| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/4.0.0+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/4.0.0.0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/3.22.0.1 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/3.22.0.0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/3.20.1.0 |
| msstats |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| bioconductor-msstats | 4.0.0 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input|msstats_input: msstats_testfile.txt input|input_src: MSstats dp_options|selected_outputs: ['raw_data', 'featurelevel_data', 'quant_sample_matrix', 'quant_group_long'] dp_options|out_plots_opt|selected_vis_outputs: ['ProfilePlot', 'profile_wsum_plot'] |
name: value name: value name: value name: value name: value |
msstats_testfile.txt value |
| Test-2 |
input|msstats_input: msstats_testfile.tsv input|input_src: MSstats group|comparison_matrix: comparison_matrix.csv group|select_outputs: model_qc group|comparison_plots_opt|select_comparison_plots: ResidualPlots group|group_comparison: yes |
name: value name: value name: value |
msstats_testfile.tsv comparison_matrix.csv value |
| Test-3 |
input|evidence: test_MQ_evidence.tabular input|proteinGroups: test_MQ_proteingroups.tabular input|annotation: test_MQ_annotation.txt input|input_src: MaxQuant dp_options|selected_outputs: ['featurelevel_data', 'proteinlevel_data'] dp_options|out_plots_opt|selected_vis_outputs: ConditionPlot group|comparison_matrix: test_MQ_group12_comparison_matrix.csv group|select_outputs: comparison_result group|comparison_plots_opt|select_comparison_plots: QQPlots group|group_comparison: yes |
name: value name: value name: value name: value name: value |
test_MQ_evidence.tabular test_MQ_proteingroups.tabular test_MQ_annotation.txt test_MQ_group12_comparison_matrix.csv value |
| Test-4 |
input|openms_input: openms_input.tabular input|input_src: OpenMS dp_options|selected_outputs: ['featurelevel_data', 'proteinlevel_data'] dp_options|out_plots_opt|selected_vis_outputs: ConditionPlot group|comparison_matrix: openms_comparisonmatrix.tabular group|comparison_plots_opt|select_comparison_plots: Heatmap group|group_comparison: yes |
name: value name: value name: value name: value |
openms_input.tabular openms_comparisonmatrix.tabular value |
| Test-5 |
input|skyline_input: skyline_input_first100.csv input|annotation: skyline_annotations.csv input|input_src: Skyline dp_options|selected_outputs: ['log', 'featurelevel_data', 'quant_sample_long'] dp_options|summarize|MBimpute: False dp_options|censoredInt: NA dp_options|out_plots_opt|selected_vis_outputs: ProfilePlot dp_options|out_plots_opt|width: 10 dp_options|out_plots_opt|height: 7 dp_options|out_plots_opt|proc_plots_advanced|featureName: Peptide group|comparison_matrix: comparison_matrix_skyline.tabular group|comparison_plots_opt|select_comparison_plots: ['VolcanoPlot', 'ComparisonPlot'] group|comparison_plots_opt|comparison_vis_options|FCcutoff: 2 group|comparison_plots_opt|comparison_vis_options|which_Comparison|comparison_list: comparison_list_skyline.tabular group|comparison_plots_opt|comparison_vis_options|which_Comparison|select: list group|group_comparison: yes |
name: value name: value name: value name: value name: value name: value name: value |
skyline_input_first100.csv skyline_annotations.csv comparison_matrix_skyline.tabular comparison_list_skyline.tabular value |
| Test-6 |
input|skyline_input: skyline_input_first100.csv input|annotation: skyline_annotations.csv input|input_src: Skyline dp_options|selected_outputs: ['log', 'featurelevel_data', 'quant_sample_matrix'] dp_options|summarize|MBimpute: True dp_options|censoredInt: 0 |
name: value name: value name: value |
skyline_input_first100.csv skyline_annotations.csv value |
| Test-7 |
input|openswath_input: test_swath_input_data.tabular input|annotation: test_swath_annotations.tabular input|input_src: OpenSWATH dp_options|out_plots_opt|selected_vis_outputs: QCPlot |
name: value name: value |
test_swath_input_data.tabular test_swath_annotations.tabular value |
| Test-8 |
input|openswath_input: test_swath_input_data.tabular input|annotation: test_swath_annotations.tabular input|input_src: OpenSWATH dp_options|selected_outputs: ['r_script', 'featurelevel_data', 'quant_sample_long'] group|comparison_matrix: test_swath_group12_comparison_matrix.csv group|select_outputs: comparison_result group|comparison_plots_opt|select_comparison_plots: ['VolcanoPlot', 'ResidualPlots'] group|group_comparison: yes |
name: value name: value name: value name: value name: value |
test_swath_input_data.tabular test_swath_annotations.tabular test_swath_group12_comparison_matrix.csv value |