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comparison cemitool.xml @ 1:53230429a90c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
author iuc
date Mon, 19 Aug 2024 10:47:06 +0000
parents a081fc047ccb
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0:a081fc047ccb 1:53230429a90c
14 #if $pathways 14 #if $pathways
15 -P '$pathways' 15 -P '$pathways'
16 #end if 16 #end if
17 #if $interactions 17 #if $interactions
18 -I '$interactions' 18 -I '$interactions'
19 #end if
20 #if str($beta):
21 -B $beta
19 #end if 22 #end if
20 -f $advanced_parameters.filter 23 -f $advanced_parameters.filter
21 -i $advanced_parameters.filter_pval 24 -i $advanced_parameters.filter_pval
22 -a $advanced_parameters.apply_vst 25 -a $advanced_parameters.apply_vst
23 -n $advanced_parameters.n_genes 26 -n $advanced_parameters.n_genes
49 representation analysis (ORA). To do this you must provide a pathway list in the form of GMT 52 representation analysis (ORA). To do this you must provide a pathway list in the form of GMT
50 file. CEMiTool will then analyze how these pathways are represented in the modules." /> 53 file. CEMiTool will then analyze how these pathways are represented in the modules." />
51 <param name="interactions" type="data" format="tabular" optional="true" label="Interactions data" help="Interaction data, 54 <param name="interactions" type="data" format="tabular" optional="true" label="Interactions data" help="Interaction data,
52 such as protein-protein interactions can be added in order to generate annotated module graphs. 55 such as protein-protein interactions can be added in order to generate annotated module graphs.
53 Interaction files contains two columns for interacting pairs of genes"/> 56 Interaction files contains two columns for interacting pairs of genes"/>
57 <param name="beta" type="integer" min="0" label="Beta value" optional="true"
58 help="The beta value is a parameter that lies in the core of the weighted gene co-expression network analysis (WGCNA)."/>
54 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Outputs selector"> 59 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Outputs selector">
55 <option value="report" selected="true">Report</option> 60 <option value="report" selected="true">Report</option>
56 <option value="tables">Tables</option> 61 <option value="tables">Tables</option>
57 <option value="plots">Plots</option> 62 <option value="plots">Plots</option>
58 </param> 63 </param>