| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfileconverter/IDFileConverter/2.8+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfileconverter/IDFileConverter/2.6+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfileconverter/IDFileConverter/2.5+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfileconverter/IDFileConverter/2.3.0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfileconverter/IDFileConverter/2.2.0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfileconverter/IDFileConverter/2.1.0 |
| IDFileConverter |
| 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: IDFileConverter_1_input1.mascotXML out_type: idXML mz_file: IDFileConverter_1_input2.mzML mz_name: peptideprophet_analyzed: False score_type: qvalue adv_opts_cond|ignore_proteins_per_peptide: False adv_opts_cond|scan_regex: adv_opts_cond|no_spectra_data_override: False adv_opts_cond|no_spectra_references_override: False adv_opts_cond|add_ionmatch_annotation: 0.0 adv_opts_cond|concatenate_peptides: False adv_opts_cond|number_of_hits: 1 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 |
IDFileConverter_1_input1.mascotXML IDFileConverter_1_input2.mzML value |
| Test-2 |
in: PepXMLFile_test.pepxml out_type: idXML mz_file: PepXMLFile_test.mzML mz_name: PepXMLFile_test peptideprophet_analyzed: False score_type: qvalue adv_opts_cond|ignore_proteins_per_peptide: False adv_opts_cond|scan_regex: adv_opts_cond|no_spectra_data_override: False adv_opts_cond|no_spectra_references_override: False adv_opts_cond|add_ionmatch_annotation: 0.0 adv_opts_cond|concatenate_peptides: False adv_opts_cond|number_of_hits: 1 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 |
PepXMLFile_test.pepxml PepXMLFile_test.mzML value |
| Test-3 |
in: IDFileConverter_3_input.protXML out_type: idXML mz_name: peptideprophet_analyzed: False score_type: qvalue adv_opts_cond|ignore_proteins_per_peptide: False adv_opts_cond|scan_regex: adv_opts_cond|no_spectra_data_override: False adv_opts_cond|no_spectra_references_override: False adv_opts_cond|add_ionmatch_annotation: 0.0 adv_opts_cond|concatenate_peptides: False adv_opts_cond|number_of_hits: 1 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 |
IDFileConverter_3_input.protXML value |
| Test-4 |
in: IDFileConverter_1_input1.mascotXML out_type: idXML mz_file: IDFileConverter_1_input2.mzML mz_name: peptideprophet_analyzed: False score_type: qvalue adv_opts_cond|ignore_proteins_per_peptide: False adv_opts_cond|scan_regex: scan=(?<SCAN>\d+) adv_opts_cond|no_spectra_data_override: False adv_opts_cond|no_spectra_references_override: False adv_opts_cond|add_ionmatch_annotation: 0.0 adv_opts_cond|concatenate_peptides: False adv_opts_cond|number_of_hits: 1 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 |
IDFileConverter_1_input1.mascotXML IDFileConverter_1_input2.mzML value |
| Test-5 |
in: IDFileConverter_6_input1.pepXML out_type: idXML mz_file: IDFileConverter_1_input2.mzML mz_name: F025589.dat.mzML peptideprophet_analyzed: False score_type: qvalue adv_opts_cond|ignore_proteins_per_peptide: False adv_opts_cond|scan_regex: adv_opts_cond|no_spectra_data_override: False adv_opts_cond|no_spectra_references_override: False adv_opts_cond|add_ionmatch_annotation: 0.0 adv_opts_cond|concatenate_peptides: False adv_opts_cond|number_of_hits: 1 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 |
IDFileConverter_6_input1.pepXML IDFileConverter_1_input2.mzML value |
| Test-6 |
in: IDFileConverter_7_input1.xml out_type: idXML mz_name: peptideprophet_analyzed: False score_type: qvalue adv_opts_cond|ignore_proteins_per_peptide: False adv_opts_cond|scan_regex: adv_opts_cond|no_spectra_data_override: False adv_opts_cond|no_spectra_references_override: False adv_opts_cond|add_ionmatch_annotation: 0.0 adv_opts_cond|concatenate_peptides: False adv_opts_cond|number_of_hits: 1 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 |
IDFileConverter_7_input1.xml value |
| Test-7 |
in: IDFileConverter_8_input.mzid out_type: idXML mz_name: peptideprophet_analyzed: False score_type: qvalue adv_opts_cond|ignore_proteins_per_peptide: False adv_opts_cond|scan_regex: adv_opts_cond|no_spectra_data_override: False adv_opts_cond|no_spectra_references_override: False adv_opts_cond|add_ionmatch_annotation: 0.0 adv_opts_cond|concatenate_peptides: False adv_opts_cond|number_of_hits: 1 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 |
IDFileConverter_8_input.mzid value |
| Test-8 |
in: IDFileConverter_9_input.idXML out_type: mzid mz_name: peptideprophet_analyzed: False score_type: qvalue adv_opts_cond|ignore_proteins_per_peptide: False adv_opts_cond|scan_regex: adv_opts_cond|no_spectra_data_override: False adv_opts_cond|no_spectra_references_override: False adv_opts_cond|add_ionmatch_annotation: 0.0 adv_opts_cond|concatenate_peptides: False adv_opts_cond|number_of_hits: 1 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 |
IDFileConverter_9_input.idXML value |
| Test-9 |
in: IDFileConverter_10_input.pepXML out_type: idXML mz_name: peptideprophet_analyzed: False score_type: qvalue adv_opts_cond|ignore_proteins_per_peptide: False adv_opts_cond|scan_regex: adv_opts_cond|no_spectra_data_override: False adv_opts_cond|no_spectra_references_override: False adv_opts_cond|add_ionmatch_annotation: 0.0 adv_opts_cond|concatenate_peptides: False adv_opts_cond|number_of_hits: 1 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 |
IDFileConverter_10_input.pepXML value |
| Test-10 |
in: IDFileConverter_11_input.tsv out_type: idXML mz_name: peptideprophet_analyzed: False score_type: qvalue adv_opts_cond|ignore_proteins_per_peptide: False adv_opts_cond|scan_regex: adv_opts_cond|no_spectra_data_override: False adv_opts_cond|no_spectra_references_override: False adv_opts_cond|add_ionmatch_annotation: 0.0 adv_opts_cond|concatenate_peptides: False adv_opts_cond|number_of_hits: 1 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 |
IDFileConverter_11_input.tsv value |
| Test-11 |
in: IDFileConverter_12_input.psms out_type: idXML mz_name: peptideprophet_analyzed: False score_type: qvalue adv_opts_cond|ignore_proteins_per_peptide: False adv_opts_cond|scan_regex: adv_opts_cond|no_spectra_data_override: False adv_opts_cond|no_spectra_references_override: False adv_opts_cond|add_ionmatch_annotation: 0.0 adv_opts_cond|concatenate_peptides: False adv_opts_cond|number_of_hits: 1 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 |
IDFileConverter_12_input.psms value |
| Test-12 |
in: IDFileConverter_12_input.psms out_type: idXML mz_name: peptideprophet_analyzed: False score_type: PEP adv_opts_cond|ignore_proteins_per_peptide: False adv_opts_cond|scan_regex: adv_opts_cond|no_spectra_data_override: False adv_opts_cond|no_spectra_references_override: False adv_opts_cond|add_ionmatch_annotation: 0.0 adv_opts_cond|concatenate_peptides: False adv_opts_cond|number_of_hits: 1 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 |
IDFileConverter_12_input.psms value |
| Test-13 |
in: IDFileConverter_12_input.psms out_type: idXML mz_name: peptideprophet_analyzed: False score_type: score adv_opts_cond|ignore_proteins_per_peptide: False adv_opts_cond|scan_regex: adv_opts_cond|no_spectra_data_override: False adv_opts_cond|no_spectra_references_override: False adv_opts_cond|add_ionmatch_annotation: 0.0 adv_opts_cond|concatenate_peptides: False adv_opts_cond|number_of_hits: 1 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 |
IDFileConverter_12_input.psms value |
| Test-14 |
in: MSGFPlusAdapter_1_out.mzid out_type: idXML mz_file: spectra.mzML mz_name: peptideprophet_analyzed: False score_type: qvalue adv_opts_cond|ignore_proteins_per_peptide: False adv_opts_cond|scan_regex: adv_opts_cond|no_spectra_data_override: False adv_opts_cond|no_spectra_references_override: False adv_opts_cond|add_ionmatch_annotation: 0.0 adv_opts_cond|concatenate_peptides: False adv_opts_cond|number_of_hits: 1 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 |
MSGFPlusAdapter_1_out.mzid spectra.mzML value |
| Test-15 |
in: IDFileConverter_16_input.pepXML out_type: idXML mz_name: peptideprophet_analyzed: False score_type: qvalue adv_opts_cond|ignore_proteins_per_peptide: False adv_opts_cond|scan_regex: adv_opts_cond|no_spectra_data_override: False adv_opts_cond|no_spectra_references_override: False adv_opts_cond|add_ionmatch_annotation: 0.0 adv_opts_cond|concatenate_peptides: False adv_opts_cond|number_of_hits: 1 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 |
IDFileConverter_16_input.pepXML value |
| Test-16 |
in: IDFileConverter_17_input.idXML out_type: pepXML mz_name: peptideprophet_analyzed: False score_type: qvalue adv_opts_cond|ignore_proteins_per_peptide: False adv_opts_cond|scan_regex: adv_opts_cond|no_spectra_data_override: False adv_opts_cond|no_spectra_references_override: False adv_opts_cond|add_ionmatch_annotation: 0.0 adv_opts_cond|concatenate_peptides: False adv_opts_cond|number_of_hits: 1 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 |
IDFileConverter_17_input.idXML value |
| Test-17 |
in: IDFileConverter_18_input.idXML out_type: pepXML mz_name: peptideprophet_analyzed: False score_type: qvalue adv_opts_cond|ignore_proteins_per_peptide: False adv_opts_cond|scan_regex: adv_opts_cond|no_spectra_data_override: False adv_opts_cond|no_spectra_references_override: False adv_opts_cond|add_ionmatch_annotation: 0.0 adv_opts_cond|concatenate_peptides: False adv_opts_cond|number_of_hits: 1 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 |
IDFileConverter_18_input.idXML value |
| Test-18 |
in: IDFileConverter_19_input.idXML out_type: pepXML mz_name: peptideprophet_analyzed: False score_type: qvalue adv_opts_cond|ignore_proteins_per_peptide: False adv_opts_cond|scan_regex: adv_opts_cond|no_spectra_data_override: False adv_opts_cond|no_spectra_references_override: False adv_opts_cond|add_ionmatch_annotation: 0.0 adv_opts_cond|concatenate_peptides: False adv_opts_cond|number_of_hits: 1 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 |
IDFileConverter_19_input.idXML value |
| Test-19 |
in: IDFileConverter_20_input.idXML out_type: pepXML mz_name: peptideprophet_analyzed: False score_type: qvalue adv_opts_cond|ignore_proteins_per_peptide: False adv_opts_cond|scan_regex: adv_opts_cond|no_spectra_data_override: False adv_opts_cond|no_spectra_references_override: False adv_opts_cond|add_ionmatch_annotation: 0.0 adv_opts_cond|concatenate_peptides: False adv_opts_cond|number_of_hits: 1 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 |
IDFileConverter_20_input.idXML value |
| Test-20 |
in: IDFileConverter_21_input.idXML out_type: idXML mz_file: IDMapper_4_input.mzML mz_name: peptideprophet_analyzed: False score_type: qvalue adv_opts_cond|ignore_proteins_per_peptide: False adv_opts_cond|scan_regex: adv_opts_cond|no_spectra_data_override: False adv_opts_cond|no_spectra_references_override: False adv_opts_cond|add_ionmatch_annotation: 0.0 adv_opts_cond|concatenate_peptides: False adv_opts_cond|number_of_hits: 1 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 |
IDFileConverter_21_input.idXML IDMapper_4_input.mzML value |
| Test-21 |
in: MSGFPlusAdapter_1_out.mzid out_type: idXML mz_file: spectra.mzML mz_name: peptideprophet_analyzed: False score_type: qvalue adv_opts_cond|ignore_proteins_per_peptide: False adv_opts_cond|scan_regex: adv_opts_cond|no_spectra_data_override: False adv_opts_cond|no_spectra_references_override: False adv_opts_cond|add_ionmatch_annotation: 0.01 adv_opts_cond|concatenate_peptides: False adv_opts_cond|number_of_hits: 1 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 |
MSGFPlusAdapter_1_out.mzid spectra.mzML value |
| Test-22 |
in: IDFileConverter_23_input.mzid out_type: idXML mz_name: peptideprophet_analyzed: False score_type: qvalue adv_opts_cond|ignore_proteins_per_peptide: False adv_opts_cond|scan_regex: adv_opts_cond|no_spectra_data_override: False adv_opts_cond|no_spectra_references_override: False adv_opts_cond|add_ionmatch_annotation: 0.0 adv_opts_cond|concatenate_peptides: False adv_opts_cond|number_of_hits: 1 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 |
IDFileConverter_23_input.mzid value |
| Test-23 |
in: IDFileConverter_24_input.pep.xml out_type: idXML mz_name: peptideprophet_analyzed: False score_type: qvalue adv_opts_cond|ignore_proteins_per_peptide: False adv_opts_cond|scan_regex: adv_opts_cond|no_spectra_data_override: False adv_opts_cond|no_spectra_references_override: False adv_opts_cond|add_ionmatch_annotation: 0.0 adv_opts_cond|concatenate_peptides: False adv_opts_cond|number_of_hits: 1 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 |
IDFileConverter_24_input.pep.xml value |
| Test-24 |
in: IDFileConverter_25_input.idXML out_type: pepXML mz_name: peptideprophet_analyzed: False score_type: qvalue adv_opts_cond|ignore_proteins_per_peptide: False adv_opts_cond|scan_regex: adv_opts_cond|no_spectra_data_override: False adv_opts_cond|no_spectra_references_override: False adv_opts_cond|add_ionmatch_annotation: 0.0 adv_opts_cond|concatenate_peptides: False adv_opts_cond|number_of_hits: 1 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 |
IDFileConverter_25_input.idXML value |
| Test-25 |
in: IDFileConverter_26_input.mzid out_type: idXML mz_name: peptideprophet_analyzed: False score_type: qvalue adv_opts_cond|ignore_proteins_per_peptide: False adv_opts_cond|scan_regex: adv_opts_cond|no_spectra_data_override: False adv_opts_cond|no_spectra_references_override: False adv_opts_cond|add_ionmatch_annotation: 0.0 adv_opts_cond|concatenate_peptides: False adv_opts_cond|number_of_hits: 1 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 |
IDFileConverter_26_input.mzid value |
| Test-26 |
in: IDFileConverter_27_input.idXML out_type: FASTA mz_name: peptideprophet_analyzed: False score_type: qvalue adv_opts_cond|ignore_proteins_per_peptide: False adv_opts_cond|scan_regex: adv_opts_cond|no_spectra_data_override: False adv_opts_cond|no_spectra_references_override: False adv_opts_cond|add_ionmatch_annotation: 0.0 adv_opts_cond|concatenate_peptides: False adv_opts_cond|number_of_hits: 1 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 |
IDFileConverter_27_input.idXML value |
| Test-27 |
in: IDFileConverter_27_input.idXML out_type: FASTA mz_name: peptideprophet_analyzed: False score_type: qvalue adv_opts_cond|ignore_proteins_per_peptide: False adv_opts_cond|scan_regex: adv_opts_cond|no_spectra_data_override: False adv_opts_cond|no_spectra_references_override: False adv_opts_cond|add_ionmatch_annotation: 0.0 adv_opts_cond|concatenate_peptides: False adv_opts_cond|number_of_hits: -1 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 |
IDFileConverter_27_input.idXML value |
| Test-28 |
in: IDFileConverter_27_input.idXML out_type: FASTA mz_name: peptideprophet_analyzed: False score_type: qvalue adv_opts_cond|ignore_proteins_per_peptide: False adv_opts_cond|scan_regex: adv_opts_cond|no_spectra_data_override: False adv_opts_cond|no_spectra_references_override: False adv_opts_cond|add_ionmatch_annotation: 0.0 adv_opts_cond|concatenate_peptides: True adv_opts_cond|number_of_hits: 1 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 |
IDFileConverter_27_input.idXML value |
| Test-29 |
in: IDFileConverter_27_input.idXML out_type: FASTA mz_name: peptideprophet_analyzed: False score_type: qvalue adv_opts_cond|ignore_proteins_per_peptide: False adv_opts_cond|scan_regex: adv_opts_cond|no_spectra_data_override: False adv_opts_cond|no_spectra_references_override: False adv_opts_cond|add_ionmatch_annotation: 0.0 adv_opts_cond|concatenate_peptides: True adv_opts_cond|number_of_hits: 2 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 |
IDFileConverter_27_input.idXML value |
| Test-30 |
in: IDFileConverter_31_input.mzid out_type: idXML mz_name: peptideprophet_analyzed: False score_type: qvalue adv_opts_cond|ignore_proteins_per_peptide: False adv_opts_cond|scan_regex: adv_opts_cond|no_spectra_data_override: False adv_opts_cond|no_spectra_references_override: False adv_opts_cond|add_ionmatch_annotation: 0.0 adv_opts_cond|concatenate_peptides: False adv_opts_cond|number_of_hits: 1 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 |
IDFileConverter_31_input.mzid value |