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comparison glob_report.xml @ 17:f93c868203cc draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults commit 4406735e44aba20859c252be39f4e99df28c7a92
author rnateam
date Sat, 27 Oct 2018 13:23:06 -0400
parents 79df97a1bc0f
children
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16:79df97a1bc0f 17:f93c868203cc
1 <tool id="glob_report" name="cluster_collection_report" version="0.4" > 1 <tool id="glob_report" name="cluster_collection_report" version="0.5" >
2 <requirements> 2 <requirements>
3 <requirement type="package" version="0.5.2">graphclust-wrappers</requirement> 3 <requirement type="package" version="0.6.0">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="1.1.2">infernal</requirement> 8 <requirement type="package" version="1.1.2">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='1.3.26'>graphicsmagick</requirement> 10 <requirement type="package" version='1.3.30'>graphicsmagick</requirement>
11 <requirement type="package" version='0.6.1'>rscape</requirement> 11 <requirement type="package" version='0.6.1'>rscape</requirement>
12 <requirement type="package" version='6.0'>unzip</requirement> 12 <requirement type="package" version='6.0'>unzip</requirement>
13
14 </requirements> 13 </requirements>
15 <stdio> 14 <command detect_errors="exit_code">
16 <exit_code range="1:" /> 15 <![CDATA[
17 </stdio>
18 <command>
19 <![CDATA[
20 unzip $FASTA &> /dev/null && 16 unzip $FASTA &> /dev/null &&
21 17 mkdir ./CMSEARCH &&
22 mkdir ./CMSEARCH && 18 mkdir ./MODEL &&
23 mkdir ./MODEL && 19 #import re
24
25 #set $inputFiles = ""
26
27 #for $cms_res in $cmsearch_results: 20 #for $cms_res in $cmsearch_results:
28 ###set $inputFiles += str($cms_res.element_identifier)+',' 21 #set $safename_cm = re.sub('[^\w\-_\.]', '_', $cms_res.element_identifier)
29 ln -f -s '$cms_res' ./CMSEARCH/$cms_res.element_identifier && 22 ln -f -s '$cms_res' ./CMSEARCH/$safename_cm &&
30 #end for 23 #end for
31 #set $inputFiles = $inputFiles[:-1]
32
33 #set $inputFilesTrees = ""
34
35 #for $mods in $model_tree_files: 24 #for $mods in $model_tree_files:
36 ###set $inputFilesTrees += str($mods.element_identifier)+',' 25 #set $safename_tr = re.sub('[^\w\-_\.]', '_', $mods.element_identifier)
37 ln -f -s '$mods' ./MODEL/$mods.element_identifier && 26 ln -f -s '$mods' ./MODEL/$safename_tr &&
38 #end for 27 #end for
39 #set $inputFilesTrees = $inputFilesTrees[:-1]
40
41 28
42 'glob_res.pl' 29 'glob_res.pl'
43 ##'$inputFiles'
44 $merge_cluster_ol 30 $merge_cluster_ol
45 $merge_overlap 31 $merge_overlap
46 $min_cluster_size 32 $min_cluster_size
47 $cm_min_bitscore 33 $cm_min_bitscore
48 $cm_max_eval 34 $cm_max_eval
49 $cm_bitscore_sig 35 $cm_bitscore_sig
50 $partition_type '' 36 $partition_type ''
51 $cut_type 37 $cut_type
52 ##'$inputFilesTrees'
53 $results_top_num 38 $results_top_num
54 #if $iteration_num.iteration_num_selector: 39 #if $iteration_num.iteration_num_selector:
55 $iteration_num.CI 40 $iteration_num.CI
56 $final_partition_soft 41 $final_partition_soft
57 $final_partition_used_cmsearch 42 $final_partition_used_cmsearch
155 <data name="final_soft" format="txt" from_work_dir="RESULTS/partitions/final_partition.soft" label="soft_part" /> 140 <data name="final_soft" format="txt" from_work_dir="RESULTS/partitions/final_partition.soft" label="soft_part" />
156 <data name="final_used_cmsearch" format="txt" from_work_dir="RESULTS/partitions/final_partition.used_cmsearch" label="final_partition_used_cmsearch" /> 141 <data name="final_used_cmsearch" format="txt" from_work_dir="RESULTS/partitions/final_partition.used_cmsearch" label="final_partition_used_cmsearch" />
157 <data name="evaluation" format="txt" from_work_dir="RESULTS/evaluation.txt" label="evaluation_of_clusters" /> 142 <data name="evaluation" format="txt" from_work_dir="RESULTS/evaluation.txt" label="evaluation_of_clusters" />
158 <data name="combined_cm_out" format="txt" from_work_dir="combined_cm_out" label="combined_cmsearch_output" /> 143 <data name="combined_cm_out" format="txt" from_work_dir="combined_cm_out" label="combined_cmsearch_output" />
159 <collection name="clusters" type="list" label="CLUSTERS"> 144 <collection name="clusters" type="list" label="CLUSTERS">
160 <discover_datasets pattern="(?P&lt;name&gt;^.*\.all$)" directory="RESULTS" /> 145 <discover_datasets format="txt" pattern="(?P&lt;name&gt;^.*\.all$)" directory="RESULTS" />
146 </collection>
147 <collection name="allFasta" type="list" label="sequences.fa">
148 <discover_datasets format="fasta" pattern="(?P&lt;name&gt;^.*\.all.fa$)" directory="RESULTS" />
161 </collection> 149 </collection>
162 <collection name="partitions" type="list" label="Partitions"> 150 <collection name="partitions" type="list" label="Partitions">
163 <discover_datasets pattern="(?P&lt;name&gt;^.*$)" directory="RESULTS/partitions" /> 151 <discover_datasets pattern="(?P&lt;name&gt;^.*$)" directory="RESULTS/partitions" />
164 </collection> 152 </collection>
165 <collection name="topSecondaryStruct" type="list" label="Top $results_top_num alirna.ps"> 153 <collection name="topSecondaryStruct" type="list" label="Top $results_top_num alirna.ps">
176 <tests> 164 <tests>
177 <test> 165 <test>
178 <param name="FASTA" value="FASTA.zip" ftype="searchgui_archive"/> 166 <param name="FASTA" value="FASTA.zip" ftype="searchgui_archive"/>
179 <param name="cmsearch_results" value="1.1.tree,1.2.tree"/> 167 <param name="cmsearch_results" value="1.1.tree,1.2.tree"/>
180 <param name="model_tree_files" value="1.1.model.tree.fa,1.2.model.tree.fa"/> 168 <param name="model_tree_files" value="1.1.model.tree.fa,1.2.model.tree.fa"/>
181 <param name="combined_cm_out" value="combined_cm_out"/>
182 <param name="partition_type" value="0"/> 169 <param name="partition_type" value="0"/>
183 <param name="cut_type" value="0"/> 170 <param name="cut_type" value="0"/>
184 <conditional name="iteration_num"> 171 <conditional name="iteration_num">
185 <param name="iteration_num_selector" value="false"/> 172 <param name="iteration_num_selector" value="false"/>
186 </conditional> 173 </conditional>
188 <param name="merge_overlap" value="0.51"/> 175 <param name="merge_overlap" value="0.51"/>
189 <param name="min_cluster_size" value="3"/> 176 <param name="min_cluster_size" value="3"/>
190 <param name="cm_min_bitscore" value="20"/> 177 <param name="cm_min_bitscore" value="20"/>
191 <param name="cm_max_eval" value="0.001"/> 178 <param name="cm_max_eval" value="0.001"/>
192 <param name="cm_bitscore_sig" value="0"/> 179 <param name="cm_bitscore_sig" value="0"/>
180 <param name="results_top_num" value="5"/>
193 <output name="final_stats" file="RESULTS/cluster.final.stats" /> 181 <output name="final_stats" file="RESULTS/cluster.final.stats" />
182 <output name="combined_cm_out" file="combined_cm_out"/>
183 <output name="evaluation" file="evaluation1.txt"/>
194 <output_collection name="clusters" type="list"> 184 <output_collection name="clusters" type="list">
195 <element name="1.cluster.all" file="RESULTS/1.cluster.all" compare="contains"/> 185 <element name="1.cluster.all" file="RESULTS/1.cluster.all" compare="contains"/>
196 <element name="2.cluster.all" file="RESULTS/2.cluster.all" compare="contains"/> 186 <element name="2.cluster.all" file="RESULTS/2.cluster.all" compare="contains"/>
197
198 </output_collection> 187 </output_collection>
199 <output_collection name="partitions"> 188 <output_collection name="partitions">
200 <element name="final_overlap.map" file="RESULTS/partitions/final_overlap.map" compare="contains"> 189 <element name="final_overlap.map" file="RESULTS/partitions/final_overlap.map" compare="contains">
201 <assert_contents> 190 <assert_contents>
202 <has_text text="1.1 1.1 " /> 191 <has_text text="1.1 1.1 " />
213 <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" />
214 <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" />
215 <element name="final_partition.soft" file="RESULTS/partitions/final_partition.soft" /> 204 <element name="final_partition.soft" file="RESULTS/partitions/final_partition.soft" />
216 <element name="final_partition.used_cmsearch" file="RESULTS/partitions/final_partition.used_cmsearch" compare="contains"/> 205 <element name="final_partition.used_cmsearch" file="RESULTS/partitions/final_partition.used_cmsearch" compare="contains"/>
217 </output_collection> 206 </output_collection>
218 <param name="results_top_num" value="5"/>
219 <output_collection name="topSecondaryStruct" type="list"> 207 <output_collection name="topSecondaryStruct" type="list">
220 <element name="1.cluster.top5.alirna.png" file="1.cluster.top5.alirna.png" ftype="png" compare="sim_size" /> 208 <element name="1.cluster.top5.alirna.png" file="1.cluster.top5.alirna.png" ftype="png" compare="sim_size" />
221 <element name="2.cluster.top5.alirna.png" file="2.cluster.top5.alirna.png" ftype="png" compare="sim_size" /> 209 <element name="2.cluster.top5.alirna.png" file="2.cluster.top5.alirna.png" ftype="png" compare="sim_size" />
222 </output_collection> 210 </output_collection>
223 <output_collection name="topDot" type="list"> 211 <output_collection name="topDot" type="list">
245 Cluster members are finally ranked by their CM bitscore. 233 Cluster members are finally ranked by their CM bitscore.
246 234
247 ]]> 235 ]]>
248 </help> 236 </help>
249 <citations> 237 <citations>
250 <citation type="bibtex">@inproceedings{costa2010fast, 238 <citation type="doi">10.5281/zenodo.597695</citation>
251 title={Fast neighborhood subgraph pairwise distance kernel},
252 author={Costa, Fabrizio and De Grave, Kurt},
253 booktitle={Proceedings of the 26th International Conference on Machine Learning},
254 pages={255--262},
255 year={2010},
256 organization={Omnipress}
257 }
258 </citation>
259 </citations> 239 </citations>
260 </tool> 240 </tool>