False unmatched_action: warn aaa_max: 0 mismatches_max: 0 IL_equivalent: False enzyme|name: auto enzyme|specificity: none adv_opts_cond|force: False adv_opts_cond|test: true adv_opts_cond|adv_opts_selector: advanced OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
PeptideIndexer_1.idXML PeptideIndexer_1.fasta value |
| Test-5 |
in: PeptideIndexer_1.idXML fasta: PeptideIndexer_1.fasta decoy_string: decoy_string_position: prefix missing_decoy_action: error write_protein_sequence: False write_protein_description: False keep_unreferenced_proteins: False unmatched_action: warn aaa_max: 4 mismatches_max: 0 IL_equivalent: False enzyme|name: auto enzyme|specificity: none adv_opts_cond|force: False adv_opts_cond|test: true adv_opts_cond|adv_opts_selector: advanced OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
PeptideIndexer_1.idXML PeptideIndexer_1.fasta value |
| Test-6 |
in: PeptideIndexer_2.idXML fasta: PeptideIndexer_1.fasta decoy_string: decoy_string_position: prefix missing_decoy_action: error write_protein_sequence: False write_protein_description: False keep_unreferenced_proteins: False unmatched_action: warn aaa_max: 3 mismatches_max: 0 IL_equivalent: False enzyme|name: auto enzyme|specificity: none adv_opts_cond|force: False adv_opts_cond|test: true adv_opts_cond|adv_opts_selector: advanced OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
PeptideIndexer_2.idXML PeptideIndexer_1.fasta value |
| Test-7 |
in: PeptideIndexer_3.idXML fasta: PeptideIndexer_1.fasta decoy_string: DECOY_ decoy_string_position: prefix missing_decoy_action: error write_protein_sequence: False write_protein_description: False keep_unreferenced_proteins: False unmatched_action: warn aaa_max: 4 mismatches_max: 0 IL_equivalent: False enzyme|name: auto enzyme|specificity: full adv_opts_cond|force: False adv_opts_cond|test: true adv_opts_cond|adv_opts_selector: advanced OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
PeptideIndexer_3.idXML PeptideIndexer_1.fasta value |
| Test-8 |
in: PeptideIndexer_3.idXML fasta: PeptideIndexer_1.fasta decoy_string: decoy_string_position: prefix missing_decoy_action: error write_protein_sequence: False write_protein_description: False keep_unreferenced_proteins: False unmatched_action: warn aaa_max: 4 mismatches_max: 0 IL_equivalent: False enzyme|name: auto enzyme|specificity: semi adv_opts_cond|force: False adv_opts_cond|test: true adv_opts_cond|adv_opts_selector: advanced OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
PeptideIndexer_3.idXML PeptideIndexer_1.fasta value |
| Test-9 |
in: PeptideIndexer_3.idXML fasta: PeptideIndexer_1.fasta decoy_string: decoy_string_position: prefix missing_decoy_action: error write_protein_sequence: False write_protein_description: False keep_unreferenced_proteins: False unmatched_action: remove aaa_max: 4 mismatches_max: 0 IL_equivalent: False enzyme|name: auto enzyme|specificity: none adv_opts_cond|force: False adv_opts_cond|test: true adv_opts_cond|adv_opts_selector: advanced OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
PeptideIndexer_3.idXML PeptideIndexer_1.fasta value |
| Test-10 |
in: PeptideIndexer_10_input.idXML fasta: PeptideIndexer_10_input.fasta decoy_string: decoy_string_position: prefix missing_decoy_action: error write_protein_sequence: True write_protein_description: False keep_unreferenced_proteins: False unmatched_action: error aaa_max: 3 mismatches_max: 0 IL_equivalent: True enzyme|name: auto enzyme|specificity: auto adv_opts_cond|force: False adv_opts_cond|test: true adv_opts_cond|adv_opts_selector: advanced OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
PeptideIndexer_10_input.idXML PeptideIndexer_10_input.fasta value |
| Test-11 |
in: PeptideIndexer_1.idXML fasta: PeptideIndexer_1.fasta decoy_string: decoy_string_position: prefix missing_decoy_action: error write_protein_sequence: False write_protein_description: False keep_unreferenced_proteins: False unmatched_action: warn aaa_max: 4 mismatches_max: 0 IL_equivalent: False enzyme|name: auto enzyme|specificity: none adv_opts_cond|force: False adv_opts_cond|test: true adv_opts_cond|adv_opts_selector: advanced OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
PeptideIndexer_1.idXML PeptideIndexer_1.fasta value |
| Test-12 |
in: empty.idXML fasta: PeptideIndexer_1.fasta decoy_string: decoy_string_position: prefix missing_decoy_action: error write_protein_sequence: False write_protein_description: False keep_unreferenced_proteins: False unmatched_action: error aaa_max: 4 mismatches_max: 0 IL_equivalent: False enzyme|name: auto enzyme|specificity: auto adv_opts_cond|force: False adv_opts_cond|test: true adv_opts_cond|adv_opts_selector: advanced OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
empty.idXML PeptideIndexer_1.fasta value |
| Test-13 |
in: PeptideIndexer_14.idXML fasta: PeptideIndexer_2.fasta decoy_string: decoy_string_position: prefix missing_decoy_action: error write_protein_sequence: True write_protein_description: False keep_unreferenced_proteins: False unmatched_action: error aaa_max: 4 mismatches_max: 0 IL_equivalent: False enzyme|name: auto enzyme|specificity: none adv_opts_cond|force: False adv_opts_cond|test: true adv_opts_cond|adv_opts_selector: advanced OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
PeptideIndexer_14.idXML PeptideIndexer_2.fasta value |