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date Thu, 06 Dec 2018 08:27:31 -0500
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1 <tool id="kegg_maps_visualization" name="KEGG maps visualization" version="2018.12.06.1">
2 <description>of quantified genes/proteins</description>
3 <requirements>
4 <requirement type="package" version="1.18.0">bioconductor-pathview</requirement>
5 <requirement type="package" version="1.18.0">bioconductor-keggrest</requirement>
6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[
8 Rscript $__tool_directory__/kegg_maps_visualization.R
9 #if $input.ids == "text"
10 --id_list="$input.txt"
11 #else
12 --input="$input.file"
13 --id_column="$input.ncol"
14 --header="$input.header"
15 #end if
16 #if $species.pathways.pathways_id != "pathways_file"
17 --pathways_id="$species.pathways.pids"
18 #else
19 --pathways_input="$species.pathways.file"
20 --header2="$species.pathways.header2"
21 --pathway_col="$species.pathways.ncol2"
22 #end if
23 --id_type="$id_type"
24 --native_kegg="$native"
25
26
27 #if $input.ids=="file" and $input.foldchange.fc=="true"
28 --fold_change_data="$input.foldchange.fc"
29 --fold_change_col="$input.foldchange.fc_col"
30 #else
31 --fold_change_data="false"
32 #end if
33
34 --species=${species.ref_file}
35 --pathways_list=$__tool_directory__/${ filter( lambda x: str( x[0] ) == str( $species.ref_file ), $__app__.tool_data_tables['kegg_pathways_list_index'].get_fields() )[0][-1] }
36 --output="$text_output"
37
38 ]]></command>
39 <inputs>
40 <conditional name="species">
41 <param name="ref_file" type="select" label="Select species" >
42 <option value="hsa">Human (H. sapiens)</option>
43 <option value="mmu">Mouse (M. musculus)</option>
44 <option value="rno">Rat (R. norvegicus)</option>
45 </param>
46 <when value="hsa">
47 <conditional name="pathways">
48 <param name="pathways_id" type="select" label="Provide your pathway(s)" help="Enter KEGG pathway name(s) or KEGG pathway id(s)">
49 <option value="pathways_names">KEGG pathway name(s)</option>
50 <option value="pathways_ids">KEGG pathway id(s)</option>
51 <option value="pathways_file">KEGG pathway id(s) from file</option>
52 </param>
53 <when value="pathways_names">
54 <param name="pids" type="select" label="Select pathway(s)" multiple="true" help='You can select one or several pathway(s), you can write the beginning of your pathways to search using autocomplete'>
55 <options from_data_table="hsa_pathways">
56 <filter type="sort_by" column="1"/>
57 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
58 </options>
59 </param>
60 </when>
61 <when value="pathways_ids">
62 <param name="pids" type="text" label="Copy/paste your pathway id(s)" help='IDs must be separated by tab, space or carriage return into the form field, for example: "hsa00010 hsa05412"'>
63 <sanitizer invalid_char=''>
64 <valid initial="string.printable">
65 <remove value="&apos;"/>
66 </valid>
67 <mapping>
68 <add source="&#x20;" target=""/>
69 </mapping>
70 </sanitizer>
71 </param>
72 </when>
73 <when value="pathways_file">
74 <param name="file" type="data" format="txt,tabular" label="Select a file with a column of pathways id" help="Pathway id format : 'path:hsa00010' or 'hsa00010' or '00010'" />
75 <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contains a header?" />
76 <param name="ncol2" type="text" value="c1" label="The column which contains your pathways ids" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />
77 </when>
78 </conditional>
79 </when>
80 <when value="mmu">
81 <conditional name="pathways">
82 <param name="pathways_id" type="select" label="Provide your pathway(s)" help="Enter KEGG pathway name(s) or KEGG pathway id(s)">
83 <option value="pathways_names">KEGG pathway name(s)</option>
84 <option value="pathways_ids">KEGG pathway id(s)</option>
85 <option value="pathways_file">KEGG pathway id(s) from file</option>
86 </param>
87 <when value="pathways_names">
88 <param name="pids" type="select" label="Select pathway(s)" multiple="true" help='You can select one or several pathway(s), you can write the beginning of your pathways to search using autocomplete'>
89 <options from_data_table="mmu_pathways">
90 <filter type="sort_by" column="1"/>
91 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
92 </options>
93 </param>
94 </when>
95 <when value="pathways_ids">
96 <param name="pids" type="text" label="Copy/paste your pathway id(s)" help='IDs must be separated by tab, space or carriage return into the form field, for example: "mmu00053 mmu00340"'>
97 <sanitizer invalid_char=''>
98 <valid initial="string.printable">
99 <remove value="&apos;"/>
100 </valid>
101 <mapping>
102 <add source="&#x20;" target=""/>
103 </mapping>
104 </sanitizer>
105 </param>
106 </when>
107 <when value="pathways_file">
108 <param name="file" type="data" format="txt,tabular" label="Select a file with a column of pathways id " help="Pathway id format : 'path:mmu00053' or 'mmu00053' or '00053'" />
109 <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
110 <param name="ncol2" type="text" value="c1" label="The column which contains your pathways ids" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />
111 </when>
112 </conditional>
113 </when>
114 <when value="rno">
115 <conditional name="pathways">
116 <param name="pathways_id" type="select" label="Enter your pathway(s) name/id" help="Enter KEGG pathway name(s) or KEGG pathway id(s)">
117 <option value="pathways_names">KEGG pathway name(s)</option>
118 <option value="pathways_ids">KEGG pathway id(s)</option>
119 <option value="pathways_file">KEGG pathway id(s) from file</option>
120 </param>
121 <when value="pathways_names">
122 <param name="pids" type="select" label="Select pathway(s)" multiple="true" help='You can select one or several pathway(s), you can write the beginning of your pathways to search using autocomplete'>
123 <options from_data_table="rno_pathways">
124 <filter type="sort_by" column="1"/>
125 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
126 </options>
127 </param>
128 </when>
129 <when value="pathways_ids">
130 <param name="pids" type="text" label="Copy/paste your pathway id(s)" help='IDs must be separated by tab, space or carriage return into the form field, for example: "hsa00010 hsa05412"'>
131 <sanitizer invalid_char=''>
132 <valid initial="string.printable">
133 <remove value="&apos;"/>
134 </valid>
135 <mapping>
136 <add source="&#x20;" target=""/>
137 </mapping>
138 </sanitizer>
139 </param>
140 </when>
141 <when value="pathways_file">
142 <param name="file" type="data" format="txt,tabular" label="Select a file with a column of pathways id" help="Pathway id format : 'path:hsa00010' or 'hsa00010' or '00010'" />
143 <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contains a header?" />
144 <param name="ncol2" type="text" value="c1" label="The column which contains your pathways ids" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />
145 </when>
146 </conditional>
147 </when>
148 </conditional>
149 <param name="id_type" type="select" label="Select your identifiers type for the genes to map on the pathway(s):">
150 <option value="geneID" selected="true">Entrez gene ID</option>
151 <option value="keggid">KEGG genes ID</option>
152 <option value="uniprotID">Uniprot Accession number</option>
153 </param>
154 <conditional name="input" >
155 <param name="ids" type="select" label="Enter your identifiers" help="Copy/paste or ID list from a file (e.g. table)" >
156 <option value="text">Copy/paste your identifiers</option>
157 <option value="file" selected="true">Input file containing your identifiers</option>
158 </param>
159 <when value="text" >
160 <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by tab, space or carriage return into the form field, for example: P31946 P62258' >
161 <sanitizer invalid_char=''>
162 <valid initial="string.printable">
163 <remove value="&apos;"/>
164 </valid>
165 <mapping initial="none">
166 <add source="&apos;" target="__sq__"/>
167 </mapping>
168 </sanitizer>
169 </param>
170 </when>
171 <when value="file" >
172 <param name="file" type="data" format="txt,tabular" label="Select a file that contains your list of IDs" help="" />
173 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contains a header?" />
174 <param name="ncol" type="text" value="c1" label="The column which contains your IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />
175 <conditional name="foldchange" >
176 <param name="fc" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Do you have fold change values to represent on the graph ?"/>
177 <when value="true">
178 <param name="fc_col" type="text" label="Please enter column(s) number of fold change data separated by ','. 3 columns max" help="For example : c1,c3,c4"/>
179 </when>
180 <when value="false"/>
181 </conditional>
182 </when>
183 </conditional>
184 <param name="native" type="select" label="Choose the output graphical format">
185 <option value="true">KEGG map (.png)</option>
186 <option value="false">Graphviz layout engine (.pdf)</option>
187 </param>
188 </inputs>
189 <outputs>
190 <data name="text_output" format="tsv" label="KEGG maps visualization text output"/>
191 <collection type="list" label="KEGG maps visualization from ${input.file.name}" name="graphviz_output_from_file">
192 <filter>native=="false" and input["ids"] == "file"</filter>
193 <discover_datasets pattern="(?P&lt;designation&gt;.+\..*)\.pdf" ext="pdf" />
194 </collection>
195 <collection type="list" label="KEGG maps visualization from ${input.file.name}" name="kegg_graph_output_from_file">
196 <filter>native=="true" and input["ids"] == "file"</filter>
197 <discover_datasets pattern="(?P&lt;designation&gt;.+\..*)\.png" ext="png"/>
198 </collection>
199 <collection type="list" label="KEGG maps visualization" name="graphviz_output_from_list">
200 <filter>native=="false" and input["ids"] == "text"</filter>
201 <discover_datasets pattern="(?P&lt;designation&gt;.+\..*)\.pdf" ext="pdf" />
202 </collection>
203 <collection type="list" label="KEGG maps visualization" name="kegg_graph_output_from_list">
204 <filter>native=="true" and input["ids"] == "text"</filter>
205 <discover_datasets pattern="(?P&lt;designation&gt;.+\..*)\.png" ext="png" />
206 </collection>
207 </outputs>
208 <tests>
209 <!--test>
210 <conditional name="input">
211 <param name="ids" value="file"/>
212 <param name="file" value="Lacombe_et_al_2017_OK.txt"/>
213 <param name="header" value="true"/>
214 <param name="ncol" value="c1"/>
215 </conditional>
216 <conditional name="pathways">
217 <param name="pathways_id" value="pathways_ids"/>
218 <param name="pids" value="04514,05167,00010"/>
219 </conditional>
220 <param name="id_type" value="uniprotID"/>
221 <param name="species" value="hsa"/>
222 <param name="native" value="true"/>
223 <output name="kegg_from_file" file="hsa04514.pathview.png" compare="sim_size"/>
224 <output name="kegg_from_file" file="hsa05167.pathview.png" compare="sim_size"/>
225 <output name="kegg_from_file" file="hsa00010.pathview.png" compare="sim_size"/>
226 </test-->
227 </tests>
228 <help><![CDATA[
229 This tool map a list identifiers to KEGG pathway with the R package 'pathview'.
230
231 You can map Entrez gene ID, KEGG genes ID or Uniprot accession number from three species : human, mouse and rat.
232
233 If your input have another type of IDs, please use the ID_Converter tool.
234
235 **Input:**
236
237
238 - KEGG Pathways IDs to be used for mapping can be set by:
239 - chosing from the KEGG pathways name list
240 - giving a list (copy/paste)
241 - importing a list from a dataset (column) - output of KEGG pathways identification and coverage can be used (1st column)
242 - Identifiers to map can be either a list of Entrez genes IDs, KEGG genes ID or Uniprot accession number or in a column of a file (tabular, tsv, txt).
243 - Fold change values (up to three columns) from a dataset (same dataset as identifiers to map) can be added.
244
245 You can see below an example of an input file with identifiers (uniprot_AC) and fold_change values.
246
247 .. csv-table:: Simulated data
248 :header: "Uniprot_AC","Protein.name","Number_of_peptides","fc_values 1","fc_values 2","fc_values 3"
249
250 "P15924","Desmoplakin","69","0.172302292051025","-0.757435966487116","0.0411240398990759"
251 "P02538","Keratin, type II cytoskeletal 6A","53","-0.988842456122076","0.654626325100182","-0.219153396366064"
252 "P02768","Serum albumin","44","-0.983493243315454","0.113752002761474","-0.645886132600729"
253 "P08779","Keratin, type I cytoskeletal 16","29","0.552302597284443","-0.329045605110646","2.10616106806788"
254
255 |
256
257
258 .. class:: warningmark
259
260 If there's more than one id per line in the defined column, it will be split to have only one id per line. For example this table:
261
262 .. csv-table:: Simulated data
263 :header: "Ensembl_Gene","UniProt.AC","UniProt.ID"
264
265 "ENSG00000136881","Q14032","BAAT_HUMAN"
266 "ENSG00000170099","P08185;G3V350;G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
267 "ENSG00000244731","P0C0L4","CO4A_HUMAN"
268
269 |
270
271 will become:
272
273 .. csv-table:: Simulated data
274 :header: "Ensembl_Gene","UniProt.AC","UniProt.ID"
275
276 "ENSG00000136881","Q14032","BAAT_HUMAN"
277 "ENSG00000170099","P08185","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
278 "ENSG00000170099","G3V350","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
279 "ENSG00000170099","G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
280 "ENSG00000244731","P0C0L4","CO4A_HUMAN"
281
282 |
283
284 **Output:**
285
286 - a **collection dataset** named 'KEGG maps visualization from <dataset>', one file (png or pdf) for each given pathway.
287 - a **summary text file** (.tsv) of the mapping(s) with the following columns
288 - **KEGG pathway ID**: KEGG pathway(s) used to map given genes/proteins ids
289 - **pathway name**: name(s) of KEGG pathway(s) used for mapping
290 - **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
291 - **nb of Entrez gene ID used**: number of Entrez gene IDs used for mapping
292 - **nb of Entrez gene ID mapped**: number of Entrez gene IDs mapped on a given pathway
293 - **nb of Entrez gene ID in the pathway**: number total of Entrez gene IDs in a given pathway
294 - **ratio of Entrez gene ID mapped**: number of Entrez gene IDs mapped / number total of Entrez gene IDs
295 - **Entrez gene ID mapped**: list of mapped Entrez gene IDs
296 - **uniprot_AC mapped** (only when Uniprot accession number is given): list of Uniprot accession number corresponding to the mapped Entrez gene IDs
297
298 -----
299
300 .. class:: infomark
301
302 **Database:**
303
304 KEGG Pathways names list are from http://rest.kegg.jp/list/pathway/
305
306 User manual / Documentation: http://www.bioconductor.org/packages/release/bioc/html/pathview.html
307
308
309 -----
310
311 .. class:: infomark
312
313 **Authors**
314
315 David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
316
317 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
318
319 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
320
321 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
322 ]]></help>
323 <citations>
324 <citation type="doi">10.1093/nar/gkx372</citation>
325 <citation type="bibtex">
326 @misc{renameTODO,
327 author = {Weijun Luo},
328 year = {2013},
329 title = {pathview},
330 url = {https://bioconductor.org/packages/release/bioc/html/pathview.html},
331 }</citation>
332 </citations>
333 </tool>