Mercurial > repos > greg > phylogenomics_analysis

comparison phylogenomics_analysis.xml @ 2:56ff8d706414 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Wed, 04 Jan 2017 09:31:35 -0500
parents b1e7de636060
children fd6773b7bb3f
comparison
equal deleted inserted replaced
1:b1e7de636060 2:56ff8d706414
58 #end if 58 #end if
59 #end if 59 #end if
60 #end if 60 #end if
61 #end if 61 #end if
62 --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds" 62 --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
63 --num_threads \${GALAXY_SLOTS:-4} 63 --num_threads \${GALAXY_SLOTS:-4} &&
64 echo "Sequence alignments and corresponding phylogenies: `ls -l phylogenomicsAnalysis_dir/orthogroups_fasta | wc -l` files" > $output &&
65 ls phylogenomicsAnalysis_dir/orthogroups_fasta >> $output &&
66 mv phylogenomicsAnalysis_dir/orthogroups_fasta/* $output.extra_files_path
64 ]]> 67 ]]>
65 </command> 68 </command>
66 <inputs> 69 <inputs>
67 <param name="orthogroup_fna" format="fasta" type="data" label="Gene family classification coding sequences (CDS) fasta file for which orthogroup fasta files were created"/> 70 <param name="orthogroup_fna" format="fasta" type="data" label="Gene family classification coding sequences (CDS) fasta file for which orthogroup fasta files were created"/>
68 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold"> 71 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
168 </conditional> 171 </conditional>
169 </when> 172 </when>
170 </conditional> 173 </conditional>
171 </inputs> 174 </inputs>
172 <outputs> 175 <outputs>
173 <collection name="transcripts" type="list"> 176 <data name="output" format="txt" label="Sequence alignments and corresponding phylogenies on ${on_string}"/>
174 <discover_datasets pattern="__name__" directory="phylogenomicsAnalysis_dir" visible="true" ext="fasta" />
175 </collection>
176 </outputs> 177 </outputs>
177 <tests> 178 <tests>
178 <test> 179 <test>
179 <param name="input" value="" ftype="fasta" /> 180 <param name="input" value="" ftype="fasta" />
180 <param name="prediction_method" value="transdecoder"/> 181 <param name="prediction_method" value="transdecoder"/>
181 <param name="target_gene_family_assembly" value="no"/> 182 <param name="target_gene_family_assembly" value="no"/>
182 <param name="strand_specific" value="yes"/> 183 <param name="strand_specific" value="yes"/>
183 <param name="dereplicate" value="yes"/> 184 <param name="dereplicate" value="yes"/>
184 <param name="min_length" value="200"/> 185 <param name="min_length" value="200"/>
185 <output_collection name="orthos" type="list"> 186 <output_collection name="orthos" type="list">
186
187 </output_collection> 187 </output_collection>
188 </test> 188 </test>
189 </tests> 189 </tests>
190 <help> 190 <help>
191 This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of 191 This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of