| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_isobaricanalyzer/IsobaricAnalyzer/2.6+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_isobaricanalyzer/IsobaricAnalyzer/2.5+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_isobaricanalyzer/IsobaricAnalyzer/2.3.0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_isobaricanalyzer/IsobaricAnalyzer/2.2.0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_isobaricanalyzer/IsobaricAnalyzer/2.1.0 |
| IsobaricAnalyzer |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| openms | 2.5 | package |
| openms-thirdparty | 2.5 | package |
| blast | 2.9.0 | package |
| openjdk | 8.0.192 | package |
| ctdopts | 1.4 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
type: itraq4plex in: IsobaricAnalyzer_input_1.mzML extraction|select_activation: extraction|reporter_mass_shift: 0.1 extraction|min_precursor_intensity: 1.0 extraction|keep_unannotated_precursor: True extraction|min_reporter_intensity: 0.0 extraction|discard_low_intensity_quantifications: False extraction|min_precursor_purity: 0.0 extraction|precursor_isotope_deviation: 10.0 extraction|purity_interpolation: True itraq4plex|channel_114_description: l1 itraq4plex|channel_115_description: l2 itraq4plex|channel_116_description: l3 itraq4plex|channel_117_description: lung itraq4plex|reference_channel: 114 itraq4plex|correction_matrix: "0.0/1.0/5.9/0.2" "0.0/2.0/5.6/0.1" "0.0/3.0/4.5/0.1" "0.1/4.0/3.5/0.1" itraq8plex|channel_113_description: itraq8plex|channel_114_description: itraq8plex|channel_115_description: itraq8plex|channel_116_description: itraq8plex|channel_117_description: itraq8plex|channel_118_description: itraq8plex|channel_119_description: itraq8plex|channel_121_description: itraq8plex|reference_channel: 113 itraq8plex|correction_matrix: "0.00/0.00/6.89/0.22" "0.00/0.94/5.90/0.16" "0.00/1.88/4.90/0.10" "0.00/2.82/3.90/0.07" "0.06/3.77/2.99/0.00" "0.09/4.71/1.88/0.00" "0.14/5.66/0.87/0.00" "0.27/7.44/0.18/0.00" quantification|isotope_correction: True quantification|normalization: False tmt10plex|channel_126_description: tmt10plex|channel_127N_description: tmt10plex|channel_127C_description: tmt10plex|channel_128N_description: tmt10plex|channel_128C_description: tmt10plex|channel_129N_description: tmt10plex|channel_129C_description: tmt10plex|channel_130N_description: tmt10plex|channel_130C_description: tmt10plex|channel_131_description: tmt10plex|reference_channel: 126 tmt10plex|correction_matrix: "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" tmt11plex|channel_126_description: tmt11plex|channel_127N_description: tmt11plex|channel_127C_description: tmt11plex|channel_128N_description: tmt11plex|channel_128C_description: tmt11plex|channel_129N_description: tmt11plex|channel_129C_description: tmt11plex|channel_130N_description: tmt11plex|channel_130C_description: tmt11plex|channel_131N_description: tmt11plex|channel_131C_description: tmt11plex|reference_channel: 126 tmt11plex|correction_matrix: "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" tmt16plex|channel_126_description: tmt16plex|channel_127N_description: tmt16plex|channel_127C_description: tmt16plex|channel_128N_description: tmt16plex|channel_128C_description: tmt16plex|channel_129N_description: tmt16plex|channel_129C_description: tmt16plex|channel_130N_description: tmt16plex|channel_130C_description: tmt16plex|channel_131N_description: tmt16plex|channel_131C_description: tmt16plex|channel_132N_description: tmt16plex|channel_132C_description: tmt16plex|channel_133N_description: tmt16plex|channel_133C_description: tmt16plex|channel_134N_description: tmt16plex|reference_channel: 126 tmt16plex|correction_matrix: "0.0/0.0/8.02/0.0" "0.0/0.68/7.46/0.0" "0.0/0.71/6.94/0.0" "0.0/1.88/6.67/0.0" "0.0/1.34/5.59/0.0" "0.0/2.41/5.48/0.0" "0.0/2.34/5.19/0.0" "0.0/3.53/4.57/0.0" "0.0/2.67/4.16/0.0" "0.0/3.92/3.73/0.0" "0.0/3.69/3.14/0.0" "0.0/3.22/2.76/0.0" "0.0/4.11/2.0/0.0" "0.0/3.85/1.58/0.0" "0.0/4.63/1.18/0.0" "0.0/5.22/0.86/0.0" tmt6plex|channel_126_description: tmt6plex|channel_127_description: tmt6plex|channel_128_description: tmt6plex|channel_129_description: tmt6plex|channel_130_description: tmt6plex|channel_131_description: tmt6plex|reference_channel: 126 tmt6plex|correction_matrix: "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" 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 |
IsobaricAnalyzer_input_1.mzML value |
| Test-2 |
type: itraq4plex in: TMTTenPlexMethod_test.mzML extraction|select_activation: High-energy collision-induced dissociation extraction|reporter_mass_shift: 0.002 extraction|min_precursor_intensity: 1.0 extraction|keep_unannotated_precursor: True extraction|min_reporter_intensity: 0.0 extraction|discard_low_intensity_quantifications: False extraction|min_precursor_purity: 0.0 extraction|precursor_isotope_deviation: 10.0 extraction|purity_interpolation: True itraq4plex|channel_114_description: itraq4plex|channel_115_description: itraq4plex|channel_116_description: itraq4plex|channel_117_description: itraq4plex|reference_channel: 114 itraq4plex|correction_matrix: "0.0/1.0/5.9/0.2" "0.0/2.0/5.6/0.1" "0.0/3.0/4.5/0.1" "0.1/4.0/3.5/0.1" itraq8plex|channel_113_description: itraq8plex|channel_114_description: itraq8plex|channel_115_description: itraq8plex|channel_116_description: itraq8plex|channel_117_description: itraq8plex|channel_118_description: itraq8plex|channel_119_description: itraq8plex|channel_121_description: itraq8plex|reference_channel: 113 itraq8plex|correction_matrix: "0.00/0.00/6.89/0.22" "0.00/0.94/5.90/0.16" "0.00/1.88/4.90/0.10" "0.00/2.82/3.90/0.07" "0.06/3.77/2.99/0.00" "0.09/4.71/1.88/0.00" "0.14/5.66/0.87/0.00" "0.27/7.44/0.18/0.00" quantification|isotope_correction: True quantification|normalization: False tmt10plex|channel_126_description: tmt10plex|channel_127N_description: tmt10plex|channel_127C_description: tmt10plex|channel_128N_description: tmt10plex|channel_128C_description: tmt10plex|channel_129N_description: tmt10plex|channel_129C_description: tmt10plex|channel_130N_description: tmt10plex|channel_130C_description: tmt10plex|channel_131_description: tmt10plex|reference_channel: 126 tmt10plex|correction_matrix: "0.0/0.0/5.0/0.0" "0.0/0.2/4.6/0.0" "0.0/0.2/4.6/0.3" "0.0/0.9/4.7/0.2" "0.0/0.5/3.2/0.0" "0.0/0.7/3.3/0.0" "0.0/1.3/2.5/0.0" "0.0/1.2/2.8/2.7" "0.0/1.5/2.0/0.0" "0.0/1.5/1.9/0.0" tmt11plex|channel_126_description: tmt11plex|channel_127N_description: tmt11plex|channel_127C_description: tmt11plex|channel_128N_description: tmt11plex|channel_128C_description: tmt11plex|channel_129N_description: tmt11plex|channel_129C_description: tmt11plex|channel_130N_description: tmt11plex|channel_130C_description: tmt11plex|channel_131N_description: tmt11plex|channel_131C_description: tmt11plex|reference_channel: 126 tmt11plex|correction_matrix: "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" tmt16plex|channel_126_description: tmt16plex|channel_127N_description: tmt16plex|channel_127C_description: tmt16plex|channel_128N_description: tmt16plex|channel_128C_description: tmt16plex|channel_129N_description: tmt16plex|channel_129C_description: tmt16plex|channel_130N_description: tmt16plex|channel_130C_description: tmt16plex|channel_131N_description: tmt16plex|channel_131C_description: tmt16plex|channel_132N_description: tmt16plex|channel_132C_description: tmt16plex|channel_133N_description: tmt16plex|channel_133C_description: tmt16plex|channel_134N_description: tmt16plex|reference_channel: 126 tmt16plex|correction_matrix: "0.0/0.0/8.02/0.0" "0.0/0.68/7.46/0.0" "0.0/0.71/6.94/0.0" "0.0/1.88/6.67/0.0" "0.0/1.34/5.59/0.0" "0.0/2.41/5.48/0.0" "0.0/2.34/5.19/0.0" "0.0/3.53/4.57/0.0" "0.0/2.67/4.16/0.0" "0.0/3.92/3.73/0.0" "0.0/3.69/3.14/0.0" "0.0/3.22/2.76/0.0" "0.0/4.11/2.0/0.0" "0.0/3.85/1.58/0.0" "0.0/4.63/1.18/0.0" "0.0/5.22/0.86/0.0" tmt6plex|channel_126_description: tmt6plex|channel_127_description: tmt6plex|channel_128_description: tmt6plex|channel_129_description: tmt6plex|channel_130_description: tmt6plex|channel_131_description: tmt6plex|reference_channel: 126 tmt6plex|correction_matrix: "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" 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 |
TMTTenPlexMethod_test.mzML value |
| Test-3 |
type: itraq4plex in: TMTTenPlexMethod_test.mzML extraction|select_activation: High-energy collision-induced dissociation extraction|reporter_mass_shift: 0.002 extraction|min_precursor_intensity: 1.0 extraction|keep_unannotated_precursor: True extraction|min_reporter_intensity: 0.0 extraction|discard_low_intensity_quantifications: False extraction|min_precursor_purity: 0.0 extraction|precursor_isotope_deviation: 10.0 extraction|purity_interpolation: True itraq4plex|channel_114_description: itraq4plex|channel_115_description: itraq4plex|channel_116_description: itraq4plex|channel_117_description: itraq4plex|reference_channel: 114 itraq4plex|correction_matrix: "0.0/1.0/5.9/0.2" "0.0/2.0/5.6/0.1" "0.0/3.0/4.5/0.1" "0.1/4.0/3.5/0.1" itraq8plex|channel_113_description: itraq8plex|channel_114_description: itraq8plex|channel_115_description: itraq8plex|channel_116_description: itraq8plex|channel_117_description: itraq8plex|channel_118_description: itraq8plex|channel_119_description: itraq8plex|channel_121_description: itraq8plex|reference_channel: 113 itraq8plex|correction_matrix: "0.00/0.00/6.89/0.22" "0.00/0.94/5.90/0.16" "0.00/1.88/4.90/0.10" "0.00/2.82/3.90/0.07" "0.06/3.77/2.99/0.00" "0.09/4.71/1.88/0.00" "0.14/5.66/0.87/0.00" "0.27/7.44/0.18/0.00" quantification|isotope_correction: True quantification|normalization: False tmt10plex|channel_126_description: tmt10plex|channel_127N_description: tmt10plex|channel_127C_description: tmt10plex|channel_128N_description: tmt10plex|channel_128C_description: tmt10plex|channel_129N_description: tmt10plex|channel_129C_description: tmt10plex|channel_130N_description: tmt10plex|channel_130C_description: tmt10plex|channel_131_description: tmt10plex|reference_channel: 126 tmt10plex|correction_matrix: "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" tmt11plex|channel_126_description: tmt11plex|channel_127N_description: tmt11plex|channel_127C_description: tmt11plex|channel_128N_description: tmt11plex|channel_128C_description: tmt11plex|channel_129N_description: tmt11plex|channel_129C_description: tmt11plex|channel_130N_description: tmt11plex|channel_130C_description: tmt11plex|channel_131N_description: tmt11plex|channel_131C_description: tmt11plex|reference_channel: 126 tmt11plex|correction_matrix: "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" tmt16plex|channel_126_description: tmt16plex|channel_127N_description: tmt16plex|channel_127C_description: tmt16plex|channel_128N_description: tmt16plex|channel_128C_description: tmt16plex|channel_129N_description: tmt16plex|channel_129C_description: tmt16plex|channel_130N_description: tmt16plex|channel_130C_description: tmt16plex|channel_131N_description: tmt16plex|channel_131C_description: tmt16plex|channel_132N_description: tmt16plex|channel_132C_description: tmt16plex|channel_133N_description: tmt16plex|channel_133C_description: tmt16plex|channel_134N_description: tmt16plex|reference_channel: 126 tmt16plex|correction_matrix: "0.0/0.0/8.02/0.0" "0.0/0.68/7.46/0.0" "0.0/0.71/6.94/0.0" "0.0/1.88/6.67/0.0" "0.0/1.34/5.59/0.0" "0.0/2.41/5.48/0.0" "0.0/2.34/5.19/0.0" "0.0/3.53/4.57/0.0" "0.0/2.67/4.16/0.0" "0.0/3.92/3.73/0.0" "0.0/3.69/3.14/0.0" "0.0/3.22/2.76/0.0" "0.0/4.11/2.0/0.0" "0.0/3.85/1.58/0.0" "0.0/4.63/1.18/0.0" "0.0/5.22/0.86/0.0" tmt6plex|channel_126_description: tmt6plex|channel_127_description: tmt6plex|channel_128_description: tmt6plex|channel_129_description: tmt6plex|channel_130_description: tmt6plex|channel_131_description: tmt6plex|reference_channel: 126 tmt6plex|correction_matrix: "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" 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 |
TMTTenPlexMethod_test.mzML value |
| Test-4 |
type: tmt10plex in: MS3_nonHierarchical.mzML extraction|select_activation: Collision-induced dissociation extraction|reporter_mass_shift: 0.002 extraction|min_precursor_intensity: 1.0 extraction|keep_unannotated_precursor: True extraction|min_reporter_intensity: 0.0 extraction|discard_low_intensity_quantifications: False extraction|min_precursor_purity: 0.0 extraction|precursor_isotope_deviation: 10.0 extraction|purity_interpolation: True itraq4plex|channel_114_description: itraq4plex|channel_115_description: itraq4plex|channel_116_description: itraq4plex|channel_117_description: itraq4plex|reference_channel: 114 itraq4plex|correction_matrix: "0.0/1.0/5.9/0.2" "0.0/2.0/5.6/0.1" "0.0/3.0/4.5/0.1" "0.1/4.0/3.5/0.1" itraq8plex|channel_113_description: itraq8plex|channel_114_description: itraq8plex|channel_115_description: itraq8plex|channel_116_description: itraq8plex|channel_117_description: itraq8plex|channel_118_description: itraq8plex|channel_119_description: itraq8plex|channel_121_description: itraq8plex|reference_channel: 113 itraq8plex|correction_matrix: "0.00/0.00/6.89/0.22" "0.00/0.94/5.90/0.16" "0.00/1.88/4.90/0.10" "0.00/2.82/3.90/0.07" "0.06/3.77/2.99/0.00" "0.09/4.71/1.88/0.00" "0.14/5.66/0.87/0.00" "0.27/7.44/0.18/0.00" quantification|isotope_correction: True quantification|normalization: False tmt10plex|channel_126_description: tmt10plex|channel_127N_description: tmt10plex|channel_127C_description: tmt10plex|channel_128N_description: tmt10plex|channel_128C_description: tmt10plex|channel_129N_description: tmt10plex|channel_129C_description: tmt10plex|channel_130N_description: tmt10plex|channel_130C_description: tmt10plex|channel_131_description: tmt10plex|reference_channel: 126 tmt10plex|correction_matrix: "0.0/0.0/5.09/0.0" "0.0/0.25/5.27/0.0" "0.0/0.37/5.36/0.15" "0.0/0.65/4.17/0.1" "0.08/0.49/3.06/0.0" "0.01/0.71/3.07/0.0" "0.0/1.32/2.62/0.0" "0.02/1.28/2.75/2.53" "0.03/2.08/2.23/0.0" "0.08/1.99/1.65/0.0" tmt11plex|channel_126_description: tmt11plex|channel_127N_description: tmt11plex|channel_127C_description: tmt11plex|channel_128N_description: tmt11plex|channel_128C_description: tmt11plex|channel_129N_description: tmt11plex|channel_129C_description: tmt11plex|channel_130N_description: tmt11plex|channel_130C_description: tmt11plex|channel_131N_description: tmt11plex|channel_131C_description: tmt11plex|reference_channel: 126 tmt11plex|correction_matrix: "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" tmt16plex|channel_126_description: tmt16plex|channel_127N_description: tmt16plex|channel_127C_description: tmt16plex|channel_128N_description: tmt16plex|channel_128C_description: tmt16plex|channel_129N_description: tmt16plex|channel_129C_description: tmt16plex|channel_130N_description: tmt16plex|channel_130C_description: tmt16plex|channel_131N_description: tmt16plex|channel_131C_description: tmt16plex|channel_132N_description: tmt16plex|channel_132C_description: tmt16plex|channel_133N_description: tmt16plex|channel_133C_description: tmt16plex|channel_134N_description: tmt16plex|reference_channel: 126 tmt16plex|correction_matrix: "0.0/0.0/8.02/0.0" "0.0/0.68/7.46/0.0" "0.0/0.71/6.94/0.0" "0.0/1.88/6.67/0.0" "0.0/1.34/5.59/0.0" "0.0/2.41/5.48/0.0" "0.0/2.34/5.19/0.0" "0.0/3.53/4.57/0.0" "0.0/2.67/4.16/0.0" "0.0/3.92/3.73/0.0" "0.0/3.69/3.14/0.0" "0.0/3.22/2.76/0.0" "0.0/4.11/2.0/0.0" "0.0/3.85/1.58/0.0" "0.0/4.63/1.18/0.0" "0.0/5.22/0.86/0.0" tmt6plex|channel_126_description: tmt6plex|channel_127_description: tmt6plex|channel_128_description: tmt6plex|channel_129_description: tmt6plex|channel_130_description: tmt6plex|channel_131_description: tmt6plex|reference_channel: 126 tmt6plex|correction_matrix: "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" 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 |
MS3_nonHierarchical.mzML value |