| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/mqppep_anova/mqppep_anova/0.1.19+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/mqppep_anova/mqppep_anova/0.1.18+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/mqppep_anova/mqppep_anova/0.1.17+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/mqppep_anova/mqppep_anova/0.1.16+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/mqppep_anova/mqppep_anova/0.1.15+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/mqppep_anova/mqppep_anova/0.1.13+galaxy0 |
| mqppep_anova |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| bioconductor-preprocesscore | 1.56.0 | package |
| gmp | 6.2.1 | package |
| numpy | 1.23.4 | package |
| openblas | 0.3.3 | package |
| pandas | 1.5.1 | package |
| perl-dbd-sqlite | 1.70 | package |
| perl | 5.32.1 | package |
| pyahocorasick | 1.4.4 | package |
| python | 3.10.6 | package |
| r-base | 4.1.3 | package |
| r-caret | 6.0_93 | package |
| r-data.table | 1.14.4 | package |
| r-dbi | 1.1.3 | package |
| r-ggplot2 | 3.3.6 | package |
| r-gplots | 3.1.3 | package |
| r-latex2exp | 0.9.5 | package |
| r-optparse | 1.7.3 | package |
| r-reshape2 | 1.4.4 | package |
| r-rmarkdown | 2.17 | package |
| r-sessioninfo | 1.2.2 | package |
| r-sqldf | 0.4_11 | package |
| r-stringr | 1.4.1 | package |
| r-tinytex | 0.42 | package |
| r-vioplot | 0.3.7 | package |
| Additional information about this tool |
(printenv | sort) &&
cp '$__tool_directory__/mqppep_anova_script.Rmd' . &&
cp '$__tool_directory__/mqppep_anova.R' . &&
cp '$__tool_directory__/kinase_name_uniprot_lut.tabular.bz2' . &&
cp '$__tool_directory__/kinase_uniprot_description_lut.tabular.bz2' . &&
cp '$__tool_directory__/mqppep_anova_preamble.tex' . &&
cp '$__tool_directory__/perpage.tex' . &&
cp '$__tool_directory__/KSEA_impl_flowchart.pdf' . &&
Rscript mqppep_anova.R
--inputFile '$input_file'
--alphaFile '$alpha_file'
--preproc_sqlite '$preproc_sqlite'
--firstDataColumn '$intensity_column_regex_f'
--imputationMethod $imputation.imputation_method
#if $imputation.imputation_method == "random"
--meanPercentile '$imputation.meanPercentile'
--sdPercentile '$imputation.sdPercentile'
#end if
--regexSampleNames '$sample_names_regex_f'
--regexSampleGrouping '$sample_grouping_regex_f'
#if $group_filter.group_filter_method == "none"
--sampleGroupFilter 'none'
#else
--sampleGroupFilter '$group_filter.group_filter_method'
--sampleGroupFilterPatterns '$group_filter_patterns_f'
--sampleGroupFilterMode '$group_filter.group_filter_mode'
#end if
--intensityMinValuesPerClass '$intnsty_min_vals_per_smpl_grp'
--imputedDataFile '$imputed_data_file'
--imputedQNLTDataFile '$imp_qn_lt_file'
--ksea_sqlite '$ksea_sqlite'
--kseaMinSubstrateCount '$ksea_min_substrate_count'
--ksea_cutoff_threshold '$ksea_cutoff_threshold'
--ksea_cutoff_statistic 'FDR'
--kseaUseAbsoluteLog2FC '$ksea_use_absolute_log2_fc'
--minQuality '$ksea_min_quality'
--anova_ksea_metadata '$anova_ksea_metadata'
--reportFile '$report_file'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input_file: test_input_for_anova.tabular alpha_file: alpha_levels.tabular preproc_sqlite: test_input_for_anova.sqlite intensity_column_regex: ^Intensity[^_] imputation|imputation_method: median sample_names_regex: \.\d+[A-Z]$ sample_grouping_regex: \d+ |
name: value name: value |
test_input_for_anova.tabular alpha_levels.tabular test_input_for_anova.sqlite value |
| Test-2 |
input_file: test_input_for_anova.tabular alpha_file: alpha_levels.tabular preproc_sqlite: test_input_for_anova.sqlite intensity_column_regex: ^Intensity[^_] imputation|imputation_method: mean sample_names_regex: \.\d+[A-Z]$ sample_grouping_regex: \d+ intnsty_min_vals_per_smpl_grp: 1 group_filter|group_filter_method: none ksea_min_substrate_count: 1 ksea_cutoff_threshold: 0.5 |
name: value name: value |
test_input_for_anova.tabular alpha_levels.tabular test_input_for_anova.sqlite value |
| Test-3 |
input_file: test_input_for_anova.tabular alpha_file: alpha_levels.tabular preproc_sqlite: test_input_for_anova.sqlite intensity_column_regex: ^Intensity[^_] imputation|imputation_method: group-median sample_names_regex: \.\d+[A-Z]$ sample_grouping_regex: \d+ intnsty_min_vals_per_smpl_grp: 1 group_filter|group_filter_method: none ksea_min_substrate_count: 1 ksea_cutoff_threshold: 0.5 |
name: value name: value |
test_input_for_anova.tabular alpha_levels.tabular test_input_for_anova.sqlite value |
| Test-4 |
input_file: test_input_for_anova.tabular alpha_file: alpha_levels.tabular preproc_sqlite: test_input_for_anova.sqlite intensity_column_regex: ^Intensity[^_] imputation|meanPercentile: 1 imputation|sdPercentile: 1.0 imputation|imputation_method: random sample_names_regex: \.\d+[A-Z]$ sample_grouping_regex: \d+ |
name: value name: value |
test_input_for_anova.tabular alpha_levels.tabular test_input_for_anova.sqlite value |