Mercurial > repos > iuc > cemitool

annotate cemitool.xml @ 2:9d93999d9028 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit f5a9be967de99a62addf6b3c7c01a10ba3572466
author iuc
date Thu, 22 Aug 2024 17:49:08 +0000
parents 81bffdf16b71
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
1 <tool id="cemitool" name="CEMiTool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
2 <description>gene co-expression network analyses</description>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
3 <macros>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
4 <import>macros.xml</import>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
5 </macros>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
6 <expand macro='xrefs'/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
7 <expand macro="requirements" />
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
9 Rscript '$__tool_directory__/CEMiTool.R'
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
10 -M '$expression_matrix'
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
11 #if $annotation
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
12 -A '$annotation'
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
13 #end if
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
14 #if $pathways
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
15 -P '$pathways'
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
16 #end if
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
17 #if $interactions
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
18 -I '$interactions'
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
19 #end if
1
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
20 #if str($beta):
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
21 -B $beta
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
22 #end if
0
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
23 -f $advanced_parameters.filter
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
24 -i $advanced_parameters.filter_pval
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
25 -a $advanced_parameters.apply_vst
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
26 -n $advanced_parameters.n_genes
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
27 -e $advanced_parameters.eps
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
28 -c $advanced_parameters.cor_method
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
29 -y $advanced_parameters.cor_function
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
30 -x $advanced_parameters.network_type
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
31 -t $advanced_parameters.tom_type
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
32 -m $advanced_parameters.merge_similar
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
33 -r $advanced_parameters.rank_method
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
34 -g $advanced_parameters.min_ngen
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
35 -d $advanced_parameters.diss_thresh
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
36 -h $advanced_parameters.center_func
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
37 -o $advanced_parameters.ora_pval
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
38 -l $advanced_parameters.gsea_scale
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
39 -w $advanced_parameters.gsea_min_size
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
40 -z $advanced_parameters.gsea_max_size
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
41 -v $advanced_parameters.sample_column_name
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
42 ]]></command>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
43 <inputs>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
44 <param name="expression_matrix" type="data" format="tabular" label="Expression matrix"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
45 <param name="annotation" type="data" format="tabular" optional="true" label="Sample annotation"
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
46 help="It allows to build a more complete object and generate richer reports about the
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
47 expression data. Sample annotation can be supplied in a data.frame that specifies a
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
48 class for each sample. Classes can represent different conditions, phenotypes, cell lines,
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
49 time points, etc. " />
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
50 <param name="pathways" type="data" format="tabular,txt" label="Pathways list" optional="true" help="CEMiTool can
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
51 determine which biological functions are associated with the modules by performing an over
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
52 representation analysis (ORA). To do this you must provide a pathway list in the form of GMT
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
53 file. CEMiTool will then analyze how these pathways are represented in the modules." />
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
54 <param name="interactions" type="data" format="tabular" optional="true" label="Interactions data" help="Interaction data,
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
55 such as protein-protein interactions can be added in order to generate annotated module graphs.
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
56 Interaction files contains two columns for interacting pairs of genes"/>
1
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
57 <param name="beta" type="integer" min="0" label="Beta value" optional="true"
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
58 help="The beta value is a parameter that lies in the core of the weighted gene co-expression network analysis (WGCNA)."/>
0
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
59 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Outputs selector">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
60 <option value="report" selected="true">Report</option>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
61 <option value="tables">Tables</option>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
62 <option value="plots">Plots</option>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
63 </param>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
64 <section name="advanced_parameters" title="Advanced parameters">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
65 <param argument="filter" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Filter" help="If enabled, it will filter expression data" />
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
66 <param argument="filter_pval" type="float" min="0" max="1" value="0.1" label="Filter P-value" help="P-value threshold for filtering" />
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
67 <param argument="apply_vst" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="VST" help="If enabled, it apply Variance Stabilizing Transform before filtering genes" />
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
68 <param argument="n_genes" type="integer" min="0" value="1000" label="Number of genes" help="Number of genes left after filtering" />
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
69 <param argument="eps" type="float" min="0" max="1" value="0.1" label="EPS" help="A value for accepted R-squared interval between subsequent beta values" />
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
70 <param name="cor_method" type="select" label="Correlation method" help="Correlation coefficient to be computed">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
71 <option value="pearson">Pearson</option>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
72 <option value="spearman">Spearman</option>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
73 </param>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
74 <param name="cor_function" type="select" label="Correlation function" help="Correlation function to be used">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
75 <option value="cor">Correlation (cor)</option>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
76 <option value="bicor">Biweight Midcorrelation (bicor)</option>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
77 </param>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
78 <param name="network_type" type="select" label="Network type" help="Indicates if network type should be computed as 'signed' or 'unsigned'">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
79 <option value="signed">Signed</option>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
80 <option value="unsigned" selected="true">Unsigned</option>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
81 </param>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
82 <param name="tom_type" type="select" label="TOM type" help="Indicates if TOM type should be computed as 'signed' or 'unsigned'">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
83 <option value="signed">Signed</option>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
84 <option value="unsigned">Unsigned</option>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
85 </param>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
86 <param argument="merge_similar" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Merge similar" help="If enabled, merge similar modules" />
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
87 <param argument="rank_method" type="select" label="Rank method" help="Indicate how to rank genes">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
88 <option value="mean">Mean</option>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
89 <option value="median">Median</option>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
90 </param>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
91 <param argument="min_ngen" type="integer" min="0" value="30" label="Minimal number of genes per module"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
92 <param argument="diss_thresh" type="float" min="0" max="1" value="0.8" label="Merging correlation threshold" help="Module merging correlation threshold for eigengene similarity" />
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
93 <param argument="center_func" type="select" label="Cetrality measure to show in the plot">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
94 <option value="mean">Mean</option>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
95 <option value="median">Median</option>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
96 </param>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
97 <param argument="ora_pval" type="float" min="0" max="1" value="0.05" label="P-value for overrepresentation analysis"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
98 <param argument="gsea_scale" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Z-score transformation for GSEA analysis" help="If enabled, it applies z-score transformation" />
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
99 <param argument="gsea_min_size" type="integer" min="0" value="15" label="Minimum size of gene sets for GSEA analysis"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
100 <param argument="gsea_max_size" type="integer" min="0" value="1000" label="Maximum size of gene sets for GSEA analysis"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
101 <param argument="sample_column_name" type="text" value="SampleName" label="Sample column name" help="This is only required if an annotation file is provided">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
102 <sanitizer invalid_char="">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
103 <valid initial="string.letters,string.digits">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
104 <add value="_" />
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
105 <add value="-" />
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
106 <add value=":" />
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
107 </valid>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
108 </sanitizer>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
109 <validator type="regex">[0-9a-zA-Z:-_]+</validator>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
110 </param>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
111 </section>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
112 </inputs>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
113 <outputs>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
114 <collection name="plots" type="list" label="${tool.name} on ${on_string}: Plots">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
115 <discover_datasets pattern="__designation_and_ext__" format="pdf" directory="Plots" />
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
116 <filter>"plots" in outputs</filter>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
117 </collection>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
118 <data name="module" format="tabular" from_work_dir="Tables/module.tsv" label="${tool.name} on ${on_string}: Module">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
119 <filter>"tables" in outputs</filter>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
120 </data>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
121 <data name="modules_genes" format="tabular" from_work_dir="Tables/modules_genes.gmt" label="${tool.name} on ${on_string}: Module genes">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
122 <filter>"tables" in outputs</filter>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
123 </data>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
124 <data name="parameters" format="tabular" from_work_dir="Tables/parameters.tsv" label="${tool.name} on ${on_string}: Parameters">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
125 <filter>"tables" in outputs</filter>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
126 </data>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
127 <data name="selected_genes" format="txt" from_work_dir="Tables/selected_genes.txt" label="${tool.name} on ${on_string}: Selected genes">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
128 <filter>"tables" in outputs</filter>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
129 </data>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
130 <data name="summary_eigengene" format="tabular" from_work_dir="Tables/summary_eigengene.tsv" label="${tool.name} on ${on_string}: Summary eigengenes">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
131 <filter>"tables" in outputs</filter>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
132 </data>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
133 <data name="summary_mean" format="tabular" from_work_dir="Tables/summary_mean.tsv" label="${tool.name} on ${on_string}: Summary mean">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
134 <filter>"tables" in outputs</filter>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
135 </data>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
136 <data name="summary_median" format="tabular" from_work_dir="Tables/summary_median.tsv" label="${tool.name} on ${on_string}: Summary median">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
137 <filter>"tables" in outputs</filter>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
138 </data>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
139 <data name="interactions_output" format="tabular" from_work_dir="Tables/interactions.tsv" label="${tool.name} on ${on_string}: Interactions">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
140 <filter>"tables" in outputs</filter>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
141 <filter>interactions</filter>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
142 </data>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
143 <data name='output_html' format='html' from_work_dir="Reports/Report/report.html" label="${tool.name} on ${on_string}: HTML report">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
144 <filter>"report" in outputs</filter>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
145 </data>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
146 </outputs>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
147 <tests>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
148 <test expect_num_outputs="1">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
149 <!--Test expression matrix input-->
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
150 <param name="expression_matrix" value="expression_matrix.tab"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
151 <param name="outputs" value="report"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
152 <section name="advanced_parameters">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
153 <param name="filter" value="True"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
154 <param name="filter_pval" value="0.1"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
155 <param name="apply_vst" value="false"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
156 <param name="n_genes" value="1000"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
157 <param name="eps" value="0.1"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
158 <param name="cor_method" value="pearson"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
159 <param name="cor_function" value="cor"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
160 <param name="network_type" value="signed"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
161 <param name="tom_type" value="signed"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
162 <param name="merge_similar" value="false"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
163 <param name="rank_method" value="mean"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
164 <param name="min_ngen" value="30"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
165 <param name="diss_thresh" value="0.8"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
166 <param name="center_func" value="mean"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
167 <param name="ora_pval" value="0.05"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
168 <param name="gsea_scale" value="true"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
169 <param name="gsea_min_size" value="15"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
170 <param name="gsea_max_size" value="1000"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
171 </section>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
172 <output name="output_html">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
173 <assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
174 <has_text text="EPSTI1"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
175 <has_text text="RSAD2"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
176 <has_text text="XAF1"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
177 <has_text text="OAS2"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
178 <has_text text="Gene Set Enrichment Analysis"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
179 <has_text text="SPARC"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
180 </assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
181 </output>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
182 </test>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
183
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
184 <test expect_num_outputs="8">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
185 <!--Test all inputs and output tables-->
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
186 <param name="expression_matrix" value="expression_matrix.tab"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
187 <param name="annotation" value="sample_annotation.tab"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
188 <param name="pathways" value="pathways.gmt"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
189 <param name="interactions" value="interactions.tab"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
190 <param name="outputs" value="tables"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
191 <section name="advanced_parameters">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
192 <param name="filter" value="True"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
193 <param name="filter_pval" value="0.1"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
194 <param name="apply_vst" value="false"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
195 <param name="n_genes" value="1000"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
196 <param name="eps" value="0.1"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
197 <param name="cor_method" value="pearson"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
198 <param name="cor_function" value="cor"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
199 <param name="network_type" value="signed"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
200 <param name="tom_type" value="signed"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
201 <param name="merge_similar" value="false"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
202 <param name="rank_method" value="mean"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
203 <param name="min_ngen" value="30"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
204 <param name="diss_thresh" value="0.8"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
205 <param name="center_func" value="mean"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
206 <param name="ora_pval" value="0.05"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
207 <param name="gsea_scale" value="true"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
208 <param name="gsea_min_size" value="15"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
209 <param name="gsea_max_size" value="1000"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
210 </section>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
211 <output name="module">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
212 <assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
213 <has_n_lines n="110"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
214 <has_size value="2250" delta="200"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
215 </assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
216 </output>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
217 <output name="modules_genes">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
218 <assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
219 <has_n_lines n="1"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
220 <has_size value="216" delta="10"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
221 </assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
222 </output>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
223 <output name="parameters">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
224 <assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
225 <has_n_lines n="12"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
226 <has_size value="234" delta="10"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
227 </assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
228 </output>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
229 <output name="selected_genes">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
230 <assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
231 <has_n_lines n="1000"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
232 <has_size value="6496" delta="10"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
233 </assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
234 </output>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
235 <output name="summary_eigengene">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
236 <assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
237 <has_n_lines n="3"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
238 <has_size value="2241" delta="10"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
239 </assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
240 </output>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
241 <output name="summary_mean">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
242 <assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
243 <has_n_lines n="3"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
244 <has_size value="2044" delta="50"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
245 </assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
246 </output>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
247 <output name="summary_median">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
248 <assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
249 <has_n_lines n="3"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
250 <has_size value="1621" delta="10"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
251 </assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
252 </output>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
253 <output name="interactions_output">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
254 <assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
255 <has_n_lines n="277"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
256 <has_size value="7736" delta="200"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
257 </assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
258 </output>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
259 </test>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
260
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
261 <test expect_num_outputs="10">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
262 <!--Test custom inputs and plots-->
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
263 <param name="expression_matrix" value="expression_matrix.tab"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
264 <param name="annotation" value="sample_annotation.tab"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
265 <param name="pathways" value="pathways.gmt"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
266 <param name="interactions" value="interactions.tab"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
267 <param name="outputs" value="report,tables,plots"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
268 <section name="advanced_parameters">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
269 <param name="filter" value="false"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
270 <param name="filter_pval" value="0.2"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
271 <param name="apply_vst" value="true"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
272 <param name="n_genes" value="2000"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
273 <param name="eps" value="0.1"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
274 <param name="cor_method" value="spearman"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
275 <param name="cor_function" value="bicor"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
276 <param name="network_type" value="unsigned"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
277 <param name="tom_type" value="unsigned"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
278 <param name="merge_similar" value="true"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
279 <param name="rank_method" value="median"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
280 <param name="min_ngen" value="35"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
281 <param name="diss_thresh" value="0.7"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
282 <param name="center_func" value="median"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
283 <param name="ora_pval" value="0.07"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
284 <param name="gsea_scale" value="false"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
285 <param name="gsea_min_size" value="10"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
286 <param name="gsea_max_size" value="1100"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
287 </section>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
288 <output name="module">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
289 <assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
290 <has_n_lines n="1929"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
291 <has_size value="26528" delta="200"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
292 </assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
293 </output>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
294 <output name="modules_genes">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
295 <assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
296 <has_n_lines n="10"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
297 <has_size value="15814" delta="200"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
298 </assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
299 </output>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
300 <output name="parameters">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
301 <assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
302 <has_n_lines n="12"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
303 <has_size value="234" delta="10"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
304 </assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
305 </output>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
306 <output name="selected_genes">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
307 <assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
308 <has_n_lines n="1928"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
309 <has_size value="12570" delta="200"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
310 </assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
311 </output>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
312 <output name="summary_eigengene">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
313 <assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
314 <has_n_lines n="12"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
315 <has_size value="9963" delta="200"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
316 </assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
317 </output>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
318 <output name="summary_mean">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
319 <assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
320 <has_n_lines n="12"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
321 <has_size value="8898" delta="200"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
322 </assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
323 </output>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
324 <output name="summary_median">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
325 <assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
326 <has_n_lines n="12"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
327 <has_size value="6574" delta="200"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
328 </assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
329 </output>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
330 <output name="interactions_output">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
331 <assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
332 <has_n_lines n="2579"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
333 <has_size value="55341" delta="200"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
334 </assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
335 </output>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
336 <output_collection name="plots" type="list" count="10">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
337 <element name="profile" file="profiles.pdf" compare="sim_size" delta="100"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
338 </output_collection>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
339 </test>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
340
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
341 </tests>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
342 <help><![CDATA[
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
343
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
344 .. class:: infomark
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
345
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
346 **Purpose**
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
347
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
348 The CEMiTool R package provides users with an easy-to-use method to automatically implement gene co-expression network analyses, obtain key information about the
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
349 discovered gene modules using additional downstream analyses and retrieve publication-ready results via a high-quality interactive report.
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
350
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
351 .. class:: infomark
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
352
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
353 **Purpose**
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
354
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
355 ]]></help>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
356 <expand macro="citations" />
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
357 </tool>