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planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
author proteore
date Tue, 18 Dec 2018 09:23:35 -0500
parents 48f302ae5545
children f4938e47f2f8
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1 <tool id="kegg_maps_visualization" name="KEGG maps visualization" version="2018.12.12"> 1 <tool id="kegg_maps_visualization" name="KEGG maps visualization" version="2018.12.18">
2 <description>of (differentially expressed) genes/proteins</description> 2 <description>of (differentially expressed) genes/proteins</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>
11 #else 11 #else
12 --input="$input.file" 12 --input="$input.file"
13 --id_column="$input.ncol" 13 --id_column="$input.ncol"
14 --header="$input.header" 14 --header="$input.header"
15 #end if 15 #end if
16 #if $species.pathways.pathways_id != "pathways_file" 16 #if $pathways_section.species.pathways.pathways_id != "pathways_file"
17 --pathways_id="$species.pathways.pids" 17 --pathways_id="$pathways_section.species.pathways.pids"
18 #else 18 #else
19 --pathways_input="$species.pathways.file" 19 --pathways_input="$pathways_section.species.pathways.file"
20 --header2="$species.pathways.header2" 20 --header2="$pathways_section.species.pathways.header2"
21 --pathway_col="$species.pathways.ncol2" 21 --pathway_col="$pathways_section.species.pathways.ncol2"
22 #end if 22 #end if
23 --id_type="$id_type" 23 --id_type="$id_type"
24 --native_kegg="$native" 24 --native_kegg="$native"
25 25
26 26
29 --fold_change_col="$input.foldchange.fc_col" 29 --fold_change_col="$input.foldchange.fc_col"
30 #else 30 #else
31 --fold_change_data="false" 31 --fold_change_data="false"
32 #end if 32 #end if
33 33
34 --species=${species.ref_file} 34 --species=${pathways_section.species.ref_file}
35 --pathways_list=$__tool_directory__/${ filter( lambda x: str( x[0] ) == str( $species.ref_file ), $__app__.tool_data_tables['kegg_pathways_list_index'].get_fields() )[0][-1] } 35 --pathways_list=$__tool_directory__/${ filter( lambda x: str( x[0] ) == str( $pathways_section.species.ref_file ), $__app__.tool_data_tables['kegg_pathways_list_index'].get_fields() )[0][-1] }
36 --output="$text_output" 36 --output="$text_output"
37 37
38 ]]></command> 38 ]]></command>
39 <inputs> 39 <inputs>
40 <conditional name="species"> 40 <!--section name="pathways_section" title="Pathways" expanded="True"-->
41 <param name="ref_file" type="select" label="Select species" > 41 <conditional name="species">
42 <option value="hsa">Human (H. sapiens)</option> 42 <param name="ref_file" type="select" label="Species" >
43 <option value="mmu">Mouse (M. musculus)</option> 43 <option value="hsa">Human (Homo sapiens)</option>
44 <option value="rno">Rat (R. norvegicus)</option> 44 <option value="mmu">Mouse (Mus musculus)</option>
45 </param> 45 <option value="rno">Rat (Rattus norvegicus)</option>
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> 46 </param>
53 <when value="pathways_names"> 47 <when value="hsa">
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'> 48 <conditional name="pathways">
55 <options from_data_table="hsa_pathways"> 49 <param name="pathways_id" type="select" label="Enter your pathway(s)" help="Enter KEGG pathway name(s) or KEGG pathway id(s)">
56 <filter type="sort_by" column="1"/> 50 <option value="pathways_names">KEGG pathway name(s)</option>
57 <validator type="no_options" message="No indexes are available for the selected input dataset"/> 51 <option value="pathways_ids">KEGG pathway IDs</option>
58 </options> 52 <option value="pathways_file">KEGG pathway IDs from file</option>
53 </param>
54 <when value="pathways_names">
55 <param name="pids" type="select" label="Select pathway(s) (by clicking in the box)" multiple="true" help='You can select one or several pathway(s), you can write the beginning of your pathways to search using autocomplete'>
56 <options from_data_table="hsa_pathways">
57 <filter type="sort_by" column="1"/>
58 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
59 </options>
60 </param>
61 </when>
62 <when value="pathways_ids">
63 <param name="pids" type="text" label="Copy/paste your pathway IDs" help='IDs must be separated by tab, space or carriage return into the form field, for example: "hsa00010 hsa05412"'>
64 <sanitizer invalid_char=''>
65 <valid initial="string.printable">
66 <remove value="&apos;"/>
67 </valid>
68 <mapping>
69 <add source="&#x20;" target=""/>
70 </mapping>
71 </sanitizer>
72 </param>
73 </when>
74 <when value="pathways_file">
75 <param name="file" type="data" format="txt,tabular" label="Select your file" help="Pathway id format : 'path:hsa00010' or 'hsa00010' or '00010'" />
76 <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
77 <param name="ncol2" type="text" value="c1" label="Column of pathways IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />
78 </when>
79 </conditional>
80 </when>
81 <when value="mmu">
82 <conditional name="pathways">
83 <param name="pathways_id" type="select" label="Enter your pathway(s)" help="Enter KEGG pathway name(s) or KEGG pathway id(s)">
84 <option value="pathways_names">KEGG pathway name(s)</option>
85 <option value="pathways_ids">KEGG pathway IDs</option>
86 <option value="pathways_file">KEGG pathway IDs from file</option>
59 </param> 87 </param>
60 </when> 88 <when value="pathways_names">
61 <when value="pathways_ids"> 89 <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'>
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"'> 90 <options from_data_table="mmu_pathways">
91 <filter type="sort_by" column="1"/>
92 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
93 </options>
94 </param>
95 </when>
96 <when value="pathways_ids">
97 <param name="pids" type="text" label="Copy/paste your pathway IDs" help='IDs must be separated by tab, space or carriage return into the form field, for example: "mmu00053 mmu00340"'>
98 <sanitizer invalid_char=''>
99 <valid initial="string.printable">
100 <remove value="&apos;"/>
101 </valid>
102 <mapping>
103 <add source="&#x20;" target=""/>
104 </mapping>
105 </sanitizer>
106 </param>
107 </when>
108 <when value="pathways_file">
109 <param name="file" type="data" format="txt,tabular" label="Enter your file" help="Pathway id format : 'path:mmu00053' or 'mmu00053' or '00053'" />
110 <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
111 <param name="ncol2" type="text" value="c1" label="Column of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />
112 </when>
113 </conditional>
114 </when>
115 <when value="rno">
116 <conditional name="pathways">
117 <param name="pathways_id" type="select" label="Enter your pathway(s) name/id" help="Enter KEGG pathway name(s) or KEGG pathway id(s)">
118 <option value="pathways_names">KEGG pathway name(s)</option>
119 <option value="pathways_ids">KEGG pathway IDs</option>
120 <option value="pathways_file">KEGG pathway IDs from file</option>
121 </param>
122 <when value="pathways_names">
123 <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'>
124 <options from_data_table="rno_pathways">
125 <filter type="sort_by" column="1"/>
126 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
127 </options>
128 </param>
129 </when>
130 <when value="pathways_ids">
131 <param name="pids" type="text" label="Copy/paste your pathway IDs" help='IDs must be separated by tab, space or carriage return into the form field, for example: "hsa00010 hsa05412"'>
132 <sanitizer invalid_char=''>
133 <valid initial="string.printable">
134 <remove value="&apos;"/>
135 </valid>
136 <mapping>
137 <add source="&#x20;" target=""/>
138 </mapping>
139 </sanitizer>
140 </param>
141 </when>
142 <when value="pathways_file">
143 <param name="file" type="data" format="txt,tabular" label="Select your file" help="Pathway id format : 'path:hsa00010' or 'hsa00010' or '00010'" />
144 <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
145 <param name="ncol2" type="text" value="c1" label="Column of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />
146 </when>
147 </conditional>
148 </when>
149 </conditional>
150 <!--/section-->
151 <!--section name="genes_section" title="Genes/prot" expanded="True"-->
152 <param name="id_type" type="select" label="Select ID type for genes to map to the pathway(s):">
153 <option value="geneID" selected="true">Entrez Gene ID</option>
154 <option value="keggid">KEGG Genes ID</option>
155 <option value="uniprotID">UniProt Accession number</option>
156 </param>
157 <conditional name="input" >
158 <param name="ids" type="select" label="Enter your IDs" help="Copy/paste or ID from file (e.g. table)" >
159 <option value="text">Copy/paste your IDs</option>
160 <option value="file" selected="true">Input file containing your IDs</option>
161 </param>
162 <when value="text" >
163 <param name="txt" type="text" label="Copy/paste your IDs" help='IDs must be separated by tab, space or carriage return into the form field, for example: P31946 P62258' >
63 <sanitizer invalid_char=''> 164 <sanitizer invalid_char=''>
64 <valid initial="string.printable"> 165 <valid initial="string.printable">
65 <remove value="&apos;"/> 166 <remove value="&apos;"/>
66 </valid> 167 </valid>
67 <mapping> 168 <mapping initial="none">
68 <add source="&#x20;" target=""/> 169 <add source="&apos;" target="__sq__"/>
69 </mapping> 170 </mapping>
70 </sanitizer> 171 </sanitizer>
71 </param> 172 </param>
72 </when> 173 </when>
73 <when value="pathways_file"> 174 <when value="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'" /> 175 <param name="file" type="data" format="txt,tabular" label="Select your file" help="" />
75 <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contains a header?" /> 176 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain 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' /> 177 <param name="ncol" type="text" value="c1" label="Column if 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' />
77 </when> 178 <conditional name="foldchange" >
78 </conditional> 179 <param name="fc" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Map quantitative data on the pathway?"/>
79 </when> 180 <when value="true">
80 <when value="mmu"> 181 <param name="fc_col" type="text" label="Column(s) number of quantitative data (separated by ','. 3 columns max)" help="For example : c1,c3,c4"/>
81 <conditional name="pathways"> 182 </when>
82 <param name="pathways_id" type="select" label="Provide your pathway(s)" help="Enter KEGG pathway name(s) or KEGG pathway id(s)"> 183 <when value="false"/>
83 <option value="pathways_names">KEGG pathway name(s)</option> 184 </conditional>
84 <option value="pathways_ids">KEGG pathway id(s)</option> 185 </when>
85 <option value="pathways_file">KEGG pathway id(s) from file</option> 186 </conditional>
86 </param> 187 <!--/section-->
87 <when value="pathways_names"> 188 <param name="native" type="select" label="Graphical format">
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> 189 <option value="true">KEGG map (.png)</option>
186 <option value="false">Graphviz layout engine (.pdf)</option> 190 <option value="false">Graphviz layout engine (.pdf)</option>
187 </param> 191 </param>
188 </inputs> 192 </inputs>
189 <outputs> 193 <outputs>
224 <output name="kegg_from_file" file="hsa05167.pathview.png" compare="sim_size"/> 228 <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"/> 229 <output name="kegg_from_file" file="hsa00010.pathview.png" compare="sim_size"/>
226 </test--> 230 </test-->
227 </tests> 231 </tests>
228 <help><![CDATA[ 232 <help><![CDATA[
229 This tool map a list identifiers to KEGG pathway with the R package 'pathview'. 233
230 234 **Description**
231 You can map Entrez gene ID, KEGG genes ID or Uniprot accession number from three species : human, mouse and rat. 235
232 236 This tool based on the Pathview R package, is set for pathway based data integration and visualization.
233 If your input have another type of IDs, please use the ID_Converter tool. 237
234 238 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.
235 **Input:** 239
236 240 **Input**
237 241
238 - KEGG Pathways IDs to be used for mapping can be set by: 242 1. "Enter your pathway(s)": target KEGG Pathways to be specify can be set by:
239 - chosing from the KEGG pathways name list 243
240 - giving a list (copy/paste) 244 - choosing from the KEGG pathways name list
241 - importing a list from a dataset (column) - output of KEGG pathways identification and coverage can be used (1st column) 245 - giving a list of KEGG pathway IDs (e.g.hsa00010) (copy/paste mode)
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). 246 - selecting a list from a dataset (column) - for instance, output from the "KEGG pathways identification and coverage" tool can be used (1st column, c1)
243 - Fold change values (up to three columns) from a dataset (same dataset as identifiers to map) can be added. 247 2. "Select ID type for genes to map on the pathway(s)": Identifiers to map can be either a list of Entrez genes IDs, KEGG genes ID or Uniprot accession number. IDs to be mapped can be either provided by copy/paste or a file (tabular, tsv, txt) with a column containing the IDs.
244 248 3. "Map quantitative data on the pathway ?": Yes/No (default is No). Fold change values (up to three columns) from a dataset (same file as identifiers to map) can be graphically represented on the final figure (using a range of color representing the fold-change values).
245 You can see below an example of an input file with identifiers (uniprot_AC) and fold_change values. 249
250 Below is an example of an input file with identifiers (uniprot_AC) and fold_change values.
246 251
247 .. csv-table:: Simulated data 252 .. csv-table:: Simulated data
248 :header: "Uniprot_AC","Protein.name","Number_of_peptides","fc_values 1","fc_values 2","fc_values 3" 253 :header: "Uniprot_AC","Protein.name","Number_of_peptides","fc_values 1","fc_values 2","fc_values 3"
249 254
250 "P15924","Desmoplakin","69","0.172302292051025","-0.757435966487116","0.0411240398990759" 255 "P15924","Desmoplakin","69","0.172302292051025","-0.757435966487116","0.0411240398990759"
252 "P02768","Serum albumin","44","-0.983493243315454","0.113752002761474","-0.645886132600729" 257 "P02768","Serum albumin","44","-0.983493243315454","0.113752002761474","-0.645886132600729"
253 "P08779","Keratin, type I cytoskeletal 16","29","0.552302597284443","-0.329045605110646","2.10616106806788" 258 "P08779","Keratin, type I cytoskeletal 16","29","0.552302597284443","-0.329045605110646","2.10616106806788"
254 259
255 | 260 |
256 261
257
258 .. class:: warningmark 262 .. class:: warningmark
259 263
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: 264 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:
261 265
262 .. csv-table:: Simulated data 266 .. csv-table:: Simulated data
263 :header: "Ensembl_Gene","UniProt.AC","UniProt.ID" 267 :header: "Ensembl_Gene","UniProt.AC","UniProt.ID"
264 268
265 "ENSG00000136881","Q14032","BAAT_HUMAN" 269 "ENSG00000136881","Q14032","BAAT_HUMAN"
266 "ENSG00000170099","P08185;G3V350;G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN" 270 "ENSG00000170099","P08185;G3V350;G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
267 "ENSG00000244731","P0C0L4","CO4A_HUMAN" 271 "ENSG00000244731","P0C0L4","CO4A_HUMAN"
268 272
269 | 273 |
270 274
271 will become: 275 will be converted as follow:
272 276
273 .. csv-table:: Simulated data 277 .. csv-table:: Simulated data
274 :header: "Ensembl_Gene","UniProt.AC","UniProt.ID" 278 :header: "Ensembl_Gene","UniProt.AC","UniProt.ID"
275 279
276 "ENSG00000136881","Q14032","BAAT_HUMAN" 280 "ENSG00000136881","Q14032","BAAT_HUMAN"
279 "ENSG00000170099","G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN" 283 "ENSG00000170099","G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
280 "ENSG00000244731","P0C0L4","CO4A_HUMAN" 284 "ENSG00000244731","P0C0L4","CO4A_HUMAN"
281 285
282 | 286 |
283 287
288 -----
289
284 **Output:** 290 **Output:**
285 291
286 - a **collection dataset** named 'KEGG maps visualization from <dataset>', one file (png or pdf) for each given pathway. 292 - a **collection dataset** named 'KEGG maps visualization from <dataset>', one file (png or pdf) for each given pathway.
293
287 - a **summary text file** (.tsv) of the mapping(s) with the following columns 294 - 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 295 - **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 296 - **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 297 - **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 298 - **nb of Entrez gene ID used**: number of Entrez gene IDs used for mapping
297 304
298 ----- 305 -----
299 306
300 .. class:: infomark 307 .. class:: infomark
301 308
302 **Database:** 309 **Data source (release date)**
303 310
304 KEGG Pathways names list are from http://rest.kegg.jp/list/pathway/ 311 KEGG Pathways names list are from http://rest.kegg.jp/list/pathway/
305 312
306 User manual / Documentation: http://www.bioconductor.org/packages/release/bioc/html/pathview.html 313 User manual / Documentation: http://www.bioconductor.org/packages/release/bioc/html/pathview.html
307 314
308
309 ----- 315 -----
310 316
311 .. class:: infomark 317 .. class:: infomark
312 318
313 **Authors** 319 **Authors**
314 320
315 David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR 321 Luo, Weijun, Brouwer, Cory (2013). “Pathview: an R/Bioconductor package for pathway-based data integration and visualization.” Bioinformatics, 29(14), 1830-1831. doi: 10.1093/bioinformatics/btt285.
316 322
317 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform 323 -----
324
325 .. class:: infomark
326
327 **Galaxy integration**
328
329 David Christiany, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
330
331 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
318 332
319 This work has been partially funded through the French National Agency for Research (ANR) IFB project. 333 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
320 334
321 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. 335 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
322 ]]></help> 336 ]]></help>