| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermultiplex/FeatureFinderMultiplex/2.8+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermultiplex/FeatureFinderMultiplex/2.6+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermultiplex/FeatureFinderMultiplex/2.5+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermultiplex/FeatureFinderMultiplex/2.3.0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermultiplex/FeatureFinderMultiplex/2.2.0.1 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermultiplex/FeatureFinderMultiplex/2.2.0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermultiplex/FeatureFinderMultiplex/2.1.0 |
| FeatureFinderMultiplex |
| 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: FeatureFinderMultiplex_1_input.mzML algorithm|labels: [Dimethyl0][Dimethyl8] algorithm|charge: 1:4 algorithm|isotopes_per_peptide: 3:6 algorithm|rt_typical: 90.0 algorithm|rt_band: 10.0 algorithm|rt_min: 5.0 algorithm|mz_tolerance: 40.0 algorithm|mz_unit: ppm algorithm|intensity_cutoff: 10.0 algorithm|peptide_similarity: 0.8 algorithm|averagine_similarity: 0.75 algorithm|averagine_similarity_scaling: 0.75 algorithm|missed_cleavages: 1 algorithm|spectrum_type: automatic algorithm|averagine_type: peptide algorithm|knock_out: False labels|Arg6: 6.0201290268 labels|Arg10: 10.0082686 labels|Lys4: 4.0251069836 labels|Lys6: 6.0201290268 labels|Lys8: 8.0141988132 labels|Leu3: 3.01883 labels|Dimethyl0: 28.0313 labels|Dimethyl4: 32.056407 labels|Dimethyl6: 34.063117 labels|Dimethyl8: 36.07567 labels|ICPL0: 105.021464 labels|ICPL4: 109.046571 labels|ICPL6: 111.041593 labels|ICPL10: 115.0667 adv_opts_cond|force: False adv_opts_cond|test: true adv_opts_cond|adv_opts_selector: advanced OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG', 'out_multiplets_FLAG'] |
name: value name: value name: value |
FeatureFinderMultiplex_1_input.mzML value |
| Test-2 |
in: FeatureFinderMultiplex_2_input.mzML algorithm|labels: [][Lys8,Arg10] algorithm|charge: 1:4 algorithm|isotopes_per_peptide: 3:6 algorithm|rt_typical: 40.0 algorithm|rt_band: 5.0 algorithm|rt_min: 2.0 algorithm|mz_tolerance: 6.0 algorithm|mz_unit: ppm algorithm|intensity_cutoff: 1000.0 algorithm|peptide_similarity: 0.5 algorithm|averagine_similarity: 0.4 algorithm|averagine_similarity_scaling: 0.75 algorithm|missed_cleavages: 0 algorithm|spectrum_type: automatic algorithm|averagine_type: peptide algorithm|knock_out: False labels|Arg6: 6.0201290268 labels|Arg10: 10.0082686 labels|Lys4: 4.0251069836 labels|Lys6: 6.0201290268 labels|Lys8: 8.0141988132 labels|Leu3: 3.01883 labels|Dimethyl0: 28.0313 labels|Dimethyl4: 32.056407 labels|Dimethyl6: 34.063117 labels|Dimethyl8: 36.07567 labels|ICPL0: 105.021464 labels|ICPL4: 109.046571 labels|ICPL6: 111.041593 labels|ICPL10: 115.0667 adv_opts_cond|force: False adv_opts_cond|test: true adv_opts_cond|adv_opts_selector: advanced OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG', 'out_multiplets_FLAG'] |
name: value name: value name: value |
FeatureFinderMultiplex_2_input.mzML value |
| Test-3 |
in: FeatureFinderMultiplex_3_input.mzML algorithm|labels: [] algorithm|charge: 5:15 algorithm|isotopes_per_peptide: 5:10 algorithm|rt_typical: 45.0 algorithm|rt_band: 5.0 algorithm|rt_min: 2.0 algorithm|mz_tolerance: 6.0 algorithm|mz_unit: ppm algorithm|intensity_cutoff: 200.0 algorithm|peptide_similarity: 0.5 algorithm|averagine_similarity: 0.4 algorithm|averagine_similarity_scaling: 0.75 algorithm|missed_cleavages: 0 algorithm|spectrum_type: automatic algorithm|averagine_type: RNA algorithm|knock_out: False labels|Arg6: 6.0201290268 labels|Arg10: 10.0082686 labels|Lys4: 4.0251069836 labels|Lys6: 6.0201290268 labels|Lys8: 8.0141988132 labels|Leu3: 3.01883 labels|Dimethyl0: 28.0313 labels|Dimethyl4: 32.056407 labels|Dimethyl6: 34.063117 labels|Dimethyl8: 36.07567 labels|ICPL0: 105.021464 labels|ICPL4: 109.046571 labels|ICPL6: 111.041593 labels|ICPL10: 115.0667 adv_opts_cond|force: False adv_opts_cond|test: true adv_opts_cond|adv_opts_selector: advanced OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG', 'out_multiplets_FLAG'] |
name: value name: value name: value |
FeatureFinderMultiplex_3_input.mzML value |
| Test-4 |
in: FeatureFinderMultiplex_4_input.mzML algorithm|labels: [] algorithm|charge: 5:15 algorithm|isotopes_per_peptide: 5:10 algorithm|rt_typical: 45.0 algorithm|rt_band: 5.0 algorithm|rt_min: 2.0 algorithm|mz_tolerance: 6.0 algorithm|mz_unit: ppm algorithm|intensity_cutoff: 200.0 algorithm|peptide_similarity: 0.5 algorithm|averagine_similarity: 0.4 algorithm|averagine_similarity_scaling: 0.75 algorithm|missed_cleavages: 0 algorithm|spectrum_type: automatic algorithm|averagine_type: DNA algorithm|knock_out: False labels|Arg6: 6.0201290268 labels|Arg10: 10.0082686 labels|Lys4: 4.0251069836 labels|Lys6: 6.0201290268 labels|Lys8: 8.0141988132 labels|Leu3: 3.01883 labels|Dimethyl0: 28.0313 labels|Dimethyl4: 32.056407 labels|Dimethyl6: 34.063117 labels|Dimethyl8: 36.07567 labels|ICPL0: 105.021464 labels|ICPL4: 109.046571 labels|ICPL6: 111.041593 labels|ICPL10: 115.0667 adv_opts_cond|force: False adv_opts_cond|test: true adv_opts_cond|adv_opts_selector: advanced OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG', 'out_multiplets_FLAG'] |
name: value name: value name: value |
FeatureFinderMultiplex_4_input.mzML value |
| Test-5 |
in: FeatureFinderMultiplex_5_input.mzML algorithm|labels: [Dimethyl0][Dimethyl6] algorithm|charge: 1:5 algorithm|isotopes_per_peptide: 3:6 algorithm|rt_typical: 50.0 algorithm|rt_band: 3.0 algorithm|rt_min: 8.0 algorithm|mz_tolerance: 10.0 algorithm|mz_unit: ppm algorithm|intensity_cutoff: 10000000.0 algorithm|peptide_similarity: 0.95 algorithm|averagine_similarity: 0.8 algorithm|averagine_similarity_scaling: 0.95 algorithm|missed_cleavages: 3 algorithm|spectrum_type: profile algorithm|averagine_type: peptide algorithm|knock_out: False labels|Arg6: 6.0201290268 labels|Arg10: 10.0082686 labels|Lys4: 4.0251069836 labels|Lys6: 6.0201290268 labels|Lys8: 8.0141988132 labels|Leu3: 3.01883 labels|Dimethyl0: 28.0313 labels|Dimethyl4: 32.056407 labels|Dimethyl6: 34.063117 labels|Dimethyl8: 36.07567 labels|ICPL0: 105.021464 labels|ICPL4: 109.046571 labels|ICPL6: 111.041593 labels|ICPL10: 115.0667 adv_opts_cond|force: False adv_opts_cond|test: true adv_opts_cond|adv_opts_selector: advanced OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG', 'out_multiplets_FLAG'] |
name: value name: value name: value |
FeatureFinderMultiplex_5_input.mzML value |
| Test-6 |
in: FeatureFinderMultiplex_6_input.mzML algorithm|labels: [Dimethyl0][Dimethyl6] algorithm|charge: 1:5 algorithm|isotopes_per_peptide: 3:6 algorithm|rt_typical: 50.0 algorithm|rt_band: 3.0 algorithm|rt_min: 8.0 algorithm|mz_tolerance: 10.0 algorithm|mz_unit: ppm algorithm|intensity_cutoff: 10000000.0 algorithm|peptide_similarity: 0.95 algorithm|averagine_similarity: 0.8 algorithm|averagine_similarity_scaling: 1.0 algorithm|missed_cleavages: 3 algorithm|spectrum_type: profile algorithm|averagine_type: peptide algorithm|knock_out: False labels|Arg6: 6.0201290268 labels|Arg10: 10.0082686 labels|Lys4: 4.0251069836 labels|Lys6: 6.0201290268 labels|Lys8: 8.0141988132 labels|Leu3: 3.01883 labels|Dimethyl0: 28.0313 labels|Dimethyl4: 32.056407 labels|Dimethyl6: 34.063117 labels|Dimethyl8: 36.07567 labels|ICPL0: 105.021464 labels|ICPL4: 109.046571 labels|ICPL6: 111.041593 labels|ICPL10: 115.0667 adv_opts_cond|force: False adv_opts_cond|test: true adv_opts_cond|adv_opts_selector: advanced OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG', 'out_multiplets_FLAG'] |
name: value name: value name: value |
FeatureFinderMultiplex_6_input.mzML value |
| Test-7 |
in: FeatureFinderMultiplex_7_input.mzML algorithm|labels: [][Dimethyl4] algorithm|charge: 1:4 algorithm|isotopes_per_peptide: 3:6 algorithm|rt_typical: 40.0 algorithm|rt_band: 5.0 algorithm|rt_min: 2.0 algorithm|mz_tolerance: 6.0 algorithm|mz_unit: ppm algorithm|intensity_cutoff: 1000.0 algorithm|peptide_similarity: 0.5 algorithm|averagine_similarity: 0.4 algorithm|averagine_similarity_scaling: 0.75 algorithm|missed_cleavages: 0 algorithm|spectrum_type: automatic algorithm|averagine_type: peptide algorithm|knock_out: False labels|Arg6: 6.0201290268 labels|Arg10: 10.0082686 labels|Lys4: 4.0251069836 labels|Lys6: 6.0201290268 labels|Lys8: 8.0141988132 labels|Leu3: 3.01883 labels|Dimethyl0: 28.0313 labels|Dimethyl4: 31.0094 labels|Dimethyl6: 34.063117 labels|Dimethyl8: 36.07567 labels|ICPL0: 105.021464 labels|ICPL4: 109.046571 labels|ICPL6: 111.041593 labels|ICPL10: 115.0667 adv_opts_cond|force: False adv_opts_cond|test: true adv_opts_cond|adv_opts_selector: advanced OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG', 'out_multiplets_FLAG'] |
name: value name: value name: value |
FeatureFinderMultiplex_7_input.mzML value |
| Test-8 |
in: FeatureFinderMultiplex_8_input.mzML algorithm|labels: [Dimethyl0][Dimethyl4][Dimethyl8] algorithm|charge: 1:7 algorithm|isotopes_per_peptide: 3:8 algorithm|rt_typical: 50.0 algorithm|rt_band: 3.0 algorithm|rt_min: 8.0 algorithm|mz_tolerance: 10.0 algorithm|mz_unit: ppm algorithm|intensity_cutoff: 10.0 algorithm|peptide_similarity: 0.2 algorithm|averagine_similarity: 0.25 algorithm|averagine_similarity_scaling: 0.95 algorithm|missed_cleavages: 4 algorithm|spectrum_type: automatic algorithm|averagine_type: peptide algorithm|knock_out: True labels|Arg6: 6.0201290268 labels|Arg10: 10.0082686 labels|Lys4: 4.0251069836 labels|Lys6: 6.0201290268 labels|Lys8: 8.0141988132 labels|Leu3: 3.01883 labels|Dimethyl0: 28.0313 labels|Dimethyl4: 32.056407 labels|Dimethyl6: 34.063117 labels|Dimethyl8: 36.07567 labels|ICPL0: 105.021464 labels|ICPL4: 109.046571 labels|ICPL6: 111.041593 labels|ICPL10: 115.0667 adv_opts_cond|force: False adv_opts_cond|test: true adv_opts_cond|adv_opts_selector: advanced OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG', 'out_multiplets_FLAG'] |
name: value name: value name: value |
FeatureFinderMultiplex_8_input.mzML value |
| Test-9 |
in: FeatureFinderMultiplex_9_input.mzML algorithm|labels: [0][6.03705] algorithm|charge: 2:8 algorithm|isotopes_per_peptide: 3:8 algorithm|rt_typical: 40.0 algorithm|rt_band: 0.0 algorithm|rt_min: 4.0 algorithm|mz_tolerance: 10.0 algorithm|mz_unit: ppm algorithm|intensity_cutoff: 1000.0 algorithm|peptide_similarity: 0.5 algorithm|averagine_similarity: 0.4 algorithm|averagine_similarity_scaling: 0.95 algorithm|missed_cleavages: 0 algorithm|spectrum_type: centroid algorithm|averagine_type: peptide algorithm|knock_out: False labels|Arg6: 6.0201290268 labels|Arg10: 10.0082686 labels|Lys4: 4.0251069836 labels|Lys6: 6.0201290268 labels|Lys8: 8.0141988132 labels|Leu3: 3.01883 labels|Dimethyl0: 28.0313 labels|Dimethyl4: 32.056407 labels|Dimethyl6: 34.063117 labels|Dimethyl8: 36.07567 labels|ICPL0: 105.021464 labels|ICPL4: 109.046571 labels|ICPL6: 111.041593 labels|ICPL10: 115.0667 adv_opts_cond|force: False adv_opts_cond|test: true adv_opts_cond|adv_opts_selector: advanced OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG', 'out_multiplets_FLAG'] |
name: value name: value name: value |
FeatureFinderMultiplex_9_input.mzML value |
| Test-10 |
in: FeatureFinderMultiplex_10_input.mzML algorithm|labels: [Dimethyl0][Dimethyl6] algorithm|charge: 1:7 algorithm|isotopes_per_peptide: 3:6 algorithm|rt_typical: 50.0 algorithm|rt_band: 5.0 algorithm|rt_min: 8.0 algorithm|mz_tolerance: 6.0 algorithm|mz_unit: ppm algorithm|intensity_cutoff: 10.0 algorithm|peptide_similarity: 0.4 algorithm|averagine_similarity: 0.5 algorithm|averagine_similarity_scaling: 0.95 algorithm|missed_cleavages: 3 algorithm|spectrum_type: profile algorithm|averagine_type: peptide algorithm|knock_out: True labels|Arg6: 6.0201290268 labels|Arg10: 10.0082686 labels|Lys4: 4.0251069836 labels|Lys6: 6.0201290268 labels|Lys8: 8.0141988132 labels|Leu3: 3.01883 labels|Dimethyl0: 28.0313 labels|Dimethyl4: 32.056407 labels|Dimethyl6: 34.063117 labels|Dimethyl8: 36.07567 labels|ICPL0: 105.021464 labels|ICPL4: 109.046571 labels|ICPL6: 111.041593 labels|ICPL10: 115.0667 adv_opts_cond|force: False adv_opts_cond|test: true adv_opts_cond|adv_opts_selector: advanced OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG', 'out_multiplets_FLAG'] |
name: value name: value name: value |
FeatureFinderMultiplex_10_input.mzML value |
| Test-11 |
in: FeatureFinderMultiplex_11_input.mzML algorithm|labels: [] algorithm|charge: 1:4 algorithm|isotopes_per_peptide: 3:6 algorithm|rt_typical: 1e-05 algorithm|rt_band: 0.0 algorithm|rt_min: 0.0 algorithm|mz_tolerance: 10.0 algorithm|mz_unit: ppm algorithm|intensity_cutoff: 1000.0 algorithm|peptide_similarity: 0.5 algorithm|averagine_similarity: 0.7 algorithm|averagine_similarity_scaling: 0.95 algorithm|missed_cleavages: 0 algorithm|spectrum_type: automatic algorithm|averagine_type: peptide algorithm|knock_out: False labels|Arg6: 6.0201290268 labels|Arg10: 10.0082686 labels|Lys4: 4.0251069836 labels|Lys6: 6.0201290268 labels|Lys8: 8.0141988132 labels|Leu3: 3.01883 labels|Dimethyl0: 28.0313 labels|Dimethyl4: 32.056407 labels|Dimethyl6: 34.063117 labels|Dimethyl8: 36.07567 labels|ICPL0: 105.021464 labels|ICPL4: 109.046571 labels|ICPL6: 111.041593 labels|ICPL10: 115.0667 adv_opts_cond|force: False adv_opts_cond|test: true adv_opts_cond|adv_opts_selector: advanced OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG'] |
name: value name: value |
FeatureFinderMultiplex_11_input.mzML value |