Mercurial > repos > proteore > proteore_pathview_mapping

comparison kegg_pathways_visualization.xml @ 13:c59ec7fce7b3 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 7e2bd28d27e13c402acd46500f64d5c117797aa7-dirty
author proteore
date Fri, 09 Nov 2018 05:16:58 -0500
parents 9fe4a861601b
children be8115c73b0d
comparison
equal deleted inserted replaced
12:9fe4a861601b 13:c59ec7fce7b3
1 <tool id="kegg_pathways_visualization" name="KEGG pathways" version="2018.11.08"> 1 <tool id="kegg_pathways_visualization" name="KEGG pathways" version="2018.11.09">
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[
170 <when value="file" > 170 <when value="file" >
171 <param name="file" type="data" format="txt,tabular" label="Select a file that contains your list of IDs" help="" /> 171 <param name="file" type="data" format="txt,tabular" label="Select a file that contains your list of IDs" help="" />
172 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contains a header?" /> 172 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contains a header?" />
173 <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' /> 173 <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' />
174 <conditional name="foldchange" > 174 <conditional name="foldchange" >
175 <param name="fc" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Do you have fold change values to represent on the graph ?" default="false"/> 175 <param name="fc" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Do you have fold change values to represent on the graph ?"/>
176 <when value="true"> 176 <when value="true">
177 <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"/> 177 <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"/>
178 </when> 178 </when>
179 <when value="false"/> 179 <when value="false"/>
180 </conditional> 180 </conditional>
203 <filter>native=="true" and input["ids"] == "text"</filter> 203 <filter>native=="true" and input["ids"] == "text"</filter>
204 <discover_datasets pattern="(?P&lt;designation&gt;.+\..*)\.png" ext="png" /> 204 <discover_datasets pattern="(?P&lt;designation&gt;.+\..*)\.png" ext="png" />
205 </collection> 205 </collection>
206 </outputs> 206 </outputs>
207 <tests> 207 <tests>
208 <test> 208 <!--test>
209 <conditional name="input"> 209 <conditional name="input">
210 <param name="ids" value="file"/> 210 <param name="ids" value="file"/>
211 <param name="file" value="Lacombe_et_al_2017_OK.txt"/> 211 <param name="file" value="Lacombe_et_al_2017_OK.txt"/>
212 <param name="header" value="true"/> 212 <param name="header" value="true"/>
213 <param name="ncol" value="c1"/> 213 <param name="ncol" value="c1"/>
220 <param name="species" value="hsa"/> 220 <param name="species" value="hsa"/>
221 <param name="native" value="true"/> 221 <param name="native" value="true"/>
222 <output name="kegg_from_file" file="hsa04514.pathview.png" compare="sim_size"/> 222 <output name="kegg_from_file" file="hsa04514.pathview.png" compare="sim_size"/>
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 of Uniprot Accession number or Entrez gene ID to KEGG pathway with pathview R package.
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 IDs / Uniprot accession number from three species : human, mouse and rat.