Repository revision
1:4e73ea176c34

Repository 'rgcca'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/rgcca

RGCCA tool metadata
Miscellaneous
RGCCA
performs multiblock data analysis of several sets of variables (blocks) observed on the same group of individuals.
rgcca
toolshed.g2.bx.psu.edu/repos/iuc/rgcca/rgcca/3.0.2+galaxy1
3.0.2+galaxy1
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/rgcca/rgcca/3.0.2+galaxy1 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/rgcca/rgcca/3.0.0+galaxy0
rgcca
Requirements (dependencies defined in the <requirements> tag set)
name version type
rgccacmd 3.0.2 package
r-base 4.1 package
Additional information about this tool
#set data_paths = ",".join([str(_.file_name) for _ in $blocks])
        #set data_names = ",".join([str(_.element_identifier).replace(',', '_') for _ in $blocks])
        #set out_files = str($output_selector).split(",")
        Rscript '$__tool_directory__/launcher.R'
            --datasets '${data_paths}'
            --names '${data_names}'
            #if 'individuals' in $out_files
                --o1 '$individual_plot'
            #end if
            #if 'corcircle' in $out_files
                --o2 '$corcircle'
            #end if
            #if 'top_variables' in $out_files
                --o3 '$top_variables'
            #end if
            #if 'ave' in $out_files
                --o4 '$ave'
            #end if
            #if 'design' in $out_files
                --o5 '$design'
            #end if
            #if 'individual_table' in $out_files
                --o6 '$individual_table'
            #end if
            #if 'variable_table' in $out_files
                --o7 '$variable_table'
            #end if
            #if 'rdata' in $out_files
                --o8 '$rdata'
            #end if
            $parse.header
            --separator $parse.separator
            $analyse.superblock
            $analyse.scale
            #if $analyse.tau.bool == 'false'
                --penalty $analyse.tau.value
            #else
                --penalty $analyse.tau.bool
            #end if
            --ncomp $analyse.ncomp
            --scheme $analyse.scheme
            #if $analyse.method.family == '1'
                --type pca
            #else
                --type $analyse.method.type
            #end if
            #if $analyse.connection
                --connection $analyse.connection
            #end if
            #if $analyse.supervised.learning_mode == 'supervised'
                --response $analyse.supervised.block_response
            #end if
            #if $graphic.response
                --group $graphic.response
            #end if
            --compx $graphic.compx
            --compy $graphic.compy
            --nmark $graphic.nmark
            $graphic.text
            --block $graphic.blockx
            --block_y $graphic.blocky
    
None
False
Functional tests
name inputs outputs required files
Test-1 blocks: agriculture.tsv
output_selector: ['individuals', 'corcircle', 'top_variables', 'ave', 'design', 'individual_table', 'variable_table', 'rdata']
name: value
name: value
name: value
name: value
name: value
name: value
name: value
name: value
agriculture.tsv
value
Test-2 blocks: ['agriculture.tsv', 'industry.tsv', 'politic.tsv']
analyse|connection: connection.tsv
analyse|superblock: False
analyse|tau|value: 0.75
analyse|tau|bool: false
analyse|scheme: 4
output_selector: ['individuals', 'corcircle', 'top_variables', 'ave', 'design', 'individual_table', 'variable_table', 'rdata']
name: value
name: value
name: value
name: value
name: value
name: value
name: value
agriculture.tsv
industry.tsv
politic.tsv
connection.tsv
value
Test-3 blocks: ['agriculture.tsv', 'industry.tsv', 'politic.tsv']
analyse|superblock: False
analyse|supervised|block_response: 3
analyse|supervised|learning_mode: supervised
analyse|tau|value: 0.75
analyse|tau|bool: false
analyse|scheme: 4
output_selector: ['individuals', 'corcircle', 'top_variables', 'ave', 'design', 'individual_table', 'variable_table', 'rdata']
name: value
name: value
name: value
name: value
name: value
name: value
name: value
agriculture.tsv
industry.tsv
politic.tsv
value
Test-4 blocks: ['agriculture.tsv', 'industry.tsv', 'politic.tsv']
analyse|tau|value: 0.75
analyse|tau|bool: false
analyse|scheme: 4
output_selector: ['individuals', 'corcircle', 'top_variables', 'ave', 'design', 'individual_table', 'variable_table', 'rdata']
name: value
name: value
name: value
name: value
name: value
name: value
name: value
agriculture.tsv
industry.tsv
politic.tsv
value
Test-5 blocks: ['agriculture.tsv', 'industry.tsv', 'politic.tsv']
analyse|method|type: sgcca
analyse|method|family: m
analyse|tau|value: 0.75
analyse|tau|bool: false
analyse|scheme: 4
output_selector: ['individuals', 'corcircle', 'top_variables', 'ave', 'design', 'individual_table', 'variable_table', 'rdata']
name: value
name: value
name: value
name: value
name: value
name: value
name: value
agriculture.tsv
industry.tsv
politic.tsv
value
Test-6 blocks: ['agriculture.tsv', 'politic.tsv']
analyse|ncomp: 3
analyse|scale: False
analyse|method|type: pls
analyse|method|family: 2
analyse|tau|value: 0
analyse|tau|bool: false
analyse|scheme: 3
graphic|response: political_system.tsv
graphic|text: False
graphic|compx: 3
graphic|compy: 1
graphic|blockx: 2
graphic|blocky: 1
graphic|nmark: 11
output_selector: ['individuals', 'corcircle', 'top_variables', 'ave', 'design', 'individual_table', 'variable_table', 'rdata']
name: value
name: value
name: value
name: value
name: value
name: value
name: value
agriculture.tsv
politic.tsv
political_system.tsv
value