| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/cemitool/cemitool/1.30.0+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/cemitool/cemitool/1.26.0+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/cemitool/cemitool/1.18.1+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/cemitool/cemitool/1.18.1+galaxy0 |
| cemitool |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| bioconductor-cemitool | 1.30.0 | package |
| r-ggplot2 | 3.5.1 | package |
| r-getopt | 1.20.4 | package |
| Additional information about this tool |
Rscript '$__tool_directory__/CEMiTool.R'
-M '$expression_matrix'
#if $annotation
-A '$annotation'
#end if
#if $pathways
-P '$pathways'
#end if
#if $interactions
-I '$interactions'
#end if
#if str($beta):
-B $beta
#end if
-f $advanced_parameters.filter
-i $advanced_parameters.filter_pval
-a $advanced_parameters.apply_vst
-n $advanced_parameters.n_genes
-e $advanced_parameters.eps
-c $advanced_parameters.cor_method
-y $advanced_parameters.cor_function
-x $advanced_parameters.network_type
-t $advanced_parameters.tom_type
-m $advanced_parameters.merge_similar
-r $advanced_parameters.rank_method
-g $advanced_parameters.min_ngen
-d $advanced_parameters.diss_thresh
-h $advanced_parameters.center_func
-o $advanced_parameters.ora_pval
-l $advanced_parameters.gsea_scale
-w $advanced_parameters.gsea_min_size
-z $advanced_parameters.gsea_max_size
-v $advanced_parameters.sample_column_name
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
expression_matrix: expression_matrix.tab outputs: report advanced_parameters|filter: True advanced_parameters|filter_pval: 0.1 advanced_parameters|apply_vst: False advanced_parameters|n_genes: 1000 advanced_parameters|eps: 0.1 advanced_parameters|cor_method: pearson advanced_parameters|cor_function: cor advanced_parameters|network_type: signed advanced_parameters|tom_type: signed advanced_parameters|merge_similar: False advanced_parameters|rank_method: mean advanced_parameters|min_ngen: 30 advanced_parameters|diss_thresh: 0.8 advanced_parameters|center_func: mean advanced_parameters|ora_pval: 0.05 advanced_parameters|gsea_scale: True advanced_parameters|gsea_min_size: 15 advanced_parameters|gsea_max_size: 1000 |
name: value |
expression_matrix.tab value |
| Test-2 |
expression_matrix: expression_matrix.tab annotation: sample_annotation.tab pathways: pathways.gmt interactions: interactions.tab outputs: tables advanced_parameters|filter: True advanced_parameters|filter_pval: 0.1 advanced_parameters|apply_vst: False advanced_parameters|n_genes: 1000 advanced_parameters|eps: 0.1 advanced_parameters|cor_method: pearson advanced_parameters|cor_function: cor advanced_parameters|network_type: signed advanced_parameters|tom_type: signed advanced_parameters|merge_similar: False advanced_parameters|rank_method: mean advanced_parameters|min_ngen: 30 advanced_parameters|diss_thresh: 0.8 advanced_parameters|center_func: mean advanced_parameters|ora_pval: 0.05 advanced_parameters|gsea_scale: True advanced_parameters|gsea_min_size: 15 advanced_parameters|gsea_max_size: 1000 |
name: value name: value name: value name: value name: value name: value name: value name: value |
expression_matrix.tab sample_annotation.tab pathways.gmt interactions.tab value |
| Test-3 |
expression_matrix: expression_matrix.tab annotation: sample_annotation.tab pathways: pathways.gmt interactions: interactions.tab outputs: ['report', 'tables', 'plots'] advanced_parameters|filter: False advanced_parameters|filter_pval: 0.2 advanced_parameters|apply_vst: True advanced_parameters|n_genes: 2000 advanced_parameters|eps: 0.1 advanced_parameters|cor_method: spearman advanced_parameters|cor_function: bicor advanced_parameters|network_type: unsigned advanced_parameters|tom_type: unsigned advanced_parameters|merge_similar: True advanced_parameters|rank_method: median advanced_parameters|min_ngen: 35 advanced_parameters|diss_thresh: 0.7 advanced_parameters|center_func: median advanced_parameters|ora_pval: 0.07 advanced_parameters|gsea_scale: False advanced_parameters|gsea_min_size: 10 advanced_parameters|gsea_max_size: 1100 |
name: value name: value name: value name: value name: value name: value name: value name: value |
expression_matrix.tab sample_annotation.tab pathways.gmt interactions.tab value |