Mercurial > repos > rnateam > graphclust_postprocessing

comparison glob_report.xml @ 12:b5f49453af8c draft

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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
author rnateam
date Wed, 31 May 2017 14:53:30 -0400
parents e080ebe95476
children 23dc3b4545d5
comparison
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11:e080ebe95476 12:b5f49453af8c
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>