Mercurial > repos > rnateam > graphclust_postprocessing
comparison glob_report.xml @ 17:f93c868203cc draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults commit 4406735e44aba20859c252be39f4e99df28c7a92
author | rnateam |
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date | Sat, 27 Oct 2018 13:23:06 -0400 |
parents | 79df97a1bc0f |
children |
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16:79df97a1bc0f | 17:f93c868203cc |
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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 $final_partition_used_cmsearch |
155 <data name="final_soft" format="txt" from_work_dir="RESULTS/partitions/final_partition.soft" label="soft_part" /> | 140 <data name="final_soft" format="txt" from_work_dir="RESULTS/partitions/final_partition.soft" label="soft_part" /> |
156 <data name="final_used_cmsearch" format="txt" from_work_dir="RESULTS/partitions/final_partition.used_cmsearch" label="final_partition_used_cmsearch" /> | 141 <data name="final_used_cmsearch" format="txt" from_work_dir="RESULTS/partitions/final_partition.used_cmsearch" label="final_partition_used_cmsearch" /> |
157 <data name="evaluation" format="txt" from_work_dir="RESULTS/evaluation.txt" label="evaluation_of_clusters" /> | 142 <data name="evaluation" format="txt" from_work_dir="RESULTS/evaluation.txt" label="evaluation_of_clusters" /> |
158 <data name="combined_cm_out" format="txt" from_work_dir="combined_cm_out" label="combined_cmsearch_output" /> | 143 <data name="combined_cm_out" format="txt" from_work_dir="combined_cm_out" label="combined_cmsearch_output" /> |
159 <collection name="clusters" type="list" label="CLUSTERS"> | 144 <collection name="clusters" type="list" label="CLUSTERS"> |
160 <discover_datasets pattern="(?P<name>^.*\.all$)" directory="RESULTS" /> | 145 <discover_datasets format="txt" pattern="(?P<name>^.*\.all$)" directory="RESULTS" /> |
146 </collection> | |
147 <collection name="allFasta" type="list" label="sequences.fa"> | |
148 <discover_datasets format="fasta" pattern="(?P<name>^.*\.all.fa$)" 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<name>^.*$)" directory="RESULTS/partitions" /> | 151 <discover_datasets pattern="(?P<name>^.*$)" 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> |