Mercurial > repos > greg > gene_family_classifier

comparison gene_family_classifier.xml @ 132:169504db8e43 draft

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author greg
date Fri, 07 Apr 2017 08:38:49 -0400
parents 656614635ebf
children b2ae23e484e8
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131:656614635ebf 132:169504db8e43
228 <collection name="orthos" type="list"> 228 <collection name="orthos" type="list">
229 <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" /> 229 <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" />
230 </collection> 230 </collection>
231 </outputs> 231 </outputs>
232 <tests> 232 <tests>
233 <!-- Need to figure out how to test using scaffolds data.
233 <test> 234 <test>
234 <param name="input" value="transcripts.cleaned.nr.pep" ftype="fasta" /> 235 <param name="input" value="transcripts.cleaned.nr.pep" ftype="fasta" />
235 <param name="scaffold" value="22Gv1.1"/> 236 <param name="scaffold" value="plant_tribes/scaffolds/22Gv1.1"/>
236 <param name="method" value="orthomcl"/> 237 <param name="method" value="orthomcl"/>
237 <param name="classifier" value="blastp"/> 238 <param name="classifier" value="blastp"/>
238 <param name="dereplicate" value="yes"/>
239 <param name="min_length" value="200"/>
240 <output_collection name="orthos" type="list"> 239 <output_collection name="orthos" type="list">
241 <element name="proteins.blastp.22Gv1.1" file="proteins.blastp.22Gv1.1" ftype="tabular"/> 240 <element name="proteins.blastp.22Gv1.1" file="proteins.blastp.22Gv1.1" ftype="tabular" compare="contains"/>
242 <element name="proteins.blastp.22Gv1.1.bestOrthos" file="proteins.blastp.22Gv1.1.bestOrthos" ftype="tabular"/> 241 <element name="proteins.blastp.22Gv1.1.bestOrthos" file="proteins.blastp.22Gv1.1.bestOrthos" ftype="tabular"/>
243 <element name="proteins.blastp.22Gv1.1.bestOrthos.summary" file="proteins.blastp.22Gv1.1.bestOrthos.summary" ftype="tabular"/> 242 <element name="proteins.blastp.22Gv1.1.bestOrthos.summary" file="proteins.blastp.22Gv1.1.bestOrthos.summary" ftype="tabular"/>
244 </output_collection> 243 </output_collection>
245 </test> 244 </test>
245 -->
246 </tests> 246 </tests>
247 <help> 247 <help>
248 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary 248 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary
249 analyses of genome-scale gene families and transcriptomes. This tool classifies gene coding sequences either produced by 249 analyses of genome-scale gene families and transcriptomes. This tool classifies gene coding sequences either produced by
250 the AssemblyPostProcessor tool or from an external source into pre-computed orthologous gene family clusters (orthogroups) 250 the AssemblyPostProcessor tool or from an external source into pre-computed orthologous gene family clusters (orthogroups)