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comparison kegg_pathways_visualization.xml @ 16:682041ae727d draft default tip

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planemo upload commit 170560760f17fd1b77efe8bb95fedf3eb2433f0b-dirty
author proteore
date Thu, 22 Nov 2018 04:37:54 -0500
parents da82872f5c80
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15:da82872f5c80 16:682041ae727d
1 <tool id="kegg_pathways_visualization" name="KEGG pathways" version="2018.11.12"> 1 <tool id="kegg_pathways_visualization" name="KEGG pathways" version="2018.11.22">
2 <description>map visualisation (PathView)</description> 2 <description>map visualisation (PathView)</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 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
144 </when> 144 </when>
145 </conditional> 145 </conditional>
146 </when> 146 </when>
147 </conditional> 147 </conditional>
148 <param name="id_type" type="select" label="Select your identifiers type :"> 148 <param name="id_type" type="select" label="Select your identifiers type :">
149 <option value="geneID" selected="true">Entrez gene ID</option>
150 <option value="keggid">KEGG genes ID</option>
149 <option value="uniprotID">Uniprot Accession number</option> 151 <option value="uniprotID">Uniprot Accession number</option>
150 <option value="geneID">Entrez gene ID</option>
151 <option value="keggid">KEGG genes ID</option>
152 </param> 152 </param>
153 <conditional name="input" > 153 <conditional name="input" >
154 <param name="ids" type="select" label="Enter your identifiers (Uniprot AC or Entrez gene ID)" help="Copy/paste or ID list from a file (e.g. table)" > 154 <param name="ids" type="select" label="Enter your identifiers" help="Copy/paste or ID list from a file (e.g. table)" >
155 <option value="text">Copy/paste your identifiers</option> 155 <option value="text">Copy/paste your identifiers</option>
156 <option value="file" selected="true">Input file containing your identifiers</option> 156 <option value="file" selected="true">Input file containing your identifiers</option>
157 </param> 157 </param>
158 <when value="text" > 158 <when value="text" >
159 <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' > 159 <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' >
223 <output name="kegg_from_file" file="hsa05167.pathview.png" compare="sim_size"/> 223 <output name="kegg_from_file" file="hsa05167.pathview.png" compare="sim_size"/>
224 <output name="kegg_from_file" file="hsa00010.pathview.png" compare="sim_size"/> 224 <output name="kegg_from_file" file="hsa00010.pathview.png" compare="sim_size"/>
225 </test--> 225 </test-->
226 </tests> 226 </tests>
227 <help><![CDATA[ 227 <help><![CDATA[
228 This tool map a list of Uniprot Accession number or Entrez gene ID to KEGG pathway with pathview R package. 228 This tool map a list identifiers to KEGG pathway with the R package 'pathview'.
229 229
230 You can map Entrez gene IDs / Uniprot accession number from three species : human, mouse and rat. 230 You can map Entrez gene ID, KEGG genes ID or Uniprot accession number from three species : human, mouse and rat.
231 231
232 If your input have another type of IDs, please use the ID_Converter tool. 232 If your input have another type of IDs, please use the ID_Converter tool.
233 233
234 **Input:** 234 **Input:**
235 235
236 236
237 - KEGG Pathways IDs to be used for mapping can be set by: 237 - KEGG Pathways IDs to be used for mapping can be set by:
238 - chosing from the KEGG pathways name list 238 - chosing from the KEGG pathways name list
239 - giving a list (copy/paste) 239 - giving a list (copy/paste)
240 - importing a list from a dataset (column) - output of KEGG pathways identification and coverage can be used (1st column) 240 - importing a list from a dataset (column) - output of KEGG pathways identification and coverage can be used (1st column)
241 - Genes/proteins ids to map can be either a list of Entrez genes IDs / Uniprot accession number or a file (tabular, tsv, txt) containing at least one column of Entrez genes IDs / Uniprot accession number. 241 - 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).
242 - fold change values (up to three columns) from a dataset (same dataset as for Genes/proteins ids to map) 242 - Fold change values (up to three columns) from a dataset (same dataset as identifiers to map) can be added.
243 243
244 You can see below an example of an input file with identifiers (uniprot_AC) and fold_change values. 244 You can see below an example of an input file with identifiers (uniprot_AC) and fold_change values.
245 245
246 .. csv-table:: Simulated data 246 .. csv-table:: Simulated data
247 :header: "Uniprot_AC","Protein.name","Number_of_peptides","fc_values 1","fc_values 2","fc_values 3" 247 :header: "Uniprot_AC","Protein.name","Number_of_peptides","fc_values 1","fc_values 2","fc_values 3"