| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.19052.1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.19052.0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/0.3.0 |
| msconvert |
| Requirements (dependencies defined in the <requirements> tag set) |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input: small.mzML license_agreement: True output_type: mzML data_processing|peak_picking|pick_peaks_ms_levels: 1- data_processing|peak_picking|pick_peaks_algorithm: cwt data_processing|peak_picking|pick_peaks: True |
name: value |
small.mzML value |
| Test-2 |
input: small.RAW license_agreement: True output_type: mzML data_processing|peak_picking|pick_peaks_ms_levels: 1- data_processing|peak_picking|pick_peaks_algorithm: vendor data_processing|peak_picking|pick_peaks: True |
name: value |
small.RAW value |
| Test-3 |
input: ThyroglobMRM000003.d.tar license_agreement: True output_type: mzML general_options|combineIonMobilitySpectra: True general_options|scan_summing|do_scan_summing: True |
name: value |
ThyroglobMRM000003.d.tar value |
| Test-4 |
input: MassLynxTest.raw.tar license_agreement: True output_type: mzML |
name: value |
MassLynxTest.raw.tar value |
| Test-5 |
input: AgilentMassHunterTest.d.tar license_agreement: True output_type: mzXML |
name: value |
AgilentMassHunterTest.d.tar value |
| Test-6 |
input: BrukerBafTest.d.tar license_agreement: True output_type: mzML data_processing|peak_picking|pick_peaks_ms_levels: 1- data_processing|peak_picking|pick_peaks_algorithm: vendor data_processing|peak_picking|pick_peaks: True |
name: value |
BrukerBafTest.d.tar value |
| Test-7 |
input: SciexTest.wiff.tar license_agreement: True output_type: mzML general_options|multi_run_output|runIndexSet: 0 general_options|multi_run_output|do_multi_run_output: False |
name: value |
SciexTest.wiff.tar value |
| Test-8 |
input: SciexTest.wiff.tar license_agreement: True output_type: mzXML filtering|indices_0|from: 0 filtering|indices_0|to: 499 general_options|srmAsSpectra: True general_options|multi_run_output|runIndexSet: 0 general_options|multi_run_output|do_multi_run_output: False |
name: value |
SciexTest.wiff.tar value |
| Test-9 |
input: SciexTest.wiff.tar license_agreement: True output_type: mzXML filtering|indices_0|from: 0 filtering|indices_0|to: 499 general_options|srmAsSpectra: True general_options|multi_run_output|runIndexSet: 1 general_options|multi_run_output|do_multi_run_output: False |
name: value |
SciexTest.wiff.tar value |
| Test-10 |
input: SciexTest.wiff.tar license_agreement: True output_type: mzML general_options|multi_run_output|run_index_set_0|from: 0 general_options|multi_run_output|run_index_set_0|to: 1 general_options|multi_run_output|do_multi_run_output: True |
SciexTest.wiff.tar |
|
| Test-11 |
input: SciexTest.wiff.tar license_agreement: True output_type: mzML general_options|multi_run_output|do_multi_run_output: True |
SciexTest.wiff.tar |
|
| Test-12 |
input: small.mzML license_agreement: True output_type: mzML data_processing|peak_picking|pick_peaks_ms_levels: 1 data_processing|peak_picking|pick_peaks_algorithm: cwt data_processing|peak_picking|pick_peaks: True |
name: value |
small.mzML value |
| Test-13 |
input: small-peakpicking-cwt-allMS.mzML license_agreement: True output_type: mz5 settings|mz_encoding: 64 settings|intensity_encoding: 64 |
name: value |
small-peakpicking-cwt-allMS.mzML value |
| Test-14 |
input: small-peakpicking-cwt-allMS.mzML license_agreement: True output_type: mzXML settings|mz_encoding: 32 settings|intensity_encoding: 32 |
name: value |
small-peakpicking-cwt-allMS.mzML value |
| Test-15 |
input: small-peakpicking-cwt-allMS.mzML license_agreement: True output_type: mzML settings|binary_compression: numpressLinearPic |
name: value |
small-peakpicking-cwt-allMS.mzML value |
| Test-16 |
input: small-peakpicking-cwt-allMS.mzML license_agreement: True output_type: mzML settings|binary_compression: numpressLinearSlof |
name: value |
small-peakpicking-cwt-allMS.mzML value |
| Test-17 |
input: small-peakpicking-cwt-allMS.mzML license_agreement: True output_type: mzML settings|binary_compression: numpressLinear |
name: value |
small-peakpicking-cwt-allMS.mzML value |
| Test-18 |
input: small-peakpicking-cwt-allMS.mzML license_agreement: True output_type: mzML settings|binary_compression: numpressPic |
name: value |
small-peakpicking-cwt-allMS.mzML value |
| Test-19 |
input: small-peakpicking-cwt-allMS.mzML license_agreement: True output_type: mzML settings|binary_compression: numpressSlof |
name: value |
small-peakpicking-cwt-allMS.mzML value |
| Test-20 |
input: Rpal_01.mz5 license_agreement: True output_type: mzML data_processing|precursor_refinement|input_ident: Rpal_01.pepXML data_processing|precursor_refinement|thresholdScore: mvh data_processing|precursor_refinement|thresholdValue: 40- data_processing|precursor_refinement|use_mzrefinement: True settings|binary_compression: numpressLinearPic |
name: value name: value |
Rpal_01.mz5 Rpal_01.pepXML value |
| Test-21 |
input: small-peakpicking-cwt-allMS.mzML license_agreement: True output_type: mzML data_processing|charge_state_calculation|predictor_overrideExistingCharge: True data_processing|charge_state_calculation|minMultipleCharge: 2 data_processing|charge_state_calculation|maxMultipleCharge: 5 data_processing|charge_state_calculation|singleChargeFractionTIC: 0.95 data_processing|charge_state_calculation|maxKnownCharge: 8 data_processing|charge_state_calculation|charge_state_calculation_method: predictor settings|binary_compression: numpressLinearPic |
name: value |
small-peakpicking-cwt-allMS.mzML value |
| Test-22 |
input: small-peakpicking-cwt-allMS.mzML license_agreement: True output_type: mzML data_processing|charge_state_calculation|minCharge: 1 data_processing|charge_state_calculation|maxCharge: 5 data_processing|charge_state_calculation|precursorsBefore: 1 data_processing|charge_state_calculation|precursorsAfter: 1 data_processing|charge_state_calculation|halfIsoWidth: 1.5 data_processing|charge_state_calculation|defaultMinCharge: 1 data_processing|charge_state_calculation|defaultMaxCharge: 5 data_processing|charge_state_calculation|charge_state_calculation_method: turbocharger settings|binary_compression: numpressLinearPic |
name: value |
small-peakpicking-cwt-allMS.mzML value |
| Test-23 |
input: D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5 license_agreement: True output_type: mzML data_processing|etd_filtering|remove_precursor: true data_processing|etd_filtering|remove_charge_reduced: true data_processing|etd_filtering|remove_neutral_loss: false data_processing|etd_filtering|blanket_removal: false data_processing|etd_filtering|matching_tolerance: 50 data_processing|etd_filtering|matching_tolerance_units: PPM data_processing|etd_filtering|do_etd_filtering: True settings|binary_compression: numpressLinearPic |
name: value |
D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5 value |
| Test-24 |
input: small-peakpicking-cwt-allMS.mzML license_agreement: True output_type: mzML data_processing|thresholds_0|threshold_type: count data_processing|thresholds_0|value: 100 data_processing|thresholds_0|orientation: most-intense data_processing|thresholds_1|threshold_type: absolute data_processing|thresholds_1|value: 1 data_processing|thresholds_1|orientation: most-intense settings|binary_compression: numpressLinearPic |
name: value |
small-peakpicking-cwt-allMS.mzML value |
| Test-25 |
input: small-peakpicking-cwt-allMS.mzML license_agreement: True output_type: mzML data_processing|filter_mz_windows|mz_window_from: 420 data_processing|filter_mz_windows|mz_window_to: 840 data_processing|filter_mz_windows|do_mzwindow_filter: True settings|binary_compression: numpressLinearPic |
name: value |
small-peakpicking-cwt-allMS.mzML value |
| Test-26 |
input: small-peakpicking-cwt-allMS.mzML license_agreement: True output_type: mzML data_processing|ms2denoise|num_peaks: 10 data_processing|ms2denoise|window_width: 40 data_processing|ms2denoise|relax: False data_processing|ms2denoise|denoise: True settings|binary_compression: numpressLinearPic |
name: value |
small-peakpicking-cwt-allMS.mzML value |
| Test-27 |
input: small-peakpicking-cwt-allMS.mzML license_agreement: True output_type: mzML data_processing|ms2deisotope: True settings|binary_compression: numpressLinearPic |
name: value |
small-peakpicking-cwt-allMS.mzML value |
| Test-28 |
input: small-peakpicking-cwt-allMS.mzML license_agreement: True output_type: mzML filtering|activation: CID settings|binary_compression: numpressLinearPic |
name: value |
small-peakpicking-cwt-allMS.mzML value |
| Test-29 |
input: small-peakpicking-cwt-allMS.mzML license_agreement: True output_type: mzML filtering|indices_0|from: 2 filtering|indices_0|to: 4 filtering|indices_1|from: 10 filtering|indices_1|to: 10 filtering|indices_2|from: 13 filtering|indices_2|to: 15 settings|binary_compression: numpressLinearPic |
name: value |
small-peakpicking-cwt-allMS.mzML value |
| Test-30 |
input: small-peakpicking-cwt-allMS.mzML license_agreement: True output_type: mzML filtering|strip_it: True settings|binary_compression: numpressLinearPic |
name: value |
small-peakpicking-cwt-allMS.mzML value |
| Test-31 |
input: small-peakpicking-cwt-allMS.mzML license_agreement: True output_type: mzML filtering|filter_ms_levels|ms_level_from: 2 filtering|filter_ms_levels|ms_level_to: 2 filtering|filter_ms_levels|do_ms_level_filter: True settings|binary_compression: numpressLinearPic |
name: value |
small-peakpicking-cwt-allMS.mzML value |
| Test-32 |
input: small-peakpicking-cwt-allMS.mzML license_agreement: True output_type: mzML filtering|polarity: positive settings|binary_compression: numpressLinearPic |
name: value |
small-peakpicking-cwt-allMS.mzML value |
| Test-33 |
input: small-peakpicking-cwt-allMS.mzML license_agreement: True output_type: mzML filtering|analyzer: IT settings|binary_compression: numpressLinearPic |
name: value |
small-peakpicking-cwt-allMS.mzML value |
| Test-34 |
input: small-peakpicking-cwt-allMS.mzML license_agreement: True output_type: mzML filtering|scan_numbers_0|from: 3 filtering|scan_numbers_0|to: 5 filtering|scan_numbers_1|from: 11 filtering|scan_numbers_1|to: 11 filtering|scan_numbers_2|from: 14 filtering|scan_numbers_2|to: 16 settings|binary_compression: numpressLinearPic |
name: value |
small-peakpicking-cwt-allMS.mzML value |