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