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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
author iuc
date Mon, 10 Oct 2022 16:54:39 +0000
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1 <tool id="cemitool" name="CEMiTool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <description>gene co-expression network analyses</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro='xrefs'/>
7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[
9 Rscript '$__tool_directory__/CEMiTool.R'
10 -M '$expression_matrix'
11 #if $annotation
12 -A '$annotation'
13 #end if
14 #if $pathways
15 -P '$pathways'
16 #end if
17 #if $interactions
18 -I '$interactions'
19 #end if
20 -f $advanced_parameters.filter
21 -i $advanced_parameters.filter_pval
22 -a $advanced_parameters.apply_vst
23 -n $advanced_parameters.n_genes
24 -e $advanced_parameters.eps
25 -c $advanced_parameters.cor_method
26 -y $advanced_parameters.cor_function
27 -x $advanced_parameters.network_type
28 -t $advanced_parameters.tom_type
29 -m $advanced_parameters.merge_similar
30 -r $advanced_parameters.rank_method
31 -g $advanced_parameters.min_ngen
32 -d $advanced_parameters.diss_thresh
33 -h $advanced_parameters.center_func
34 -o $advanced_parameters.ora_pval
35 -l $advanced_parameters.gsea_scale
36 -w $advanced_parameters.gsea_min_size
37 -z $advanced_parameters.gsea_max_size
38 -v $advanced_parameters.sample_column_name
39 ]]></command>
40 <inputs>
41 <param name="expression_matrix" type="data" format="tabular" label="Expression matrix"/>
42 <param name="annotation" type="data" format="tabular" optional="true" label="Sample annotation"
43 help="It allows to build a more complete object and generate richer reports about the
44 expression data. Sample annotation can be supplied in a data.frame that specifies a
45 class for each sample. Classes can represent different conditions, phenotypes, cell lines,
46 time points, etc. " />
47 <param name="pathways" type="data" format="tabular,txt" label="Pathways list" optional="true" help="CEMiTool can
48 determine which biological functions are associated with the modules by performing an over
49 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." />
51 <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.
53 Interaction files contains two columns for interacting pairs of genes"/>
54 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Outputs selector">
55 <option value="report" selected="true">Report</option>
56 <option value="tables">Tables</option>
57 <option value="plots">Plots</option>
58 </param>
59 <section name="advanced_parameters" title="Advanced parameters">
60 <param argument="filter" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Filter" help="If enabled, it will filter expression data" />
61 <param argument="filter_pval" type="float" min="0" max="1" value="0.1" label="Filter P-value" help="P-value threshold for filtering" />
62 <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" />
63 <param argument="n_genes" type="integer" min="0" value="1000" label="Number of genes" help="Number of genes left after filtering" />
64 <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" />
65 <param name="cor_method" type="select" label="Correlation method" help="Correlation coefficient to be computed">
66 <option value="pearson">Pearson</option>
67 <option value="spearman">Spearman</option>
68 </param>
69 <param name="cor_function" type="select" label="Correlation function" help="Correlation function to be used">
70 <option value="cor">Correlation (cor)</option>
71 <option value="bicor">Biweight Midcorrelation (bicor)</option>
72 </param>
73 <param name="network_type" type="select" label="Network type" help="Indicates if network type should be computed as 'signed' or 'unsigned'">
74 <option value="signed">Signed</option>
75 <option value="unsigned" selected="true">Unsigned</option>
76 </param>
77 <param name="tom_type" type="select" label="TOM type" help="Indicates if TOM type should be computed as 'signed' or 'unsigned'">
78 <option value="signed">Signed</option>
79 <option value="unsigned">Unsigned</option>
80 </param>
81 <param argument="merge_similar" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Merge similar" help="If enabled, merge similar modules" />
82 <param argument="rank_method" type="select" label="Rank method" help="Indicate how to rank genes">
83 <option value="mean">Mean</option>
84 <option value="median">Median</option>
85 </param>
86 <param argument="min_ngen" type="integer" min="0" value="30" label="Minimal number of genes per module"/>
87 <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" />
88 <param argument="center_func" type="select" label="Cetrality measure to show in the plot">
89 <option value="mean">Mean</option>
90 <option value="median">Median</option>
91 </param>
92 <param argument="ora_pval" type="float" min="0" max="1" value="0.05" label="P-value for overrepresentation analysis"/>
93 <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" />
94 <param argument="gsea_min_size" type="integer" min="0" value="15" label="Minimum size of gene sets for GSEA analysis"/>
95 <param argument="gsea_max_size" type="integer" min="0" value="1000" label="Maximum size of gene sets for GSEA analysis"/>
96 <param argument="sample_column_name" type="text" value="SampleName" label="Sample column name" help="This is only required if an annotation file is provided">
97 <sanitizer invalid_char="">
98 <valid initial="string.letters,string.digits">
99 <add value="_" />
100 <add value="-" />
101 <add value=":" />
102 </valid>
103 </sanitizer>
104 <validator type="regex">[0-9a-zA-Z:-_]+</validator>
105 </param>
106 </section>
107 </inputs>
108 <outputs>
109 <collection name="plots" type="list" label="${tool.name} on ${on_string}: Plots">
110 <discover_datasets pattern="__designation_and_ext__" format="pdf" directory="Plots" />
111 <filter>"plots" in outputs</filter>
112 </collection>
113 <data name="module" format="tabular" from_work_dir="Tables/module.tsv" label="${tool.name} on ${on_string}: Module">
114 <filter>"tables" in outputs</filter>
115 </data>
116 <data name="modules_genes" format="tabular" from_work_dir="Tables/modules_genes.gmt" label="${tool.name} on ${on_string}: Module genes">
117 <filter>"tables" in outputs</filter>
118 </data>
119 <data name="parameters" format="tabular" from_work_dir="Tables/parameters.tsv" label="${tool.name} on ${on_string}: Parameters">
120 <filter>"tables" in outputs</filter>
121 </data>
122 <data name="selected_genes" format="txt" from_work_dir="Tables/selected_genes.txt" label="${tool.name} on ${on_string}: Selected genes">
123 <filter>"tables" in outputs</filter>
124 </data>
125 <data name="summary_eigengene" format="tabular" from_work_dir="Tables/summary_eigengene.tsv" label="${tool.name} on ${on_string}: Summary eigengenes">
126 <filter>"tables" in outputs</filter>
127 </data>
128 <data name="summary_mean" format="tabular" from_work_dir="Tables/summary_mean.tsv" label="${tool.name} on ${on_string}: Summary mean">
129 <filter>"tables" in outputs</filter>
130 </data>
131 <data name="summary_median" format="tabular" from_work_dir="Tables/summary_median.tsv" label="${tool.name} on ${on_string}: Summary median">
132 <filter>"tables" in outputs</filter>
133 </data>
134 <data name="interactions_output" format="tabular" from_work_dir="Tables/interactions.tsv" label="${tool.name} on ${on_string}: Interactions">
135 <filter>"tables" in outputs</filter>
136 <filter>interactions</filter>
137 </data>
138 <data name='output_html' format='html' from_work_dir="Reports/Report/report.html" label="${tool.name} on ${on_string}: HTML report">
139 <filter>"report" in outputs</filter>
140 </data>
141 </outputs>
142 <tests>
143 <test expect_num_outputs="1">
144 <!--Test expression matrix input-->
145 <param name="expression_matrix" value="expression_matrix.tab"/>
146 <param name="outputs" value="report"/>
147 <section name="advanced_parameters">
148 <param name="filter" value="True"/>
149 <param name="filter_pval" value="0.1"/>
150 <param name="apply_vst" value="false"/>
151 <param name="n_genes" value="1000"/>
152 <param name="eps" value="0.1"/>
153 <param name="cor_method" value="pearson"/>
154 <param name="cor_function" value="cor"/>
155 <param name="network_type" value="signed"/>
156 <param name="tom_type" value="signed"/>
157 <param name="merge_similar" value="false"/>
158 <param name="rank_method" value="mean"/>
159 <param name="min_ngen" value="30"/>
160 <param name="diss_thresh" value="0.8"/>
161 <param name="center_func" value="mean"/>
162 <param name="ora_pval" value="0.05"/>
163 <param name="gsea_scale" value="true"/>
164 <param name="gsea_min_size" value="15"/>
165 <param name="gsea_max_size" value="1000"/>
166 </section>
167 <output name="output_html">
168 <assert_contents>
169 <has_text text="EPSTI1"/>
170 <has_text text="RSAD2"/>
171 <has_text text="XAF1"/>
172 <has_text text="OAS2"/>
173 <has_text text="Gene Set Enrichment Analysis"/>
174 <has_text text="SPARC"/>
175 </assert_contents>
176 </output>
177 </test>
178
179 <test expect_num_outputs="8">
180 <!--Test all inputs and output tables-->
181 <param name="expression_matrix" value="expression_matrix.tab"/>
182 <param name="annotation" value="sample_annotation.tab"/>
183 <param name="pathways" value="pathways.gmt"/>
184 <param name="interactions" value="interactions.tab"/>
185 <param name="outputs" value="tables"/>
186 <section name="advanced_parameters">
187 <param name="filter" value="True"/>
188 <param name="filter_pval" value="0.1"/>
189 <param name="apply_vst" value="false"/>
190 <param name="n_genes" value="1000"/>
191 <param name="eps" value="0.1"/>
192 <param name="cor_method" value="pearson"/>
193 <param name="cor_function" value="cor"/>
194 <param name="network_type" value="signed"/>
195 <param name="tom_type" value="signed"/>
196 <param name="merge_similar" value="false"/>
197 <param name="rank_method" value="mean"/>
198 <param name="min_ngen" value="30"/>
199 <param name="diss_thresh" value="0.8"/>
200 <param name="center_func" value="mean"/>
201 <param name="ora_pval" value="0.05"/>
202 <param name="gsea_scale" value="true"/>
203 <param name="gsea_min_size" value="15"/>
204 <param name="gsea_max_size" value="1000"/>
205 </section>
206 <output name="module">
207 <assert_contents>
208 <has_n_lines n="110"/>
209 <has_size value="2250" delta="200"/>
210 </assert_contents>
211 </output>
212 <output name="modules_genes">
213 <assert_contents>
214 <has_n_lines n="1"/>
215 <has_size value="216" delta="10"/>
216 </assert_contents>
217 </output>
218 <output name="parameters">
219 <assert_contents>
220 <has_n_lines n="12"/>
221 <has_size value="234" delta="10"/>
222 </assert_contents>
223 </output>
224 <output name="selected_genes">
225 <assert_contents>
226 <has_n_lines n="1000"/>
227 <has_size value="6496" delta="10"/>
228 </assert_contents>
229 </output>
230 <output name="summary_eigengene">
231 <assert_contents>
232 <has_n_lines n="3"/>
233 <has_size value="2241" delta="10"/>
234 </assert_contents>
235 </output>
236 <output name="summary_mean">
237 <assert_contents>
238 <has_n_lines n="3"/>
239 <has_size value="2044" delta="50"/>
240 </assert_contents>
241 </output>
242 <output name="summary_median">
243 <assert_contents>
244 <has_n_lines n="3"/>
245 <has_size value="1621" delta="10"/>
246 </assert_contents>
247 </output>
248 <output name="interactions_output">
249 <assert_contents>
250 <has_n_lines n="277"/>
251 <has_size value="7736" delta="200"/>
252 </assert_contents>
253 </output>
254 </test>
255
256 <test expect_num_outputs="10">
257 <!--Test custom inputs and plots-->
258 <param name="expression_matrix" value="expression_matrix.tab"/>
259 <param name="annotation" value="sample_annotation.tab"/>
260 <param name="pathways" value="pathways.gmt"/>
261 <param name="interactions" value="interactions.tab"/>
262 <param name="outputs" value="report,tables,plots"/>
263 <section name="advanced_parameters">
264 <param name="filter" value="false"/>
265 <param name="filter_pval" value="0.2"/>
266 <param name="apply_vst" value="true"/>
267 <param name="n_genes" value="2000"/>
268 <param name="eps" value="0.1"/>
269 <param name="cor_method" value="spearman"/>
270 <param name="cor_function" value="bicor"/>
271 <param name="network_type" value="unsigned"/>
272 <param name="tom_type" value="unsigned"/>
273 <param name="merge_similar" value="true"/>
274 <param name="rank_method" value="median"/>
275 <param name="min_ngen" value="35"/>
276 <param name="diss_thresh" value="0.7"/>
277 <param name="center_func" value="median"/>
278 <param name="ora_pval" value="0.07"/>
279 <param name="gsea_scale" value="false"/>
280 <param name="gsea_min_size" value="10"/>
281 <param name="gsea_max_size" value="1100"/>
282 </section>
283 <output name="module">
284 <assert_contents>
285 <has_n_lines n="1929"/>
286 <has_size value="26528" delta="200"/>
287 </assert_contents>
288 </output>
289 <output name="modules_genes">
290 <assert_contents>
291 <has_n_lines n="10"/>
292 <has_size value="15814" delta="200"/>
293 </assert_contents>
294 </output>
295 <output name="parameters">
296 <assert_contents>
297 <has_n_lines n="12"/>
298 <has_size value="234" delta="10"/>
299 </assert_contents>
300 </output>
301 <output name="selected_genes">
302 <assert_contents>
303 <has_n_lines n="1928"/>
304 <has_size value="12570" delta="200"/>
305 </assert_contents>
306 </output>
307 <output name="summary_eigengene">
308 <assert_contents>
309 <has_n_lines n="12"/>
310 <has_size value="9963" delta="200"/>
311 </assert_contents>
312 </output>
313 <output name="summary_mean">
314 <assert_contents>
315 <has_n_lines n="12"/>
316 <has_size value="8898" delta="200"/>
317 </assert_contents>
318 </output>
319 <output name="summary_median">
320 <assert_contents>
321 <has_n_lines n="12"/>
322 <has_size value="6574" delta="200"/>
323 </assert_contents>
324 </output>
325 <output name="interactions_output">
326 <assert_contents>
327 <has_n_lines n="2579"/>
328 <has_size value="55341" delta="200"/>
329 </assert_contents>
330 </output>
331 <output_collection name="plots" type="list" count="10">
332 <element name="profile" file="profiles.pdf" compare="sim_size" delta="100"/>
333 </output_collection>
334 </test>
335
336 </tests>
337 <help><![CDATA[
338
339 .. class:: infomark
340
341 **Purpose**
342
343 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
344 discovered gene modules using additional downstream analyses and retrieve publication-ready results via a high-quality interactive report.
345
346 .. class:: infomark
347
348 **Purpose**
349
350 ]]></help>
351 <expand macro="citations" />
352 </tool>