Mercurial > repos > rnateam > graphclust_postprocessing

comparison glob_report.xml @ 6:869a6e807d76 draft

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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 057c2fd398055dc86eb2c00d8a74f301d5c231d9-dirty
author rnateam
date Wed, 22 Feb 2017 16:51:06 -0500
parents 4310ac018d05
children 870dfc90473f
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5:4310ac018d05 6:869a6e807d76
1 <tool id="glob_report" name="Report_Results" version="0.1"> 1 <tool id="glob_report" name="Report_Results" version="0.1">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="0.1.7">graphclust-wrappers</requirement> 3 <requirement type="package" version="0.1.8">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>
27 27
28 #for $mods in $model_tree_files: 28 #for $mods in $model_tree_files:
29 #set $inputFilesTrees += str($mods)+',' 29 #set $inputFilesTrees += str($mods)+','
30 #end for 30 #end for
31 #set $inputFilesTrees = $inputFilesTrees[:-1] 31 #set $inputFilesTrees = $inputFilesTrees[:-1]
32 'glob_res.pl' 32 'glob_res.pl'
33 '$inputFiles' 33 '$inputFiles'
34 $merge_cluster_ol 34 $merge_cluster_ol
35 $merge_overlap 35 $merge_overlap
36 $min_cluster_size 36 $min_cluster_size
37 $cm_min_bitscore 37 $cm_min_bitscore
156 <data name="RESULTS_zip" format="zip" from_work_dir="RESULTS.zip" label="RESULTS.zip" /> 156 <data name="RESULTS_zip" format="zip" from_work_dir="RESULTS.zip" label="RESULTS.zip" />
157 </outputs> 157 </outputs>
158 <tests> 158 <tests>
159 <test> 159 <test>
160 <param name="FASTA" value="FASTA.zip" ftype="searchgui_archive"/> 160 <param name="FASTA" value="FASTA.zip" ftype="searchgui_archive"/>
161 <param name="cmsearch_results" value="1.tabular,2.tabular"/> 161 <param name="cmsearch_results" value="1.tabular,2.tabular,3.tabular,4.tabular,5.tabular"/>
162 <param name="model_tree_files" value="1.1.model.tree.fa,1.2.model.tree.fa"/> 162 <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"/>
163 <param name="partition_type" value="0"/> 163 <param name="partition_type" value="0"/>
164 <param name="cut_type" value="0"/> 164 <param name="cut_type" value="0"/>
165 <conditional name="iteration_num"> 165 <conditional name="iteration_num">
166 <param name="iteration_num_selector" value="false"/> 166 <param name="iteration_num_selector" value="false"/>
167 </conditional> 167 </conditional>
173 <param name="cm_bitscore_sig" value="1"/> 173 <param name="cm_bitscore_sig" value="1"/>
174 <output name="final_stats" file="RESULTS/cluster.final.stats" /> 174 <output name="final_stats" file="RESULTS/cluster.final.stats" />
175 <output_collection name="clusters" type="list"> 175 <output_collection name="clusters" type="list">
176 <element name="1.cluster.all" file="RESULTS/1.cluster.all" compare="contains"/> 176 <element name="1.cluster.all" file="RESULTS/1.cluster.all" compare="contains"/>
177 <element name="2.cluster.all" file="RESULTS/2.cluster.all" compare="contains"/> 177 <element name="2.cluster.all" file="RESULTS/2.cluster.all" compare="contains"/>
178 <element name="3.cluster.all" file="RESULTS/3.cluster.all" compare="contains"/>
179 <element name="4.cluster.all" file="RESULTS/4.cluster.all" compare="contains"/>
178 </output_collection> 180 </output_collection>
179 <output_collection name="partitions"> 181 <output_collection name="partitions">
180 <element name="final_overlap.map" file="RESULTS/partitions/final_overlap.map" compare="contains"> 182 <element name="final_overlap.map" file="RESULTS/partitions/final_overlap.map" compare="contains">
181 <assert_contents> 183 <assert_contents>
182 <has_text text="1.1 1.1" /> 184 <has_text text="1.1 1.1 1.2" />
183 <has_text text="1.2 1.2" /> 185 <has_text text="1.3 1.3" />
186 <has_text text="1.4 1.4" />
187 <has_text text="1.5 1.5 " />
184 </assert_contents> 188 </assert_contents>
185 </element> 189 </element>
186 <element name="final_overlap.matrix" file="RESULTS/partitions/final_overlap.matrix" compare="contains"> 190 <element name="final_overlap.matrix" file="RESULTS/partitions/final_overlap.matrix" compare="contains">
187 <assert_contents> 191 <assert_contents>
188 <has_text text="MODEL CLASS 0 0" /> 192 <has_text text="MODEL CLASS 0 0 0 0 0" />
189 <has_text text="1.2" /> 193 <!--has_text text="1.2" />
190 <has_text text="1.1" /> 194 <has_text text="1.1" /-->
191 </assert_contents> 195 </assert_contents>
192 </element> 196 </element>
193 <element name="final_partition.hard.best" file="RESULTS/partitions/final_partition.hard.best" /> 197 <element name="final_partition.hard.best" file="RESULTS/partitions/final_partition.hard.best" />
194 <element name="final_partition.hard.merged" file="RESULTS/partitions/final_partition.hard.merged" /> 198 <element name="final_partition.hard.merged" file="RESULTS/partitions/final_partition.hard.merged" />
195 <element name="final_partition.soft" file="RESULTS/partitions/final_partition.soft" /> 199 <element name="final_partition.soft" file="RESULTS/partitions/final_partition.soft" />
197 </output_collection> 201 </output_collection>
198 <param name="results_top_num" value="5"/> 202 <param name="results_top_num" value="5"/>
199 <output_collection name="topSecondaryStruct" type="list"> 203 <output_collection name="topSecondaryStruct" type="list">
200 <element name="1.cluster.top5.alirna.png" file="1.cluster.top5.alirna.png" ftype="png" compare="sim_size" /> 204 <element name="1.cluster.top5.alirna.png" file="1.cluster.top5.alirna.png" ftype="png" compare="sim_size" />
201 <element name="2.cluster.top5.alirna.png" file="2.cluster.top5.alirna.png" ftype="png" compare="sim_size" /> 205 <element name="2.cluster.top5.alirna.png" file="2.cluster.top5.alirna.png" ftype="png" compare="sim_size" />
206 <element name="3.cluster.top5.alirna.png" file="3.cluster.top5.alirna.png" ftype="png" compare="sim_size" />
207 <element name="4.cluster.top5.alirna.png" file="4.cluster.top5.alirna.png" ftype="png" compare="sim_size" />
202 </output_collection> 208 </output_collection>
203 <output_collection name="topDot" type="list"> 209 <output_collection name="topDot" type="list">
204 <element name="1.cluster.top5.aln.png" file="1.cluster.top5.aln.png" ftype="png" compare="sim_size" /> 210 <element name="1.cluster.top5.aln.png" file="1.cluster.top5.aln.png" ftype="png" compare="sim_size" />
205 <element name="2.cluster.top5.aln.png" file="2.cluster.top5.aln.png" ftype="png" compare="sim_size" /> 211 <element name="2.cluster.top5.aln.png" file="2.cluster.top5.aln.png" ftype="png" compare="sim_size" />
212 <element name="3.cluster.top5.aln.png" file="3.cluster.top5.aln.png" ftype="png" compare="sim_size" />
213 <element name="4.cluster.top5.aln.png" file="4.cluster.top5.aln.png" ftype="png" compare="sim_size" />
206 </output_collection> 214 </output_collection>
207 <output name="RESULTS_zip" file="RESULTS.zip" ftype="zip" compare="sim_size" /> 215 <output name="RESULTS_zip" file="RESULTS.zip" ftype="zip" compare="sim_size" />
208 216
209 </test> 217 </test>
210 </tests> 218 </tests>