Mercurial > repos > rnateam > graphclust_postprocessing

comparison glob_report.xml @ 4:dbcea781900e draft

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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit f971832d2b34a182314e5201ea6895dd207c5923
author rnateam
date Mon, 13 Mar 2017 17:54:32 -0400
parents a8fde40f00fc
children fc701681ca6e
comparison
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3:a8fde40f00fc 4:dbcea781900e
1 <tool id="glob_report" name="Report_Results" version="0.1"> 1 <tool id="glob_report" name="cluster_collection_report" version="0.1">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="0.1.7">graphclust-wrappers</requirement> 3 <requirement type="package" version="0.1.10">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>
9 <requirement type="package" version='2.2.10'>viennarna</requirement> 9 <requirement type="package" version='2.2.10'>viennarna</requirement>
10 <requirement type="package" version='1.3.23'>graphicsmagick</requirement> 10 <requirement type="package" version='1.3.23'>graphicsmagick</requirement>
11 <requirement type="package" version='0.3.1'>rscape</requirement>
12
11 </requirements> 13 </requirements>
12 <stdio> 14 <stdio>
13 <exit_code range="1:" /> 15 <exit_code range="1:" />
14 </stdio> 16 </stdio>
15 <command> 17 <command>
151 <discover_datasets format="png" pattern="(?P&lt;name&gt;^.*\.alirna.png$)" /> 153 <discover_datasets format="png" pattern="(?P&lt;name&gt;^.*\.alirna.png$)" />
152 </collection> 154 </collection>
153 <collection name="topDot" type="list" label="Top $results_top_num aln.ps"> 155 <collection name="topDot" type="list" label="Top $results_top_num aln.ps">
154 <discover_datasets format="png" pattern="(?P&lt;name&gt;^.*\.aln.png$)" /> 156 <discover_datasets format="png" pattern="(?P&lt;name&gt;^.*\.aln.png$)" />
155 </collection> 157 </collection>
158 <collection name="rscapePlot" type="list" label="R-scape Plot">
159 <discover_datasets format="pdf" pattern="(?P&lt;name&gt;^.*\.pdf$)" />
160 </collection>
156 <data name="RESULTS_zip" format="zip" from_work_dir="RESULTS.zip" label="RESULTS.zip" /> 161 <data name="RESULTS_zip" format="zip" from_work_dir="RESULTS.zip" label="RESULTS.zip" />
157 </outputs> 162 </outputs>
158 <tests> 163 <tests>
159 <test> 164 <test>
160 <param name="FASTA" value="FASTA.zip" ftype="searchgui_archive"/> 165 <param name="FASTA" value="FASTA.zip" ftype="searchgui_archive"/>
161 <param name="cmsearch_results" value="1.tabular,2.tabular"/> 166 <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"/> 167 <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"/> 168 <param name="partition_type" value="0"/>
164 <param name="cut_type" value="0"/> 169 <param name="cut_type" value="0"/>
165 <conditional name="iteration_num"> 170 <conditional name="iteration_num">
166 <param name="iteration_num_selector" value="false"/> 171 <param name="iteration_num_selector" value="false"/>
167 </conditional> 172 </conditional>
173 <param name="cm_bitscore_sig" value="1"/> 178 <param name="cm_bitscore_sig" value="1"/>
174 <output name="final_stats" file="RESULTS/cluster.final.stats" /> 179 <output name="final_stats" file="RESULTS/cluster.final.stats" />
175 <output_collection name="clusters" type="list"> 180 <output_collection name="clusters" type="list">
176 <element name="1.cluster.all" file="RESULTS/1.cluster.all" compare="contains"/> 181 <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"/> 182 <element name="2.cluster.all" file="RESULTS/2.cluster.all" compare="contains"/>
183 <element name="3.cluster.all" file="RESULTS/3.cluster.all" compare="contains"/>
184 <element name="4.cluster.all" file="RESULTS/4.cluster.all" compare="contains"/>
178 </output_collection> 185 </output_collection>
179 <output_collection name="partitions"> 186 <output_collection name="partitions">
180 <element name="final_overlap.map" file="RESULTS/partitions/final_overlap.map" compare="contains"> 187 <element name="final_overlap.map" file="RESULTS/partitions/final_overlap.map" compare="contains">
181 <assert_contents> 188 <assert_contents>
182 <has_text text="1.1 1.1" /> 189 <has_text text="1.1 1.1 1.2" />
183 <has_text text="1.2 1.2" /> 190 <has_text text="1.3 1.3" />
191 <has_text text="1.4 1.4" />
192 <has_text text="1.5 1.5 " />
184 </assert_contents> 193 </assert_contents>
185 </element> 194 </element>
186 <element name="final_overlap.matrix" file="RESULTS/partitions/final_overlap.matrix" compare="contains"> 195 <element name="final_overlap.matrix" file="RESULTS/partitions/final_overlap.matrix" compare="contains">
187 <assert_contents> 196 <assert_contents>
188 <has_text text="MODEL CLASS 0 0" /> 197 <has_text text="MODEL CLASS 0 0 0 0 0" />
189 <has_text text="1.2" /> 198 <!--has_text text="1.2" />
190 <has_text text="1.1" /> 199 <has_text text="1.1" /-->
191 </assert_contents> 200 </assert_contents>
192 </element> 201 </element>
193 <element name="final_partition.hard.best" file="RESULTS/partitions/final_partition.hard.best" /> 202 <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" /> 203 <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" /> 204 <element name="final_partition.soft" file="RESULTS/partitions/final_partition.soft" />
197 </output_collection> 206 </output_collection>
198 <param name="results_top_num" value="5"/> 207 <param name="results_top_num" value="5"/>
199 <output_collection name="topSecondaryStruct" type="list"> 208 <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" /> 209 <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" /> 210 <element name="2.cluster.top5.alirna.png" file="2.cluster.top5.alirna.png" ftype="png" compare="sim_size" />
211 <element name="3.cluster.top5.alirna.png" file="3.cluster.top5.alirna.png" ftype="png" compare="sim_size" />
212 <element name="4.cluster.top5.alirna.png" file="4.cluster.top5.alirna.png" ftype="png" compare="sim_size" />
202 </output_collection> 213 </output_collection>
203 <output_collection name="topDot" type="list"> 214 <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" /> 215 <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" /> 216 <element name="2.cluster.top5.aln.png" file="2.cluster.top5.aln.png" ftype="png" compare="sim_size" />
206 </output_collection> 217 <element name="3.cluster.top5.aln.png" file="3.cluster.top5.aln.png" ftype="png" compare="sim_size" />
207 <output name="RESULTS_zip" file="RESULTS.zip" ftype="zip" compare="sim_size" /> 218 <element name="4.cluster.top5.aln.png" file="4.cluster.top5.aln.png" ftype="png" compare="sim_size" />
219 </output_collection>
220
221 <output_collection name="rscapePlot" type="list">
222 <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" />
223 <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" />
224 <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" />
225 <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" />
226 </output_collection>
227
228 <output name="RESULTS_zip" file="RESULTS.zip" ftype="zip" compare="sim_size" delta="20000"/>
208 229
209 </test> 230 </test>
210 </tests> 231 </tests>
211 <help> 232 <help>
212 <![CDATA[ 233 <![CDATA[