Mercurial > repos > rnateam > graphclust_postprocessing
comparison glob_report.xml @ 12:b5f49453af8c draft
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
author | rnateam |
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date | Wed, 31 May 2017 14:53:30 -0400 |
parents | e080ebe95476 |
children | 23dc3b4545d5 |
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11:e080ebe95476 | 12:b5f49453af8c |
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1 <tool id="glob_report" name="cluster_collection_report" version="0.1"> | 1 <tool id="glob_report" name="cluster_collection_report" version="0.1"> |
2 <requirements> | 2 <requirements> |
3 <requirement type="package" version="0.1.12">graphclust-wrappers</requirement> | 3 <requirement type="package" version="0.2.0">graphclust-wrappers</requirement> |
4 <requirement type="package" version='0.5'>perl-array-utils</requirement> | 4 <requirement type="package" version='0.5'>perl-array-utils</requirement> |
5 <requirement type="package" version='0.18.1'>scikit-learn</requirement> | 5 <requirement type="package" version='0.18.1'>scikit-learn</requirement> |
6 <requirement type="package" version='1.8.10'>locarna</requirement> | 6 <requirement type="package" version='1.8.10'>locarna</requirement> |
7 <requirement type="package" version='2.1'>rnaz</requirement> | 7 <requirement type="package" version='2.1'>rnaz</requirement> |
8 <requirement type="package" version="1.1">infernal</requirement> | 8 <requirement type="package" version="1.1">infernal</requirement> |
170 <data name="RESULTS_zip" format="zip" from_work_dir="RESULTS.zip" label="RESULTS.zip" /> | 170 <data name="RESULTS_zip" format="zip" from_work_dir="RESULTS.zip" label="RESULTS.zip" /> |
171 </outputs> | 171 </outputs> |
172 <tests> | 172 <tests> |
173 <test> | 173 <test> |
174 <param name="FASTA" value="FASTA.zip" ftype="searchgui_archive"/> | 174 <param name="FASTA" value="FASTA.zip" ftype="searchgui_archive"/> |
175 <param name="cmsearch_results" value="1.tabular,2.tabular,3.tabular,4.tabular,5.tabular"/> | 175 <param name="cmsearch_results" value="1.1.tree,1.2.tree"/> |
176 <param name="model_tree_files" value="1.1.model.tree.fa,1.2.model.tree.fa,1.3.model.tree.fa,1.4.model.tree.fa,1.5.model.tree.fa"/> | 176 <param name="model_tree_files" value="1.1.model.tree.fa,1.2.model.tree.fa"/> |
177 <param name="combined_cm_out" value="combined_cm_out"/> | |
177 <param name="partition_type" value="0"/> | 178 <param name="partition_type" value="0"/> |
178 <param name="cut_type" value="0"/> | 179 <param name="cut_type" value="0"/> |
179 <conditional name="iteration_num"> | 180 <conditional name="iteration_num"> |
180 <param name="iteration_num_selector" value="false"/> | 181 <param name="iteration_num_selector" value="false"/> |
181 </conditional> | 182 </conditional> |
182 <param name="merge_cluster_ol" value="0.66"/> | 183 <param name="merge_cluster_ol" value="0.66"/> |
183 <param name="merge_overlap" value="0.51"/> | 184 <param name="merge_overlap" value="0.51"/> |
184 <param name="min_cluster_size" value="3"/> | 185 <param name="min_cluster_size" value="3"/> |
185 <param name="cm_min_bitscore" value="20"/> | 186 <param name="cm_min_bitscore" value="20"/> |
186 <param name="cm_max_eval" value="0.001"/> | 187 <param name="cm_max_eval" value="0.001"/> |
187 <param name="cm_bitscore_sig" value="1"/> | 188 <param name="cm_bitscore_sig" value="0"/> |
188 <output name="final_stats" file="RESULTS/cluster.final.stats" /> | 189 <output name="final_stats" file="RESULTS/cluster.final.stats" /> |
189 <output_collection name="clusters" type="list"> | 190 <output_collection name="clusters" type="list"> |
190 <element name="1.cluster.all" file="RESULTS/1.cluster.all" compare="contains"/> | 191 <element name="1.cluster.all" file="RESULTS/1.cluster.all" compare="contains"/> |
191 <element name="2.cluster.all" file="RESULTS/2.cluster.all" compare="contains"/> | 192 <element name="2.cluster.all" file="RESULTS/2.cluster.all" compare="contains"/> |
192 <element name="3.cluster.all" file="RESULTS/3.cluster.all" compare="contains"/> | 193 |
193 <element name="4.cluster.all" file="RESULTS/4.cluster.all" compare="contains"/> | |
194 </output_collection> | 194 </output_collection> |
195 <output_collection name="partitions"> | 195 <output_collection name="partitions"> |
196 <element name="final_overlap.map" file="RESULTS/partitions/final_overlap.map" compare="contains"> | 196 <element name="final_overlap.map" file="RESULTS/partitions/final_overlap.map" compare="contains"> |
197 <assert_contents> | 197 <assert_contents> |
198 <has_text text="1.1 1.1 1.2" /> | 198 <has_text text="1.1 1.1 " /> |
199 <has_text text="1.3 1.3" /> | 199 <has_text text="1.2 1.2" /> |
200 <has_text text="1.4 1.4" /> | |
201 <has_text text="1.5 1.5 " /> | |
202 </assert_contents> | 200 </assert_contents> |
203 </element> | 201 </element> |
204 <element name="final_overlap.matrix" file="RESULTS/partitions/final_overlap.matrix" compare="contains"> | 202 <element name="final_overlap.matrix" file="RESULTS/partitions/final_overlap.matrix" compare="contains"> |
205 <assert_contents> | 203 <assert_contents> |
206 <has_text text="MODEL CLASS 0 0 0 0 0" /> | 204 <has_text text="MODEL CLASS 0 0" /> |
207 <!--has_text text="1.2" /> | 205 <!--has_text text="1.2" /> |
208 <has_text text="1.1" /--> | 206 <has_text text="1.1" /--> |
209 </assert_contents> | 207 </assert_contents> |
210 </element> | 208 </element> |
211 <element name="final_partition.hard.best" file="RESULTS/partitions/final_partition.hard.best" /> | 209 <element name="final_partition.hard.best" file="RESULTS/partitions/final_partition.hard.best" /> |
215 </output_collection> | 213 </output_collection> |
216 <param name="results_top_num" value="5"/> | 214 <param name="results_top_num" value="5"/> |
217 <output_collection name="topSecondaryStruct" type="list"> | 215 <output_collection name="topSecondaryStruct" type="list"> |
218 <element name="1.cluster.top5.alirna.png" file="1.cluster.top5.alirna.png" ftype="png" compare="sim_size" /> | 216 <element name="1.cluster.top5.alirna.png" file="1.cluster.top5.alirna.png" ftype="png" compare="sim_size" /> |
219 <element name="2.cluster.top5.alirna.png" file="2.cluster.top5.alirna.png" ftype="png" compare="sim_size" /> | 217 <element name="2.cluster.top5.alirna.png" file="2.cluster.top5.alirna.png" ftype="png" compare="sim_size" /> |
220 <element name="3.cluster.top5.alirna.png" file="3.cluster.top5.alirna.png" ftype="png" compare="sim_size" /> | |
221 <element name="4.cluster.top5.alirna.png" file="4.cluster.top5.alirna.png" ftype="png" compare="sim_size" /> | |
222 </output_collection> | 218 </output_collection> |
223 <output_collection name="topDot" type="list"> | 219 <output_collection name="topDot" type="list"> |
224 <element name="1.cluster.top5.aln.png" file="1.cluster.top5.aln.png" ftype="png" compare="sim_size" /> | 220 <element name="1.cluster.top5.aln.png" file="1.cluster.top5.aln.png" ftype="png" compare="sim_size" /> |
225 <element name="2.cluster.top5.aln.png" file="2.cluster.top5.aln.png" ftype="png" compare="sim_size" /> | 221 <element name="2.cluster.top5.aln.png" file="2.cluster.top5.aln.png" ftype="png" compare="sim_size" /> |
226 <element name="3.cluster.top5.aln.png" file="3.cluster.top5.aln.png" ftype="png" compare="sim_size" /> | |
227 <element name="4.cluster.top5.aln.png" file="4.cluster.top5.aln.png" ftype="png" compare="sim_size" /> | |
228 </output_collection> | 222 </output_collection> |
229 | 223 |
230 <output_collection name="rscapePlot" type="list"> | 224 <output_collection name="rscapePlot" type="list"> |
231 <element name="1.cluster.top5.result.aln_1.R2R.sto.pdf" file="1.cluster.top5.result.aln_1.R2R.sto.pdf" ftype="pdf" compare="sim_size" /> | 225 <element name="1.cluster.top5.result.aln_1.R2R.sto.pdf" file="1.cluster.top5.result.aln_1.R2R.sto.pdf" ftype="pdf" compare="sim_size" /> |
232 <element name="2.cluster.top5.result.aln_1.R2R.sto.pdf" file="2.cluster.top5.result.aln_1.R2R.sto.pdf" ftype="pdf" compare="sim_size" /> | 226 <element name="2.cluster.top5.result.aln_1.R2R.sto.pdf" file="2.cluster.top5.result.aln_1.R2R.sto.pdf" ftype="pdf" compare="sim_size" /> |
233 <element name="3.cluster.top5.result.aln_1.R2R.sto.pdf" file="3.cluster.top5.result.aln_1.R2R.sto.pdf" ftype="pdf" compare="sim_size" /> | |
234 <element name="4.cluster.top5.result.aln_1.R2R.sto.pdf" file="4.cluster.top5.result.aln_1.R2R.sto.pdf" ftype="pdf" compare="sim_size" /> | |
235 </output_collection> | 227 </output_collection> |
236 | 228 |
237 <output name="RESULTS_zip" file="RESULTS.zip" ftype="zip" compare="sim_size" delta="20000"/> | 229 <output name="RESULTS_zip" file="RESULTS.zip" ftype="zip" compare="sim_size" delta="20000"/> |
238 | 230 |
239 </test> | 231 </test> |