comparison cemitool.xml @ 1:81bffdf16b71 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc

0:3f9ff31c88bb

        #if $pathways
            -P '$pathways'
        #end if
        #if $interactions
            -I '$interactions'
        #end if
        -f $advanced_parameters.filter
        -i $advanced_parameters.filter_pval
        -a $advanced_parameters.apply_vst
        -n $advanced_parameters.n_genes

            representation analysis (ORA). To do this you must provide a pathway list in the form of GMT 
            file. CEMiTool will then analyze how these pathways are represented in the modules." />
        <param name="interactions" type="data" format="tabular" optional="true" label="Interactions data" help="Interaction data, 
            such as protein-protein interactions can be added in order to generate annotated module graphs. 
            Interaction files contains two columns for interacting pairs of genes"/>
        <param name="outputs" type="select" multiple="true" display="checkboxes" label="Outputs selector">
            <option value="report" selected="true">Report</option>
            <option value="tables">Tables</option>
            <option value="plots">Plots</option>
        </param>

1:81bffdf16b71

        #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

            representation analysis (ORA). To do this you must provide a pathway list in the form of GMT 
            file. CEMiTool will then analyze how these pathways are represented in the modules." />
        <param name="interactions" type="data" format="tabular" optional="true" label="Interactions data" help="Interaction data, 
            such as protein-protein interactions can be added in order to generate annotated module graphs. 
            Interaction files contains two columns for interacting pairs of genes"/>
        <param name="beta" type="integer" min="0" label="Beta value" optional="true"
            help="The beta value is a parameter that lies in the core of the weighted gene co-expression network analysis (WGCNA)."/>
        <param name="outputs" type="select" multiple="true" display="checkboxes" label="Outputs selector">
            <option value="report" selected="true">Report</option>
            <option value="tables">Tables</option>
            <option value="plots">Plots</option>
        </param>