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planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty
author proteore
date Thu, 27 Jun 2019 04:20:35 -0400
parents f4e02d20546b
children 940d787535a7
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1 <tool id="kegg_maps_visualization" name="Pathways visualization" version="2019.05.14"> 1 <tool id="kegg_maps_visualization" name="Pathways visualization" version="2019.06.27">
2 <description>of (differentially expressed) genes/proteins [KEGG]</description> 2 <description>of (differentially expressed) genes/proteins [KEGG]</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.18.0">bioconductor-pathview</requirement> 4 <requirement type="package" version="1.18.0">bioconductor-pathview</requirement>
5 <requirement type="package" version="1.18.0">bioconductor-keggrest</requirement> 5 <requirement type="package" version="1.18.0">bioconductor-keggrest</requirement>
6 </requirements> 6 </requirements>
36 --output="$text_output" 36 --output="$text_output"
37 37
38 ]]></command> 38 ]]></command>
39 <inputs> 39 <inputs>
40 <!--section name="pathways_section" title="Pathways" expanded="True"--> 40 <!--section name="pathways_section" title="Pathways" expanded="True"-->
41 <conditional name="species"> 41 <conditional name="species (human, mouse, rat)">
42 <param name="ref_file" type="select" label="Species" > 42 <param name="ref_file" type="select" label="Species" >
43 <option value="hsa">Human (Homo sapiens)</option> 43 <option value="hsa">Human (Homo sapiens)</option>
44 <option value="mmu">Mouse (Mus musculus)</option> 44 <option value="mmu">Mouse (Mus musculus)</option>
45 <option value="rno">Rat (Rattus norvegicus)</option> 45 <option value="rno">Rat (Rattus norvegicus)</option>
46 </param> 46 </param>
198 </when> 198 </when>
199 </conditional> 199 </conditional>
200 <!--/section--> 200 <!--/section-->
201 <param name="native" type="select" label="Graphical format"> 201 <param name="native" type="select" label="Graphical format">
202 <option value="true">KEGG map (.png)</option> 202 <option value="true">KEGG map (.png)</option>
203 <option value="false">Graphviz layout engine (.pdf)</option> 203 <option value="false">KEGG map, graphviz layout engine (.pdf)</option>
204 </param> 204 </param>
205 </inputs> 205 </inputs>
206 <outputs> 206 <outputs>
207 <data name="text_output" format="tsv" label="KEGG maps visualization text output"/> 207 <data name="text_output" format="tsv" label="KEGG maps visualization text output"/>
208 <collection type="list" label="KEGG maps visualization from ${input.file.name}" name="graphviz_output_from_file"> 208 <collection type="list" label="KEGG maps visualization from ${input.file.name}" name="graphviz_output_from_file">
244 </tests> 244 </tests>
245 <help><![CDATA[ 245 <help><![CDATA[
246 246
247 **Description** 247 **Description**
248 248
249 This tool based on the Pathview R package, is set for pathway based data integration and visualization. 249 This tool, relying on the Pathview R package, is set for pathway based data integration and visualization.
250 250
251 It maps and renders a wide variety of biological data on relevant KEGG pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. 251 It maps and renders a wide variety of biological data on relevant KEGG pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data.
252 252
253 **Input** 253 **Input**
254 254
275 .. class:: warningmark 275 .. class:: warningmark
276 276
277 If there's more than one ID per line in the specified column, it will be splitted resulting in one unique ID per line. For example this table: 277 If there's more than one ID per line in the specified column, it will be splitted resulting in one unique ID per line. For example this table:
278 278
279 .. csv-table:: Simulated data 279 .. csv-table:: Simulated data
280 :header: "Ensembl_Gene","UniProt.AC","UniProt.ID" 280 :header: "Entrez_gene_ID","UniProt.AC","UniProt.ID"
281 281
282 "ENSG00000136881","Q14032","BAAT_HUMAN" 282 "6881","Q14032","BAAT_HUMAN"
283 "ENSG00000170099","P08185;G3V350;G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN" 283 "70099","P08185;G3V350;G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
284 "ENSG00000244731","P0C0L4","CO4A_HUMAN" 284 "731","P0C0L4","CO4A_HUMAN"
285 285
286 | 286 |
287 287
288 will be converted as follow: 288 will be converted as follow:
289 289
290 .. csv-table:: Simulated data 290 .. csv-table:: Simulated data
291 :header: "Ensembl_Gene","UniProt.AC","UniProt.ID" 291 :header: "Entrez_gene_ID","UniProt.AC","UniProt.ID"
292 292
293 "ENSG00000136881","Q14032","BAAT_HUMAN" 293 "6881","Q14032","BAAT_HUMAN"
294 "ENSG00000170099","P08185","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN" 294 "70099","P08185","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
295 "ENSG00000170099","G3V350","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN" 295 "70099","G3V350","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
296 "ENSG00000170099","G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN" 296 "70099","G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
297 "ENSG00000244731","P0C0L4","CO4A_HUMAN" 297 "731","P0C0L4","CO4A_HUMAN"
298 298
299 | 299 |
300 300
301 ----- 301 -----
302 302
303 **Output:** 303 **Output:**
304 304
305 - a **collection dataset** named 'KEGG maps visualization from <dataset>', one file (png or pdf) for each given pathway. 305 - a set of graphical map, i.e. a **collection dataset** named 'KEGG maps visualization from <dataset>', one file (png or pdf) for each KEGG map.
306 306
307 - a **summary text file** (.tsv) of the mapping(s) with the following columns 307 - a **summary text file** (.tsv) of the mapping(s) with the following columns
308 - **KEGG pathway ID**: KEGG pathway(s) used to map given genes/proteins ids 308 - **KEGG pathway ID**: KEGG pathway(s) used to map given genes/proteins ids
309 - **pathway name**: name(s) of KEGG pathway(s) used for mapping 309 - **pathway name**: name(s) of KEGG pathway(s) used for mapping
310 - **nb of Uniprot_AC used** (only when Uniprot accession number is given): number of Uniprot accession number which will be converted to Entrez genes IDs 310 - **nb of Uniprot_AC used** (only when Uniprot accession number is given): number of Uniprot accession number which will be converted to Entrez genes IDs
343 343
344 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR 344 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
345 345
346 This work has been partially funded through the French National Agency for Research (ANR) IFB project. 346 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
347 347
348 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. 348 Help: contact@proteore.org for any questions or concerns about this tool.
349 ]]></help> 349 ]]></help>
350 <citations> 350 <citations>
351 <citation type="doi">10.1093/nar/gkx372</citation> 351 <citation type="doi">10.1093/nar/gkx372</citation>
352 <citation type="bibtex"> 352 <citation type="bibtex">
353 @misc{renameTODO, 353 @misc{renameTODO,